AFA results for: tSAHAda2PC3

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Go to: Gene Set Collection: mirbase.targets
Go to: Gene Set Collection: tfbsK3Z3

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
KEGG 03040	View Gene Set	2.905e-11	128	6.217e-09	1	Spliceosome	www.genome.jp/d...
KEGG 01100	View Gene Set	1.092e-08	1120	1.168e-06	2	Metabolic pathways	www.genome.jp/d...
KEGG 00970	View Gene Set	7.935e-08	41	5.66e-06	3	Aminoacyl-tRNA biosynthesis	www.genome.jp/d...
KEGG 00240	View Gene Set	1.059e-06	99	5.665e-05	4	Pyrimidine metabolism	www.genome.jp/d...
KEGG 03020	View Gene Set	4.323e-05	29	0.00185	5	RNA polymerase	www.genome.jp/d...
KEGG 00670	View Gene Set	0.0001163	17	0.00415	6	One carbon pool by folate	www.genome.jp/d...
KEGG 03030	View Gene Set	0.0001644	36	0.005027	7	DNA replication	www.genome.jp/d...
KEGG 00310	View Gene Set	0.0002577	46	0.006894	8	Lysine degradation	www.genome.jp/d...
KEGG 03018	View Gene Set	0.0003	59	0.007134	9	RNA degradation	www.genome.jp/d...
KEGG 00230	View Gene Set	0.0003692	161	0.0079	10	Purine metabolism	www.genome.jp/d...
KEGG 03410	View Gene Set	0.0004114	34	0.008004	11	Base excision repair	www.genome.jp/d...
KEGG 00290	View Gene Set	0.0007528	11	0.01342	12	Valine leucine and isoleucine biosynthesis	www.genome.jp/d...
KEGG 00020	View Gene Set	0.00185	31	0.03045	13	Citrate cycle (TCA cycle)	www.genome.jp/d...
KEGG 04740	View Gene Set	0.002281	388	0.03487	14	Olfactory transduction	www.genome.jp/d...
KEGG 04623	View Gene Set	0.00296	56	0.04223	15	Cytosolic DNA-sensing pathway	www.genome.jp/d...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
GO GO:0006396	View Gene Set	5.974e-33	578	7.982e-29	1	RNA processing	amigo.geneontol...
GO GO:0031974	View Gene Set	1.25e-28	1917	8.297e-25	2	membrane-enclosed lumen	amigo.geneontol...
GO GO:0070013	View Gene Set	1.863e-28	1845	8.297e-25	2	intracellular organelle lumen	amigo.geneontol...
GO GO:0043233	View Gene Set	2.659e-27	1881	8.881e-24	4	organelle lumen	amigo.geneontol...
GO GO:0034660	View Gene Set	5.759e-27	236	1.539e-23	5	ncRNA metabolic process	amigo.geneontol...
GO GO:0005739	View Gene Set	1.503e-26	1274	3.346e-23	6	mitochondrion	amigo.geneontol...
GO GO:0044428	View Gene Set	2.93e-24	1938	5.592e-21	7	nuclear part	amigo.geneontol...
GO GO:0022613	View Gene Set	5.338e-22	194	8.915e-19	8	ribonucleoprotein complex biogenesis	amigo.geneontol...
GO GO:0044429	View Gene Set	1.745e-21	619	2.591e-18	9	mitochondrial part	amigo.geneontol...
GO GO:0034470	View Gene Set	1.067e-20	193	1.426e-17	10	ncRNA processing	amigo.geneontol...
GO GO:0031981	View Gene Set	1.679e-20	1518	2.039e-17	11	nuclear lumen	amigo.geneontol...
GO GO:0042254	View Gene Set	8.057e-18	130	8.971e-15	12	ribosome biogenesis	amigo.geneontol...
GO GO:0030529	View Gene Set	1.016e-17	504	1.044e-14	13	ribonucleoprotein complex	amigo.geneontol...
GO GO:0008380	View Gene Set	5.245e-16	300	5.005e-13	14	RNA splicing	amigo.geneontol...
GO GO:0003723	View Gene Set	8.267e-16	732	7.363e-13	15	RNA binding	amigo.geneontol...
GO GO:0005759	View Gene Set	1.317e-15	223	1.035e-12	16	mitochondrial matrix	amigo.geneontol...
GO GO:0031980	View Gene Set	1.317e-15	223	1.035e-12	16	mitochondrial lumen	amigo.geneontol...
GO GO:0006399	View Gene Set	1.446e-15	118	1.073e-12	18	tRNA metabolic process	amigo.geneontol...
GO GO:0005654	View Gene Set	1.187e-14	939	8.348e-12	19	nucleoplasm	amigo.geneontol...
GO GO:0016071	View Gene Set	3.185e-13	381	2.127e-10	20	mRNA metabolic process	amigo.geneontol...
GO GO:0016072	View Gene Set	3.769e-13	101	2.398e-10	21	rRNA metabolic process	amigo.geneontol...
GO GO:0034641	View Gene Set	8.926e-13	4584	5.421e-10	22	cellular nitrogen compound metabolic process	amigo.geneontol...
GO GO:0006807	View Gene Set	1.103e-12	4698	6.409e-10	23	nitrogen compound metabolic process	amigo.geneontol...
GO GO:0044451	View Gene Set	2.112e-12	600	1.176e-09	24	nucleoplasm part	amigo.geneontol...
GO GO:0006364	View Gene Set	3.204e-12	97	1.712e-09	25	rRNA processing	amigo.geneontol...
GO GO:0005740	View Gene Set	4.037e-12	444	2.074e-09	26	mitochondrial envelope	amigo.geneontol...
GO GO:0005730	View Gene Set	5.155e-12	734	2.46e-09	27	nucleolus	amigo.geneontol...
GO GO:0031966	View Gene Set	5.019e-12	420	2.46e-09	27	mitochondrial membrane	amigo.geneontol...
GO GO:0006397	View Gene Set	1.644e-11	317	7.572e-09	29	mRNA processing	amigo.geneontol...
GO GO:0000375	View Gene Set	1.839e-11	106	8.192e-09	30	RNA splicing via transesterification reactions	amigo.geneontol...
GO GO:0031967	View Gene Set	2.162e-11	672	9.316e-09	31	organelle envelope	amigo.geneontol...
GO GO:0031975	View Gene Set	2.351e-11	685	9.814e-09	32	envelope	amigo.geneontol...
GO GO:0090304	View Gene Set	6.073e-11	3724	2.459e-08	33	nucleic acid metabolic process	amigo.geneontol...
GO GO:0003676	View Gene Set	7.846e-11	2979	3.083e-08	34	nucleic acid binding	amigo.geneontol...
GO GO:0010467	View Gene Set	1.141e-10	3806	4.356e-08	35	gene expression	amigo.geneontol...
GO GO:0005743	View Gene Set	1.361e-10	305	4.914e-08	36	mitochondrial inner membrane	amigo.geneontol...
GO GO:0019866	View Gene Set	1.34e-10	334	4.914e-08	36	organelle inner membrane	amigo.geneontol...
GO GO:0008033	View Gene Set	1.608e-10	78	5.652e-08	38	tRNA processing	amigo.geneontol...
GO GO:0005681	View Gene Set	2.123e-10	135	7.273e-08	39	spliceosomal complex	amigo.geneontol...
GO GO:0000377	View Gene Set	5.025e-10	97	1.598e-07	40	RNA splicing via transesterification reactions with bulged adenosine as nucleophile	amigo.geneontol...
GO GO:0000398	View Gene Set	5.025e-10	97	1.598e-07	40	nuclear mRNA splicing via spliceosome	amigo.geneontol...
GO GO:0006139	View Gene Set	4.824e-10	4294	1.598e-07	40	nucleobase nucleoside nucleotide and nucleic acid metabolic process	amigo.geneontol...
GO GO:0000313	View Gene Set	1.142e-09	49	3.468e-07	43	organellar ribosome	amigo.geneontol...
GO GO:0005761	View Gene Set	1.142e-09	49	3.468e-07	43	mitochondrial ribosome	amigo.geneontol...
GO GO:0008152	View Gene Set	1.374e-09	8439	4.079e-07	45	metabolic process	amigo.geneontol...
GO GO:0030554	View Gene Set	1.583e-09	1584	4.597e-07	46	adenyl nucleotide binding	amigo.geneontol...
GO GO:0004386	View Gene Set	1.88e-09	144	5.343e-07	47	helicase activity	amigo.geneontol...
GO GO:0044237	View Gene Set	2.469e-09	7431	6.871e-07	48	cellular metabolic process	amigo.geneontol...
GO GO:0000166	View Gene Set	2.531e-09	2257	6.9e-07	49	nucleotide binding	amigo.geneontol...
GO GO:0005524	View Gene Set	4.311e-09	1480	1.152e-06	50	ATP binding	amigo.geneontol...
GO GO:0032559	View Gene Set	4.573e-09	1503	1.198e-06	51	adenyl ribonucleotide binding	amigo.geneontol...
GO GO:0008026	View Gene Set	5.578e-09	105	1.406e-06	52	ATP-dependent helicase activity	amigo.geneontol...
GO GO:0070035	View Gene Set	5.578e-09	105	1.406e-06	52	purine NTP-dependent helicase activity	amigo.geneontol...
GO GO:0044238	View Gene Set	1.434e-08	7629	3.547e-06	54	primary metabolic process	amigo.geneontol...
GO GO:0044106	View Gene Set	1.593e-08	314	3.87e-06	55	cellular amine metabolic process	amigo.geneontol...
GO GO:0001883	View Gene Set	2.354e-08	1620	5.617e-06	56	purine nucleoside binding	amigo.geneontol...
GO GO:0001882	View Gene Set	2.744e-08	1630	6.431e-06	57	nucleoside binding	amigo.geneontol...
GO GO:0044260	View Gene Set	2.953e-08	5699	6.801e-06	58	cellular macromolecule metabolic process	amigo.geneontol...
GO GO:0006412	View Gene Set	3.653e-08	412	8.272e-06	59	translation	amigo.geneontol...
GO GO:0003824	View Gene Set	4.52e-08	5198	1.006e-05	60	catalytic activity	amigo.geneontol...
GO GO:0005634	View Gene Set	5.036e-08	5198	1.103e-05	61	nucleus	amigo.geneontol...
GO GO:0016070	View Gene Set	6.382e-08	2596	1.375e-05	62	RNA metabolic process	amigo.geneontol...
GO GO:0015931	View Gene Set	6.524e-08	118	1.384e-05	63	nucleobase nucleoside nucleotide and nucleic acid transport	amigo.geneontol...
GO GO:0071103	View Gene Set	6.854e-08	140	1.431e-05	64	DNA conformation change	amigo.geneontol...
GO GO:0043170	View Gene Set	8.186e-08	6274	1.683e-05	65	macromolecule metabolic process	amigo.geneontol...
GO GO:0016604	View Gene Set	9.623e-08	198	1.948e-05	66	nuclear body	amigo.geneontol...
GO GO:0000428	View Gene Set	1.17e-07	24	2.3e-05	67	DNA-directed RNA polymerase complex	amigo.geneontol...
GO GO:0055029	View Gene Set	1.17e-07	24	2.3e-05	67	nuclear DNA-directed RNA polymerase complex	amigo.geneontol...
GO GO:0006725	View Gene Set	1.543e-07	145	2.987e-05	69	cellular aromatic compound metabolic process	amigo.geneontol...
GO GO:0006383	View Gene Set	1.686e-07	32	3.173e-05	70	transcription from RNA polymerase III promoter	amigo.geneontol...
GO GO:0009451	View Gene Set	1.68e-07	51	3.173e-05	70	RNA modification	amigo.geneontol...
GO GO:0022618	View Gene Set	1.826e-07	76	3.389e-05	72	ribonucleoprotein complex assembly	amigo.geneontol...
GO GO:0030880	View Gene Set	2.714e-07	25	4.966e-05	73	RNA polymerase complex	amigo.geneontol...
GO GO:0006520	View Gene Set	2.77e-07	231	5.001e-05	74	cellular amino acid metabolic process	amigo.geneontol...
GO GO:0043227	View Gene Set	2.947e-07	8383	5.249e-05	75	membrane-bounded organelle	amigo.geneontol...
GO GO:0043231	View Gene Set	3.982e-07	8376	7e-05	76	intracellular membrane-bounded organelle	amigo.geneontol...
GO GO:0009058	View Gene Set	4.265e-07	4436	7.401e-05	77	biosynthetic process	amigo.geneontol...
GO GO:0044452	View Gene Set	4.584e-07	28	7.852e-05	78	nucleolar part	amigo.geneontol...
GO GO:0044446	View Gene Set	4.654e-07	5019	7.871e-05	79	intracellular organelle part	amigo.geneontol...
GO GO:0044422	View Gene Set	5.08e-07	5089	8.484e-05	80	organelle part	amigo.geneontol...
GO GO:0044455	View Gene Set	5.433e-07	133	8.962e-05	81	mitochondrial membrane part	amigo.geneontol...
GO GO:0016741	View Gene Set	9.088e-07	179	0.0001481	82	transferase activity transferring one-carbon groups	amigo.geneontol...
GO GO:0009308	View Gene Set	1.15e-06	414	0.0001719	83	amine metabolic process	amigo.geneontol...
GO GO:0044249	View Gene Set	1.152e-06	4326	0.0001719	83	cellular biosynthetic process	amigo.geneontol...
GO GO:0050657	View Gene Set	1.111e-06	102	0.0001719	83	nucleic acid transport	amigo.geneontol...
GO GO:0050658	View Gene Set	1.111e-06	102	0.0001719	83	RNA transport	amigo.geneontol...
GO GO:0051236	View Gene Set	1.111e-06	102	0.0001719	83	establishment of RNA localization	amigo.geneontol...
GO GO:0005694	View Gene Set	1.135e-06	507	0.0001719	83	chromosome	amigo.geneontol...
GO GO:0032991	View Gene Set	1.184e-06	3237	0.0001719	83	macromolecular complex	amigo.geneontol...
GO GO:0004812	View Gene Set	1.175e-06	46	0.0001719	83	aminoacyl-tRNA ligase activity	amigo.geneontol...
GO GO:0016875	View Gene Set	1.175e-06	46	0.0001719	83	ligase activity forming carbon-oxygen bonds	amigo.geneontol...
GO GO:0016876	View Gene Set	1.175e-06	46	0.0001719	83	ligase activity forming aminoacyl-tRNA and related compounds	amigo.geneontol...
GO GO:0006519	View Gene Set	1.209e-06	371	0.0001737	93	cellular amino acid and derivative metabolic process	amigo.geneontol...
GO GO:0000049	View Gene Set	1.25e-06	24	0.0001776	94	tRNA binding	amigo.geneontol...
GO GO:0032392	View Gene Set	1.303e-06	19	0.0001813	95	DNA geometric change	amigo.geneontol...
GO GO:0032508	View Gene Set	1.303e-06	19	0.0001813	95	DNA duplex unwinding	amigo.geneontol...
GO GO:0008168	View Gene Set	1.441e-06	176	0.0001984	97	methyltransferase activity	amigo.geneontol...
GO GO:0016779	View Gene Set	1.578e-06	120	0.0002151	98	nucleotidyltransferase activity	amigo.geneontol...
GO GO:0000785	View Gene Set	1.924e-06	213	0.0002597	99	chromatin	amigo.geneontol...
GO GO:0006403	View Gene Set	2.068e-06	104	0.0002763	100	RNA localization	amigo.geneontol...
GO GO:0006418	View Gene Set	2.252e-06	45	0.0002921	101	tRNA aminoacylation for protein translation	amigo.geneontol...
GO GO:0043038	View Gene Set	2.252e-06	45	0.0002921	101	amino acid activation	amigo.geneontol...
GO GO:0043039	View Gene Set	2.252e-06	45	0.0002921	101	tRNA aminoacylation	amigo.geneontol...
GO GO:0006260	View Gene Set	2.857e-06	239	0.000367	104	DNA replication	amigo.geneontol...
GO GO:0003899	View Gene Set	3.017e-06	42	0.0003803	105	DNA-directed RNA polymerase activity	amigo.geneontol...
GO GO:0034062	View Gene Set	3.017e-06	42	0.0003803	105	RNA polymerase activity	amigo.geneontol...
GO GO:0007006	View Gene Set	3.207e-06	29	0.0003989	107	mitochondrial membrane organization	amigo.geneontol...
GO GO:0016740	View Gene Set	3.225e-06	1691	0.0003989	107	transferase activity	amigo.geneontol...
GO GO:0051276	View Gene Set	3.362e-06	548	0.000412	109	chromosome organization	amigo.geneontol...
GO GO:0006268	View Gene Set	3.978e-06	12	0.0004788	110	DNA unwinding involved in replication	amigo.geneontol...
GO GO:0006400	View Gene Set	3.96e-06	18	0.0004788	110	tRNA modification	amigo.geneontol...
GO GO:0000786	View Gene Set	4.443e-06	65	0.0005299	112	nucleosome	amigo.geneontol...
GO GO:0017076	View Gene Set	4.809e-06	1934	0.0005685	113	purine nucleotide binding	amigo.geneontol...
GO GO:0006732	View Gene Set	6.125e-06	164	0.0007178	114	coenzyme metabolic process	amigo.geneontol...
GO GO:0000387	View Gene Set	7.231e-06	31	0.0008401	115	spliceosomal snRNP assembly	amigo.geneontol...
GO GO:0045333	View Gene Set	7.801e-06	100	0.0008985	116	cellular respiration	amigo.geneontol...
GO GO:0006325	View Gene Set	8.636e-06	425	0.0009861	117	chromatin organization	amigo.geneontol...
GO GO:0032553	View Gene Set	9.118e-06	1851	0.001024	118	ribonucleotide binding	amigo.geneontol...
GO GO:0032555	View Gene Set	9.118e-06	1851	0.001024	118	purine ribonucleotide binding	amigo.geneontol...
GO GO:0006261	View Gene Set	9.538e-06	74	0.001062	120	DNA-dependent DNA replication	amigo.geneontol...
GO GO:0009303	View Gene Set	1.198e-05	18	0.001323	121	rRNA transcription	amigo.geneontol...
GO GO:0015030	View Gene Set	1.256e-05	43	0.001375	122	Cajal body	amigo.geneontol...
GO GO:0034728	View Gene Set	1.388e-05	93	0.001507	123	nucleosome organization	amigo.geneontol...
GO GO:0044427	View Gene Set	1.793e-05	420	0.001932	124	chromosomal part	amigo.geneontol...
GO GO:0006323	View Gene Set	2.02e-05	119	0.00216	125	DNA packaging	amigo.geneontol...
GO GO:0030684	View Gene Set	2.301e-05	14	0.00244	126	preribosome	amigo.geneontol...
GO GO:0046112	View Gene Set	2.5e-05	12	0.00263	127	nucleobase biosynthetic process	amigo.geneontol...
GO GO:0006333	View Gene Set	2.857e-05	129	0.002982	128	chromatin assembly or disassembly	amigo.geneontol...
GO GO:0007005	View Gene Set	2.932e-05	139	0.003036	129	mitochondrion organization	amigo.geneontol...
GO GO:0009156	View Gene Set	3.131e-05	24	0.003193	130	ribonucleoside monophosphate biosynthetic process	amigo.geneontol...
GO GO:0042558	View Gene Set	3.128e-05	23	0.003193	130	pteridine and derivative metabolic process	amigo.geneontol...
GO GO:0051186	View Gene Set	3.399e-05	215	0.00344	132	cofactor metabolic process	amigo.geneontol...
GO GO:0006401	View Gene Set	3.517e-05	74	0.003533	133	RNA catabolic process	amigo.geneontol...
GO GO:0051188	View Gene Set	3.619e-05	112	0.003608	134	cofactor biosynthetic process	amigo.geneontol...
GO GO:0006405	View Gene Set	3.749e-05	44	0.00371	135	RNA export from nucleus	amigo.geneontol...
GO GO:0043543	View Gene Set	4.128e-05	72	0.004055	136	protein amino acid acylation	amigo.geneontol...
GO GO:0043021	View Gene Set	4.228e-05	39	0.004123	137	ribonucleoprotein binding	amigo.geneontol...
GO GO:0031497	View Gene Set	4.323e-05	87	0.004185	138	chromatin assembly	amigo.geneontol...
GO GO:0006839	View Gene Set	4.922e-05	75	0.004731	139	mitochondrial transport	amigo.geneontol...
GO GO:0006259	View Gene Set	5.226e-05	592	0.004987	140	DNA metabolic process	amigo.geneontol...
GO GO:0008135	View Gene Set	5.588e-05	86	0.005294	141	translation factor activity nucleic acid binding	amigo.geneontol...
GO GO:0006626	View Gene Set	5.851e-05	32	0.005429	142	protein targeting to mitochondrion	amigo.geneontol...
GO GO:0070585	View Gene Set	5.851e-05	32	0.005429	142	protein localization in mitochondrion	amigo.geneontol...
GO GO:0016853	View Gene Set	5.809e-05	132	0.005429	142	isomerase activity	amigo.geneontol...
GO GO:0051536	View Gene Set	6.763e-05	54	0.006189	145	iron-sulfur cluster binding	amigo.geneontol...
GO GO:0051540	View Gene Set	6.763e-05	54	0.006189	145	metal cluster binding	amigo.geneontol...
GO GO:0009982	View Gene Set	7.374e-05	14	0.006702	147	pseudouridine synthase activity	amigo.geneontol...
GO GO:0000184	View Gene Set	8.072e-05	30	0.007238	148	nuclear-transcribed mRNA catabolic process nonsense-mediated decay	amigo.geneontol...
GO GO:0071339	View Gene Set	8.053e-05	27	0.007238	148	MLL1 complex	amigo.geneontol...
GO GO:0009127	View Gene Set	8.403e-05	17	0.007435	150	purine nucleoside monophosphate biosynthetic process	amigo.geneontol...
GO GO:0009168	View Gene Set	8.403e-05	17	0.007435	150	purine ribonucleoside monophosphate biosynthetic process	amigo.geneontol...
GO GO:0000315	View Gene Set	9.244e-05	18	0.008072	152	organellar large ribosomal subunit	amigo.geneontol...
GO GO:0005762	View Gene Set	9.244e-05	18	0.008072	152	mitochondrial large ribosomal subunit	amigo.geneontol...
GO GO:0009108	View Gene Set	9.53e-05	77	0.008225	154	coenzyme biosynthetic process	amigo.geneontol...
GO GO:0051028	View Gene Set	9.604e-05	90	0.008225	154	mRNA transport	amigo.geneontol...
GO GO:0016887	View Gene Set	9.576e-05	339	0.008225	154	ATPase activity	amigo.geneontol...
GO GO:0006334	View Gene Set	9.957e-05	83	0.008473	157	nucleosome assembly	amigo.geneontol...
GO GO:0006473	View Gene Set	0.0001005	61	0.008495	158	protein amino acid acetylation	amigo.geneontol...
GO GO:0030532	View Gene Set	0.0001033	32	0.008683	159	small nuclear ribonucleoprotein complex	amigo.geneontol...
GO GO:0046930	View Gene Set	0.0001103	85	0.009214	160	pore complex	amigo.geneontol...
GO GO:0005840	View Gene Set	0.0001198	198	0.009942	161	ribosome	amigo.geneontol...
GO GO:0006730	View Gene Set	0.0001232	136	0.01013	162	one-carbon metabolic process	amigo.geneontol...
GO GO:0009309	View Gene Set	0.0001236	83	0.01013	162	amine biosynthetic process	amigo.geneontol...
GO GO:0018130	View Gene Set	0.0001267	63	0.01032	164	heterocycle biosynthetic process	amigo.geneontol...
GO GO:0032993	View Gene Set	0.0001329	99	0.01076	165	protein-DNA complex	amigo.geneontol...
GO GO:0000278	View Gene Set	0.0001372	489	0.01105	166	mitotic cell cycle	amigo.geneontol...
GO GO:0022904	View Gene Set	0.000152	65	0.01216	167	respiratory electron transport chain	amigo.geneontol...
GO GO:0005665	View Gene Set	0.0001539	14	0.01224	168	DNA-directed RNA polymerase II core complex	amigo.geneontol...
GO GO:0000314	View Gene Set	0.0001608	18	0.01264	169	organellar small ribosomal subunit	amigo.geneontol...
GO GO:0005763	View Gene Set	0.0001608	18	0.01264	169	mitochondrial small ribosomal subunit	amigo.geneontol...
GO GO:0003954	View Gene Set	0.0001651	44	0.01275	171	NADH dehydrogenase activity	amigo.geneontol...
GO GO:0008137	View Gene Set	0.0001651	44	0.01275	171	NADH dehydrogenase (ubiquinone) activity	amigo.geneontol...
GO GO:0050136	View Gene Set	0.0001651	44	0.01275	171	NADH dehydrogenase (quinone) activity	amigo.geneontol...
GO GO:0022403	View Gene Set	0.0001938	522	0.01488	174	cell cycle phase	amigo.geneontol...
GO GO:0070469	View Gene Set	0.0002005	77	0.0153	175	respiratory chain	amigo.geneontol...
GO GO:0019438	View Gene Set	0.0002044	17	0.01552	176	aromatic compound biosynthetic process	amigo.geneontol...
GO GO:0022402	View Gene Set	0.0002084	676	0.01569	177	cell cycle process	amigo.geneontol...
GO GO:0032259	View Gene Set	0.0002102	81	0.01569	177	methylation	amigo.geneontol...
GO GO:0043414	View Gene Set	0.0002102	81	0.01569	177	macromolecule methylation	amigo.geneontol...
GO GO:0009295	View Gene Set	0.0002141	31	0.01581	180	nucleoid	amigo.geneontol...
GO GO:0042645	View Gene Set	0.0002141	31	0.01581	180	mitochondrial nucleoid	amigo.geneontol...
GO GO:0008408	View Gene Set	0.0002188	27	0.01606	182	3'-5' exonuclease activity	amigo.geneontol...
GO GO:0016407	View Gene Set	0.0002386	86	0.01742	183	acetyltransferase activity	amigo.geneontol...
GO GO:0016607	View Gene Set	0.0002437	116	0.01769	184	nuclear speck	amigo.geneontol...
GO GO:0007606	View Gene Set	0.0002664	478	0.01914	185	sensory perception of chemical stimulus	amigo.geneontol...
GO GO:0043022	View Gene Set	0.0002664	17	0.01914	185	ribosome binding	amigo.geneontol...
GO GO:0007608	View Gene Set	0.0002773	432	0.01981	187	sensory perception of smell	amigo.geneontol...
GO GO:0000123	View Gene Set	0.0003244	50	0.02305	188	histone acetyltransferase complex	amigo.geneontol...
GO GO:0008173	View Gene Set	0.0003314	27	0.02342	189	RNA methyltransferase activity	amigo.geneontol...
GO GO:0005643	View Gene Set	0.0003406	71	0.02395	190	nuclear pore	amigo.geneontol...
GO GO:0065004	View Gene Set	0.0003466	99	0.02425	191	protein-DNA complex assembly	amigo.geneontol...
GO GO:0051537	View Gene Set	0.0003494	19	0.02431	192	2 iron 2 sulfur cluster binding	amigo.geneontol...
GO GO:0009161	View Gene Set	0.0003705	28	0.02565	193	ribonucleoside monophosphate metabolic process	amigo.geneontol...
GO GO:0042559	View Gene Set	0.0003744	13	0.02578	194	pteridine and derivative biosynthetic process	amigo.geneontol...
GO GO:0004984	View Gene Set	0.0003962	419	0.02715	195	olfactory receptor activity	amigo.geneontol...
GO GO:0005747	View Gene Set	0.0004213	46	0.02843	196	mitochondrial respiratory chain complex I	amigo.geneontol...
GO GO:0030964	View Gene Set	0.0004213	46	0.02843	196	NADH dehydrogenase complex	amigo.geneontol...
GO GO:0045271	View Gene Set	0.0004213	46	0.02843	196	respiratory chain complex I	amigo.geneontol...
GO GO:0001522	View Gene Set	0.0004335	14	0.0291	199	pseudouridine synthesis	amigo.geneontol...
GO GO:0008565	View Gene Set	0.0004414	85	0.02949	200	protein transporter activity	amigo.geneontol...

Gene Set Collection: Broad.c1.CYTOBAND

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CGP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad chr17q25	View Gene Set	5.207e-07	172	0.0001697	1	Genes in cytogenetic band chr17q25	www.broad.mit.e...
Broad chr9q34	View Gene Set	6.307e-06	204	0.001028	2	Genes in cytogenetic band chr9q34	www.broad.mit.e...
Broad chr16p13	View Gene Set	4.1e-05	254	0.004456	3	Genes in cytogenetic band chr16p13	www.broad.mit.e...
Broad chr17p13	View Gene Set	0.0001484	225	0.01209	4	Genes in cytogenetic band chr17p13	www.broad.mit.e...
Broad chr16q24	View Gene Set	0.0002753	88	0.01496	5	Genes in cytogenetic band chr16q24	www.broad.mit.e...
Broad chr22q13	View Gene Set	0.000263	179	0.01496	5	Genes in cytogenetic band chr22q13	www.broad.mit.e...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN	View Gene Set	7.576e-67	920	1.812e-63	1	Genes down-regulated in HL-60 cells (acute promyelocytic leukemia APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h.	www.broad.mit.e...
Broad KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN	View Gene Set	3.923e-46	832	4.691e-43	2	Genes down-regulated in HL-60 cells (acute promyelocytic leukemia APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h.	www.broad.mit.e...
Broad MANALO_HYPOXIA_DN	View Gene Set	6.074e-45	276	4.843e-42	3	Genes down-regulated in response to both hypoxia and overexpression of an active form of HIF1A [Gene ID=3091].	www.broad.mit.e...
Broad WEI_MYCN_TARGETS_WITH_E_BOX	View Gene Set	2.774e-37	757	1.659e-34	4	Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [Gene ID=4613].	www.broad.mit.e...
Broad PUJANA_CHEK2_PCC_NETWORK	View Gene Set	3.48e-31	744	1.665e-28	5	Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient PCC >= 0.4) with that of CHEK2 [Gene ID=11200].	www.broad.mit.e...
Broad PUJANA_BRCA1_PCC_NETWORK	View Gene Set	4.603e-30	1582	1.835e-27	6	Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of BRCA1 [Gene ID=672] across a compendium of normal tissues.	www.broad.mit.e...
Broad CAIRO_HEPATOBLASTOMA_CLASSES_UP	View Gene Set	9.414e-28	577	3.217e-25	7	Genes up-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1).	www.broad.mit.e...
Broad MOOTHA_MITOCHONDRIA	View Gene Set	2.124e-18	433	6.351e-16	8	Mitochondrial genes	www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM	View Gene Set	1.898e-17	154	5.044e-15	9	Cluster 7: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [Gene ID=4609] and down-regulated by the combination of MYC and serum.	www.broad.mit.e...
Broad WELCSH_BRCA1_TARGETS_1_DN	View Gene Set	2.555e-17	124	6.111e-15	10	Upregulated by induction of exogenous BRCA1 in EcR-293 cells	www.broad.mit.e...
Broad WONG_EMBRYONIC_STEM_CELL_CORE	View Gene Set	2.978e-17	331	6.476e-15	11	The 'core ESC-like gene module': genes coordinately up-regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module.	www.broad.mit.e...
Broad MOOTHA_HUMAN_MITODB_6_2002	View Gene Set	2.552e-16	420	5.087e-14	12	Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets.	www.broad.mit.e...
Broad SCHUHMACHER_MYC_TARGETS_UP	View Gene Set	1.064e-15	68	1.957e-13	13	Genes up-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [Gene ID=4609].	www.broad.mit.e...
Broad DODD_NASOPHARYNGEAL_CARCINOMA_DN	View Gene Set	7.111e-15	1253	1.215e-12	14	Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue.	www.broad.mit.e...
Broad GARY_CD5_TARGETS_DN	View Gene Set	1.111e-14	415	1.666e-12	15	Genes down-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [Gene ID=921] off a plasmid vector.	www.broad.mit.e...
Broad KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP	View Gene Set	1.114e-14	1180	1.666e-12	15	Genes up-regulated in TC71 and EWS502 cells (Ewing's sarcoma) upon knockdown of the EWSR1-FLII fusion [Gene ID=2130 2314].	www.broad.mit.e...
Broad PENG_GLUTAMINE_DEPRIVATION_DN	View Gene Set	5.843e-12	84	8.221e-10	17	Genes down-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation.	www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP	View Gene Set	2.606e-11	45	3.463e-09	18	Cluster 5: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [Gene ID=4609] alone or in combination with serum but not by serum alone.	www.broad.mit.e...
Broad SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN	View Gene Set	3.22e-11	46	4.053e-09	19	Cluster 6: genes down-regulated in B493-6 cells (B lymphocytes) by MYC [Gene ID=4609] in combination with serum but not affected by serum alone; they are also up-regulated by MYC alone.	www.broad.mit.e...
Broad PENG_RAPAMYCIN_RESPONSE_DN	View Gene Set	7.27e-11	69	8.694e-09	20	Genes down-regulated in BJUB cells (B-lymphoma) in response to rapamycin [PubChem=6610346] treatment.	www.broad.mit.e...
Broad TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C	View Gene Set	1.861e-10	436	2.12e-08	21	Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [Gene ID=407041 407042] microRNAs.	www.broad.mit.e...
Broad MUELLER_PLURINET	View Gene Set	2.341e-10	294	2.545e-08	22	Genes constituting the PluriNet protein-protein network shared by the pluripotent cells (embryonic stem cells embryonical carcinomas and induced pluripotent cells).	www.broad.mit.e...
Broad DANG_MYC_TARGETS_UP	View Gene Set	4.311e-10	127	4.484e-08	23	Genes up-regulated by MYC [Gene ID=4609] and whose promoters are bound by MYC according to MYC Target Gene Database.	www.broad.mit.e...
Broad MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP	View Gene Set	6.901e-10	359	6.878e-08	24	The postradiation tumor escape signature: genes up-regulated in tumors from irradiated stroma vs those from non-irradiated stroma.	www.broad.mit.e...
Broad GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN	View Gene Set	1.188e-09	148	1.137e-07	25	Genes down-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [Gene ID=2313 190] by RNAi.	www.broad.mit.e...
Broad SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY	View Gene Set	1.34e-09	31	1.233e-07	26	Cluster 3: genes strongly up-regulated in B493-6 cells (B lymphocytes) by a combination of MYC [Gene ID=4609] and serum but not by each of them alone.	www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_DN	View Gene Set	1.745e-09	136	1.546e-07	27	Genes down-regulated in MCF7 cells (breast cancer) under hypoxia conditions.	www.broad.mit.e...
Broad PUJANA_BRCA2_PCC_NETWORK	View Gene Set	4.36e-09	410	3.725e-07	28	Genes constituting the BRCA2-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of BRCA2 [Gene ID=675] across a compendium of normal tissues.	www.broad.mit.e...
Broad GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN	View Gene Set	2.24e-08	308	1.848e-06	29	Genes down-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [Gene ID=7764] locus only.	www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14	View Gene Set	3.359e-08	131	2.678e-06	30	Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 14.	www.broad.mit.e...
Broad KOBAYASHI_EGFR_SIGNALING_24HR_DN	View Gene Set	8.597e-08	243	6.426e-06	31	Genes down-regulated in H1975 cells (non-small cell lung cancer NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h.	www.broad.mit.e...
Broad DANG_BOUND_BY_MYC	View Gene Set	8.394e-08	1045	6.426e-06	31	Genes whose promoters are bound by MYC [Gene ID=4609] according to MYC Target Gene Database.	www.broad.mit.e...
Broad BERENJENO_TRANSFORMED_BY_RHOA_UP	View Gene Set	9.555e-08	485	6.795e-06	33	Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [Gene ID=387] off plasmid vector.	www.broad.mit.e...
Broad WONG_MITOCHONDRIA_GENE_MODULE	View Gene Set	9.659e-08	208	6.795e-06	33	Genes that comprise the mitochondria gene module	www.broad.mit.e...
Broad ELVIDGE_HIF1A_TARGETS_UP	View Gene Set	2.421e-07	64	1.654e-05	35	Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [Gene ID=3091] by RNAi.	www.broad.mit.e...
Broad BILD_MYC_ONCOGENIC_SIGNATURE	View Gene Set	3.82e-07	187	2.538e-05	36	Genes selected in supervised analyses to discriminate cells expressing c-Myc [Gene ID=4609] from control cells expressing GFP.	www.broad.mit.e...
Broad PAL_PRMT5_TARGETS_UP	View Gene Set	6.168e-07	178	3.987e-05	37	Genes up-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [Gene ID=10419] by RNAi.	www.broad.mit.e...
Broad PUJANA_BRCA_CENTERED_NETWORK	View Gene Set	8.682e-07	92	5.465e-05	38	Genes constituting the BRCA-centered network (BCN).	www.broad.mit.e...
Broad KIM_GASTRIC_CANCER_CHEMOSENSITIVITY	View Gene Set	9.063e-07	97	5.559e-05	39	Genes up-regulated in gastric cancer patients refractory to chemotherapy treatment with 5-fluorouracil and cisplatin [PubChem=3385 2767] compared to the sensitive state.	www.broad.mit.e...
Broad CROONQUIST_NRAS_SIGNALING_DN	View Gene Set	3.297e-06	62	0.0001971	40	Genes down-regulated in ANBL-6 cell line (multiple myeloma MM) expressing a constantly active form of NRAS [Gene ID=4893] off a plasmid vector compared to those grown in the presence of IL6 [Gene ID=3569].	www.broad.mit.e...
Broad PUJANA_ATM_PCC_NETWORK	View Gene Set	3.883e-06	1375	0.0002265	41	Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient PCC >= 0.4) with that of ATM [Gene ID=472] across a compendium of normal tissues.	www.broad.mit.e...
Broad FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN	View Gene Set	4.263e-06	43	0.0002428	42	Genes down-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen raloxifene or ICI 182780 but not by estradiol [PubChem=44959 5035 3478439 5757].	www.broad.mit.e...
Broad PUJANA_XPRSS_INT_NETWORK	View Gene Set	5.135e-06	164	0.0002856	43	Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1 BRCA2 ATM and CHEK2 [Gene ID=672 675 472 11200] in a compendium of normal tissues.	www.broad.mit.e...
Broad CROONQUIST_IL6_DEPRIVATION_DN	View Gene Set	5.327e-06	80	0.0002896	44	Genes down-regulated in the ANBL-6 cell line (multiple myeloma MM) after withdrawal of IL6 [Gene ID=3569].	www.broad.mit.e...
Broad FUJII_YBX1_TARGETS_DN	View Gene Set	6.141e-06	139	0.0003264	45	Genes down-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [Gene ID=4904] by RNAi.	www.broad.mit.e...
Broad SHEPARD_CRUSH_AND_BURN_MUTANT_UP	View Gene Set	6.902e-06	135	0.0003589	46	Human orthologs of genes up-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [Gene ID=4605].	www.broad.mit.e...
Broad CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN	View Gene Set	7.701e-06	639	0.0003919	47	Genes down-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [Gene ID=5371 5914] compared to normal promyeloblasts.	www.broad.mit.e...
Broad MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP	View Gene Set	8.017e-06	92	0.0003995	48	Genes correlated with the early tumor onset in the Emu-myc transgenic mouse lymphoma model.	www.broad.mit.e...
Broad TARTE_PLASMA_CELL_VS_PLASMABLAST_DN	View Gene Set	9.797e-06	303	0.0004694	49	Genes down-regulated in mature plasma cells compared with plasmablastic B lymphocytes.	www.broad.mit.e...
Broad GRADE_COLON_CANCER_UP	View Gene Set	9.812e-06	711	0.0004694	49	Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples.	www.broad.mit.e...
Broad BENPORATH_MYC_TARGETS_WITH_EBOX	View Gene Set	1.108e-05	229	0.0005098	51	Set 'Myc targets1': targets of c-Myc [Gene ID=4609] identified by ChIP on chip in cultured cell lines focusing on E-box???containing genes; high affinity bound subset	www.broad.mit.e...
Broad MENSSEN_MYC_TARGETS	View Gene Set	1.104e-05	16	0.0005098	51	Genes up-regulated by adenoviral expression of c-MYC [Gene ID=4609] in HUVEC cells (umbilical vein endothelium).	www.broad.mit.e...
Broad ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP	View Gene Set	1.439e-05	38	0.0006495	53	Genes up-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [Gene ID=3091 2034] by RNAi.	www.broad.mit.e...
Broad ZHANG_RESPONSE_TO_CANTHARIDIN_DN	View Gene Set	1.947e-05	60	0.0008625	54	Genes down-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701].	www.broad.mit.e...
Broad DANG_REGULATED_BY_MYC_UP	View Gene Set	2.572e-05	65	0.001119	55	Genes up-regulated by MYC [Gene ID=4609] according to the MYC Target Gene Database.	www.broad.mit.e...
Broad PENG_LEUCINE_DEPRIVATION_DN	View Gene Set	2.632e-05	50	0.001124	56	Genes down-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation.	www.broad.mit.e...
Broad SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6	View Gene Set	3.102e-05	435	0.001302	57	Cluster 6 of method A: up-regulation of these genes in patients with non???small cell lung cancer (NSCLC) predicts poor survival outcome.	www.broad.mit.e...
Broad HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP	View Gene Set	3.464e-05	59	0.001384	58	Genes up-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [Gene ID=3205 4211].	www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11	View Gene Set	3.44e-05	93	0.001384	58	Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 11.	www.broad.mit.e...
Broad SONG_TARGETS_OF_IE86_CMV_PROTEIN	View Gene Set	3.471e-05	49	0.001384	58	Cellular genes up-regulated in forskin fibroblasts by expression of CMV EI86 protein off an adenovirus vector.	www.broad.mit.e...
Broad IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR	View Gene Set	4.142e-05	100	0.001624	61	Genes in the expression cluster 'Early Progenitors Shared': up-regulated in hematopoietic progenitors from adult bone marrow and from fetal liver.	www.broad.mit.e...
Broad BROWNE_HCMV_INFECTION_14HR_UP	View Gene Set	5.648e-05	150	0.002179	62	Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not up-regulated at the previous time point 12 h.	www.broad.mit.e...
Broad MOOTHA_PGC	View Gene Set	5.879e-05	329	0.002232	63	Genes up-regulated in differentiating C2C12 cells (myoblasts) upon expression of PPARGC1A [Gene ID=10891] off an adenoviral vector.	www.broad.mit.e...
Broad TIEN_INTESTINE_PROBIOTICS_24HR_UP	View Gene Set	5.978e-05	537	0.002234	64	Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h.	www.broad.mit.e...
Broad DAIRKEE_TERT_TARGETS_UP	View Gene Set	7.872e-05	317	0.002897	65	Genes up-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [Gene ID=7015] off a retroviral vector.	www.broad.mit.e...
Broad GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN	View Gene Set	9.879e-05	160	0.00358	66	Genes down-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2 STK6 and ZNF217 [Gene ID=4605 6790 7764]	www.broad.mit.e...
Broad WHITEFORD_PEDIATRIC_CANCER_MARKERS	View Gene Set	0.0001111	92	0.003967	67	Differentially expressed genes in a panel of xenografts representing 8 common pediatric tumors compared to the normal tissues.	www.broad.mit.e...
Broad BENPORATH_ES_1	View Gene Set	0.0001243	367	0.004374	68	Set 'ES exp1': genes overexpressed in human embryonic stem cells according to 5 or more out of 20 profiling studies.	www.broad.mit.e...
Broad BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP	View Gene Set	0.0001346	190	0.004665	69	Genes up-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD).	www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_16P13_AMPLICON	View Gene Set	0.0001489	115	0.005087	70	Genes within amplicon 16p13 identified in a study of 191 breast tumor samples.	www.broad.mit.e...
Broad KIM_MYC_AMPLIFICATION_TARGETS_UP	View Gene Set	0.0001633	155	0.005501	71	Genes positively correlated with amplifications of MYC [Gene ID=4609] in SCLC (small cell lung cancer) cell lines.	www.broad.mit.e...
Broad BASSO_B_LYMPHOCYTE_NETWORK	View Gene Set	0.000168	136	0.005581	72	Genes which comprise the top 1% of highly interconnected genes (major hubs) that account for most of gene interactions in the reconstructed regulatory networks from expression profiles in B lymphocytes.	www.broad.mit.e...
Broad GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN	View Gene Set	0.0001768	51	0.005769	73	Genes from the turquoise module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC).	www.broad.mit.e...
Broad CHANG_CORE_SERUM_RESPONSE_UP	View Gene Set	0.0001785	66	0.005769	73	Up-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group.	www.broad.mit.e...
Broad ELVIDGE_HYPOXIA_BY_DMOG_DN	View Gene Set	0.0001964	56	0.006263	75	Genes down-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614].	www.broad.mit.e...
Broad STEIN_ESRRA_TARGETS_UP	View Gene Set	0.000267	368	0.008403	76	Genes up-regulated by ESRRA [Gene ID=2101] only.	www.broad.mit.e...
Broad VECCHI_GASTRIC_CANCER_EARLY_UP	View Gene Set	0.0002768	408	0.0086	77	Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples.	www.broad.mit.e...
Broad ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN	View Gene Set	0.0003005	346	0.009214	78	Genes down-regulated in normal tissue adjacent to liver tumor compared to the normal liver samples.	www.broad.mit.e...
Broad FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP	View Gene Set	0.0003228	144	0.009775	79	Genes up-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones.	www.broad.mit.e...
Broad WINNEPENNINCKX_MELANOMA_METASTASIS_UP	View Gene Set	0.0003492	152	0.01044	80	Genes from the 254-gene classifier which were up-regulated in melanoma patients with a reported distant metastasis within 4 years.	www.broad.mit.e...
Broad RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP	View Gene Set	0.0003662	589	0.01082	81	Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue.	www.broad.mit.e...
Broad SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC	View Gene Set	0.0003869	101	0.01115	82	Cluster 2: genes up-regulated in B493-6 cells (B lymphocytes) by serum alone or in combination with MYC [Gene ID=4609] but not by MYC alone.	www.broad.mit.e...
Broad LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER	View Gene Set	0.0003849	167	0.01115	82	Overexpressed genes with amplified copy number across 27 non-small cell lung cancer (NSCLC) cell lines.	www.broad.mit.e...
Broad CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP	View Gene Set	0.0004277	47	0.01218	84	Genes up-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743].	www.broad.mit.e...
Broad SHEN_SMARCA2_TARGETS_DN	View Gene Set	0.0004552	334	0.01252	85	Genes whose expression negatively correlated with that of SMARCA2 [Gene ID=6595] in prostate cancer samples.	www.broad.mit.e...
Broad BLUM_RESPONSE_TO_SALIRASIB_DN	View Gene Set	0.0004542	332	0.01252	85	Selected genes down-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [Gene ID=3265].	www.broad.mit.e...
Broad KRASNOSELSKAYA_ILF3_TARGETS_DN	View Gene Set	0.0004529	38	0.01252	85	Down-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [Gene ID=3609].	www.broad.mit.e...
Broad FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN	View Gene Set	0.0004719	76	0.0127	88	Top 100 genes positively (UP) and negatively (DN) associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [Gene ID=4297 4298].	www.broad.mit.e...
Broad MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN	View Gene Set	0.0004727	121	0.0127	88	Genes distinguishing in multiple myeloma (MM) samples with lower expression of TACI [Gene ID=23495].	www.broad.mit.e...
Broad GOLDRATH_HOMEOSTATIC_PROLIFERATION	View Gene Set	0.0004826	154	0.01283	90	Up-regulated in CD8+ [Gene ID=925] T lymphocytes undergoing homeostatic proliferation (HP) versus the naive cells; these genes are not up-regulated versus effector or memory cell population.	www.broad.mit.e...
Broad RIZ_ERYTHROID_DIFFERENTIATION	View Gene Set	0.0005628	71	0.01479	91	Selected gradually up-regulated genes in the TLX1 [Gene ID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts).	www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP	View Gene Set	0.000577	36	0.01484	92	Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors.	www.broad.mit.e...
Broad RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN	View Gene Set	0.000577	36	0.01484	92	Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors.	www.broad.mit.e...
Broad BIDUS_METASTASIS_UP	View Gene Set	0.0006227	203	0.01585	94	Genes up-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases.	www.broad.mit.e...
Broad XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN	View Gene Set	0.0006336	14	0.01595	95	Genes down-regulated synergistically in NB4 cells (acute promyelocytic leukemia APL) by tretinoin and NSC682994 [PubChem=5538 388304].	www.broad.mit.e...
Broad HEIDENBLAD_AMPLICON_8Q24_UP	View Gene Set	0.0006837	29	0.01704	96	Up-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines.	www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON	View Gene Set	0.0007199	48	0.01775	97	Genes within amplicon 16q24 identified in a copy number alterations study of 191 breast tumor samples.	www.broad.mit.e...
Broad ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN	View Gene Set	0.0007325	42	0.01788	98	Genes down-regulated in P493-6 cells (B lymphocyte) by MYC [Gene ID=4609] and up-regulated by RNAi knockdown of TFRC [Gene ID=7037].	www.broad.mit.e...
Broad GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN	View Gene Set	0.0007949	86	0.01921	99	Genes down-regulated in quiescent vs dividing CD34+ [Gene ID=8842] cells isolated from peripheral blood of normal donors.	www.broad.mit.e...
Broad UDAYAKUMAR_MED1_TARGETS_UP	View Gene Set	0.000871	129	0.02083	100	Genes up-regulated in HeLa cells after knockdown of MED1 [Gene ID=5469] by RNAi.	www.broad.mit.e...
Broad LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN	View Gene Set	0.0009212	158	0.02182	101	Genes down-regulated in Wilm's tumor samples compared to fetal kidney.	www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_7P22_AMPLICON	View Gene Set	0.000943	36	0.02211	102	Genes within amplicon 7p22 identified in a copy number alterations study of 191 breast tumor samples.	www.broad.mit.e...
Broad YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17	View Gene Set	0.0009906	165	0.02301	103	Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 17.	www.broad.mit.e...
Broad JIANG_TIP30_TARGETS_DN	View Gene Set	0.001031	23	0.02371	104	Down-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [Gene ID=10553] compared to its wild type form.	www.broad.mit.e...
Broad MOOTHA_VOXPHOS	View Gene Set	0.001052	82	0.02395	105	Genes involved in oxidative phosphorylation; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets.	www.broad.mit.e...
Broad BENPORATH_MYC_MAX_TARGETS	View Gene Set	0.001269	768	0.02863	106	Set 'Myc targets2': targets of c-Myc [Gene ID=4609] and Max [Gene ID=4149] identified by ChIP on chip in a Burkitt???s lymphoma cell line; overlap set.	www.broad.mit.e...
Broad LEE_METASTASIS_AND_RNA_PROCESSING_UP	View Gene Set	0.001288	15	0.0288	107	Components of RNA post-transcriptional modification machinery up-regulated in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [Gene ID=4830].	www.broad.mit.e...
Broad MATTIOLI_MGUS_VS_PCL	View Gene Set	0.001313	109	0.02908	108	Genes changed in MGUS (monoclonal gammopathy of undetermined significance) compared to PCL (plasma cell leukemia) samples.	www.broad.mit.e...
Broad GAJATE_RESPONSE_TO_TRABECTEDIN_DN	View Gene Set	0.001479	16	0.03246	109	Genes down-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199].	www.broad.mit.e...
Broad MARKEY_RB1_ACUTE_LOF_DN	View Gene Set	0.001544	201	0.03358	110	Genes down-regulated in adult fibroblasts with inactivated RB1 [Gene ID=5925] by Cre-lox: acute loss of function (LOF) of RB1.	www.broad.mit.e...
Broad COLLER_MYC_TARGETS_UP	View Gene Set	0.001655	12	0.03566	111	Genes regulated by forced expression of MYC [Gene ID=4609] in 293T (transformed fetal renal cell).	www.broad.mit.e...
Broad EGUCHI_CELL_CYCLE_RB1_TARGETS	View Gene Set	0.001686	19	0.03602	112	RB1 [Gene ID=5925] target genes involved in cell cycle regulation: genes down-regulated by doxorubicin [PubChem=31703] only in cells expressing RB1.	www.broad.mit.e...
Broad FAELT_B_CLL_WITH_VH3_21_UP	View Gene Set	0.001722	44	0.03644	113	Genes changed in samples from B-CLL (B-cell chronic lymphocytic leukemia) using the immunoglobulin heavy chain VH3-21 gene.	www.broad.mit.e...
Broad CASTELLANO_HRAS_AND_NRAS_TARGETS_UP	View Gene Set	0.001803	5	0.03783	114	Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS [Gene ID=3265] and NRAS [Gene ID=4893] double knockout mice.	www.broad.mit.e...
Broad CAFFAREL_RESPONSE_TO_THC_DN	View Gene Set	0.00184	25	0.03826	115	Genes down-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319].	www.broad.mit.e...
Broad PRAMOONJAGO_SOX4_TARGETS_DN	View Gene Set	0.001907	51	0.03932	116	Genes down-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [Gene ID=6659] by RNAi.	www.broad.mit.e...
Broad HELLER_HDAC_TARGETS_DN	View Gene Set	0.001939	250	0.03964	117	Genes down-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562].	www.broad.mit.e...
Broad MORI_IMMATURE_B_LYMPHOCYTE_DN	View Gene Set	0.002062	52	0.04181	118	Down-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage.	www.broad.mit.e...
Broad KAUFFMANN_DNA_REPLICATION_GENES	View Gene Set	0.002084	128	0.04189	119	Genes involved in DNA replication compiled manually by the authors.	www.broad.mit.e...
Broad MUNSHI_MULTIPLE_MYELOMA_DN	View Gene Set	0.002232	9	0.04449	120	Genes down-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin.	www.broad.mit.e...
Broad NIKOLSKY_BREAST_CANCER_19Q13.4_AMPLICON	View Gene Set	0.002435	7	0.04813	121	Genes within amplicon 19q13.4 identified in a copy number alterations study of 191 breast tumor samples.	www.broad.mit.e...

Gene Set Collection: Broad.c2.CP.BIOCARTA

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CP.KEGG

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CP.REACTOME

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad BIOCARTA_ETC_PATHWAY	View Gene Set	9.994e-05	12	0.02169	1	Electron Transport Reaction in Mitochondria	www.broad.mit.e...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad KEGG_SPLICEOSOME	View Gene Set	1.25e-10	118	2.326e-08	1	Spliceosome	www.broad.mit.e...
Broad KEGG_AMINOACYL_TRNA_BIOSYNTHESIS	View Gene Set	7.935e-08	41	7.38e-06	2	Aminoacyl-tRNA biosynthesis	www.broad.mit.e...
Broad KEGG_PYRIMIDINE_METABOLISM	View Gene Set	1.059e-06	98	6.566e-05	3	Pyrimidine metabolism	www.broad.mit.e...
Broad KEGG_RNA_POLYMERASE	View Gene Set	4.323e-05	29	0.00201	4	RNA polymerase	www.broad.mit.e...
Broad KEGG_ONE_CARBON_POOL_BY_FOLATE	View Gene Set	0.0001163	17	0.004328	5	One carbon pool by folate	www.broad.mit.e...
Broad KEGG_DNA_REPLICATION	View Gene Set	0.0001644	36	0.005097	6	DNA replication	www.broad.mit.e...
Broad KEGG_LYSINE_DEGRADATION	View Gene Set	0.000302	44	0.007022	7	Lysine degradation	www.broad.mit.e...
Broad KEGG_RNA_DEGRADATION	View Gene Set	0.0003	59	0.007022	7	RNA degradation	www.broad.mit.e...
Broad KEGG_BASE_EXCISION_REPAIR	View Gene Set	0.0004114	35	0.008502	9	Base excision repair	www.broad.mit.e...
Broad KEGG_PURINE_METABOLISM	View Gene Set	0.0005591	157	0.0104	10	Purine metabolism	www.broad.mit.e...
Broad KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS	View Gene Set	0.0007528	11	0.01273	11	Valine leucine and isoleucine biosynthesis	www.broad.mit.e...
Broad KEGG_CITRATE_CYCLE_TCA_CYCLE	View Gene Set	0.00185	32	0.02867	12	Citrate cycle (TCA cycle)	www.broad.mit.e...
Broad KEGG_OLFACTORY_TRANSDUCTION	View Gene Set	0.002281	389	0.03264	13	Olfactory transduction	www.broad.mit.e...
Broad KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY	View Gene Set	0.00296	56	0.03933	14	Cytosolic DNA-sensing pathway	www.broad.mit.e...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad REACTOME_TELOMERE_MAINTENANCE	View Gene Set	3.33e-11	77	8.789e-09	1	Genes involved in Telomere Maintenance	www.broad.mit.e...
Broad REACTOME_TRANSCRIPTION	View Gene Set	4.088e-11	188	8.789e-09	1	Genes involved in Transcription	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_I_III_AND_MITOCHONDRIAL_TRANSCRIPTION	View Gene Set	8.102e-11	120	1.161e-08	3	Genes involved in RNA Polymerase I RNA Polymerase III and Mitochondrial Transcription	www.broad.mit.e...
Broad REACTOME_PACKAGING_OF_TELOMERE_ENDS	View Gene Set	4.195e-10	49	4.509e-08	4	Genes involved in Packaging Of Telomere Ends	www.broad.mit.e...
Broad REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA	View Gene Set	9.231e-09	128	7.939e-07	5	Genes involved in Processing of Capped Intron-Containing Pre-mRNA	www.broad.mit.e...
Broad REACTOME_METABOLISM_OF_RNA	View Gene Set	1.431e-08	95	1.026e-06	6	Genes involved in Metabolism of RNA	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE	View Gene Set	2.378e-07	82	1.461e-05	7	Genes involved in RNA PolymerasePromoter Clearance	www.broad.mit.e...
Broad REACTOME_GENE_EXPRESSION	View Gene Set	5.529e-07	415	2.161e-05	8	Genes involved in Gene Expression	www.broad.mit.e...
Broad REACTOME_MRNA_SPLICING	View Gene Set	5.1e-07	97	2.161e-05	8	Genes involved in mRNA Splicing	www.broad.mit.e...
Broad REACTOME_TRNA_AMINOACYLATION	View Gene Set	4.817e-07	40	2.161e-05	8	Genes involved in tRNA Aminoacylation	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_I_PROMOTER_OPENING	View Gene Set	5.312e-07	59	2.161e-05	8	Genes involved in RNA Polymerase I Promoter Opening	www.broad.mit.e...
Broad REACTOME_SNRNP_ASSEMBLY	View Gene Set	2.449e-06	50	8.775e-05	12	Genes involved in snRNP Assembly	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER	View Gene Set	4.424e-06	20	0.0001463	13	Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter	www.broad.mit.e...
Broad REACTOME_FORMATION_AND_MATURATION_OF_MRNA_TRANSCRIPT	View Gene Set	6.362e-06	142	0.0001954	14	Genes involved in Formation and Maturation of mRNA Transcript	www.broad.mit.e...
Broad REACTOME_ELONGATION_AND_PROCESSING_OF_CAPPED_TRANSCRIPTS	View Gene Set	1.037e-05	124	0.0002974	15	Genes involved in Elongation and Processing of Capped Transcripts	www.broad.mit.e...
Broad REACTOME_GLUCOSE_REGULATION_OF_INSULIN_SECRETION	View Gene Set	2.112e-05	161	0.0005675	16	Genes involved in Glucose Regulation of Insulin Secretion	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION	View Gene Set	3.758e-05	29	0.0009505	17	Genes involved in RNA Polymerase III Transcription Initiation	www.broad.mit.e...
Broad REACTOME_METABLISM_OF_NUCLEOTIDES	View Gene Set	4.226e-05	71	0.001009	18	Genes involved in Metablism of nucleotides	www.broad.mit.e...
Broad REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION	View Gene Set	5.669e-05	20	0.001283	19	Genes involved in Mitochondrial tRNA aminoacylation	www.broad.mit.e...
Broad REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRON_CONTAINING_TRANSCRIPT	View Gene Set	7.144e-05	42	0.001536	20	Genes involved in Transport of Mature mRNA derived from an Intron-Containing Transcript	www.broad.mit.e...
Broad REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS	View Gene Set	0.0001627	11	0.003332	21	Genes involved in Purine ribonucleoside monophosphate biosynthesis	www.broad.mit.e...
Broad REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION	View Gene Set	0.0001821	23	0.00356	22	Genes involved in Cytosolic tRNA aminoacylation	www.broad.mit.e...
Broad REACTOME_INTEGRATION_OF_ENERGY_METABOLISM	View Gene Set	0.0003833	229	0.006868	23	Genes involved in Integration of energy metabolism	www.broad.mit.e...
Broad REACTOME_MICRORNA_BIOGENESIS	View Gene Set	0.0003823	18	0.006868	23	Genes involved in MicroRNA biogenesis	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION	View Gene Set	0.0004096	34	0.007045	25	Genes involved in RNA Polymerase III Transcription	www.broad.mit.e...
Broad REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE	View Gene Set	0.000609	90	0.009666	26	Genes involved in Late Phase of HIV Life Cycle	www.broad.mit.e...
Broad REACTOME_TRANSPORT_OF_THE_SLBP_INDEPENDENT_MATURE_MRNA	View Gene Set	0.0006294	32	0.009666	26	Genes involved in Transport of the SLBP independent Mature mRNA	www.broad.mit.e...
Broad REACTOME_METABOLISM_OF_MRNA	View Gene Set	0.0005957	45	0.009666	26	Genes involved in Metabolism of mRNA	www.broad.mit.e...
Broad REACTOME_CELL_CYCLE_MITOTIC	View Gene Set	0.0007766	306	0.01113	29	Genes involved in Cell Cycle Mitotic	www.broad.mit.e...
Broad REACTOME_MRNA_SPLICING_MINOR_PATHWAY	View Gene Set	0.0007605	38	0.01113	29	Genes involved in mRNA Splicing - Minor Pathway	www.broad.mit.e...
Broad REACTOME_CHAPERONIN_MEDIATED_PROTEIN_FOLDING	View Gene Set	0.000915	50	0.01203	31	Genes involved in Chaperonin-mediated protein folding	www.broad.mit.e...
Broad REACTOME_HIV_LIFE_CYCLE	View Gene Set	0.000951	103	0.01203	31	Genes involved in HIV Life Cycle	www.broad.mit.e...
Broad REACTOME_NUCLEAR_IMPORT_OF_REV_PROTEIN	View Gene Set	0.0009085	30	0.01203	31	Genes involved in Nuclear import of Rev protein	www.broad.mit.e...
Broad REACTOME_OLFACTORY_SIGNALING_PATHWAY	View Gene Set	0.0009477	371	0.01203	31	Genes involved in Olfactory Signaling Pathway	www.broad.mit.e...
Broad REACTOME_PYRUVATE_METABOLISM_AND_TCA_CYCLE	View Gene Set	0.001314	36	0.01614	35	Genes involved in Pyruvate metabolism and TCA cycle	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER	View Gene Set	0.001359	22	0.01623	36	Genes involved in RNA Polymerase III Transcription Initiation From Type 3 Promoter	www.broad.mit.e...
Broad REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS	View Gene Set	0.001416	29	0.01646	37	Genes involved in Association of TriC/CCT with target proteins during biosynthesis	www.broad.mit.e...
Broad REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE	View Gene Set	0.001533	11	0.01734	38	Genes involved in mRNA Decay by 3' to 5' Exoribonuclease	www.broad.mit.e...
Broad REACTOME_RNA_POLYMERASE_III_CHAIN_ELONGATION	View Gene Set	0.001587	12	0.0175	39	Genes involved in RNA Polymerase III Chain Elongation	www.broad.mit.e...
Broad REACTOME_REGULATION_OF_INSULIN_SECRETION	View Gene Set	0.001786	212	0.0192	40	Genes involved in Regulation of Insulin Secretion	www.broad.mit.e...
Broad REACTOME_REV_MEDIATED_NUCLEAR_EXPORT_OF_HIV1_RNA	View Gene Set	0.002106	31	0.02208	41	Genes involved in Rev-mediated nuclear export of HIV-1 RNA	www.broad.mit.e...
Broad REACTOME_ELECTRON_TRANSPORT_CHAIN	View Gene Set	0.002177	75	0.02229	42	Genes involved in Electron Transport Chain	www.broad.mit.e...
Broad REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS	View Gene Set	0.003077	37	0.03077	43	Genes involved in Activation of ATR in response to replication stress	www.broad.mit.e...
Broad REACTOME_UNWINDING_OF_DNA	View Gene Set	0.003371	11	0.03295	44	Genes involved in Unwinding of DNA	www.broad.mit.e...
Broad REACTOME_EXTENSION_OF_TELOMERES	View Gene Set	0.00372	28	0.03485	45	Genes involved in Extension of Telomeres	www.broad.mit.e...
Broad REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC	View Gene Set	0.00373	22	0.03485	45	Genes involved in Formation of tubulin folding intermediates by CCT/TriC	www.broad.mit.e...
Broad REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS	View Gene Set	0.003871	29	0.03485	45	Genes involved in Transport of Ribonucleoproteins into the Host Nucleus	www.broad.mit.e...
Broad REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY	View Gene Set	0.003891	29	0.03485	45	Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery	www.broad.mit.e...
Broad REACTOME_METABOLISM_OF_CARBOHYDRATES	View Gene Set	0.005321	119	0.0467	49	Genes involved in Metabolism of carbohydrates	www.broad.mit.e...
Broad REACTOME_VPR_MEDIATED_NUCLEAR_IMPORT_OF_PICS	View Gene Set	0.005646	31	0.04856	50	Genes involved in Vpr-mediated nuclear import of PICs	www.broad.mit.e...

Gene Set Collection: Broad.c3.TFT

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad CACGTG_V$MYC_Q2	View Gene Set	2.032e-07	734	0.000125	1	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif CACGTG which matches annotation for MYC: v-myc myelocytomatosis viral oncogene homolog (avian)	www.broad.mit.e...
Broad V$NMYC_01	View Gene Set	1.635e-06	201	0.0005026	2	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNCCACGTGNNN which matches annotation for MYCN: v-myc myelocytomatosis viral related oncogene neuroblastoma derived (avian)	www.broad.mit.e...
Broad V$MYCMAX_01	View Gene Set	2.94e-06	189	0.0006027	3	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNACCACGTGGTNN which matches annotation for MYC: v-myc myelocytomatosis viral oncogene homolog (avian)<br> MAX: MYC associated factor X	www.broad.mit.e...
Broad SGCGSSAAA_V$E2F1DP2_01	View Gene Set	1.084e-05	122	0.001666	4	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif SGCGSSAAA which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1<br> RB1: retinoblastoma 1 (including osteosarcoma)	www.broad.mit.e...
Broad V$E2F_Q3	View Gene Set	2.207e-05	162	0.002262	5	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTCGCGC. Motif does not match any known transcription factor	www.broad.mit.e...
Broad GKCGCNNNNNNNTGAYG_UNKNOWN	View Gene Set	2.179e-05	41	0.002262	5	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif GKCGCNNNNNNNTGAYG. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F1DP1RB_01	View Gene Set	4.03e-05	168	0.003432	7	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1<br> RB1: retinoblastoma 1 (including osteosarcoma)	www.broad.mit.e...
Broad V$E2F_Q4_01	View Gene Set	5.023e-05	171	0.003432	7	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NCSCGCSAAAN which matches annotation for E2F<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad KRCTCNNNNMANAGC_UNKNOWN	View Gene Set	4.505e-05	60	0.003432	7	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif KRCTCNNNNMANAGC. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F4DP1_01	View Gene Set	7.272e-05	174	0.004066	10	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGC which matches annotation for E2F4: E2F transcription factor 4 p107/p130-binding<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad V$E2F1_Q6_01	View Gene Set	6.666e-05	177	0.004066	10	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NTTTCGCGCS which matches annotation for E2F1: E2F transcription factor 1	www.broad.mit.e...
Broad V$E2F_Q4	View Gene Set	0.0001153	166	0.005066	12	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGS. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F1_Q6	View Gene Set	0.0001137	167	0.005066	12	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGS which matches annotation for E2F1: E2F transcription factor 1	www.broad.mit.e...
Broad GCCATNTTG_V$YY1_Q6	View Gene Set	0.0001011	289	0.005066	12	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif GCCATNTTG which matches annotation for YY1: YY1 transcription factor	www.broad.mit.e...
Broad V$E2F_02	View Gene Set	0.0001448	169	0.005265	15	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGC. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F_Q6	View Gene Set	0.000136	165	0.005265	15	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGS. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F1DP1_01	View Gene Set	0.0001627	169	0.005265	15	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTCSCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad V$E2F1DP2_01	View Gene Set	0.0001627	169	0.005265	15	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSSCGC which matches annotation for E2F1: E2F transcription factor 1<br> TFDP2: transcription factor Dp-2 (E2F dimerization partner 2)	www.broad.mit.e...
Broad V$E2F4DP2_01	View Gene Set	0.0001627	169	0.005265	15	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTCSCGC which matches annotation for E2F4: E2F transcription factor 4 p107/p130-binding<br> TFDP2: transcription factor Dp-2 (E2F dimerization partner 2)	www.broad.mit.e...
Broad V$USF_C	View Gene Set	0.0001761	211	0.005415	20	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif NCACGTGN. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F_01	View Gene Set	0.0002138	55	0.006262	21	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TWSGCGCGAAAAYKR. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F1_Q3	View Gene Set	0.0003282	176	0.009175	22	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NKTSSCGC which matches annotation for E2F1: E2F transcription factor 1	www.broad.mit.e...
Broad V$MAX_01	View Gene Set	0.0004473	194	0.01196	23	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NNANCACGTGNTNN which matches annotation for MAX: MYC associated factor X	www.broad.mit.e...
Broad V$ARNT_01	View Gene Set	0.0005052	196	0.01294	24	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NDDNNCACGTGNNNNN which matches annotation for ARNT: aryl hydrocarbon receptor nuclear translocator	www.broad.mit.e...
Broad V$E2F1_Q4_01	View Gene Set	0.0007572	167	0.01863	25	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGSG which matches annotation for E2F<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad V$NFMUE1_Q6	View Gene Set	0.0008829	175	0.02011	26	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif CGGCCATCT. Motif does not match any known transcription factor	www.broad.mit.e...
Broad V$E2F_Q3_01	View Gene Set	0.0008538	171	0.02011	26	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif TTTSGCGSG which matches annotation for E2F<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad V$E2F_Q6_01	View Gene Set	0.001321	167	0.02901	28	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif NKCGCGCSAAAN which matches annotation for E2F<br> TFDP1: transcription factor Dp-1	www.broad.mit.e...
Broad V$AHRARNT_02	View Gene Set	0.001538	13	0.03261	29	Genes with promoter regions [-2kb 2kb] around transcription start site containing the motif GRGKATYGCGTGMCWNSCC which matches annotation for AHR: aryl hydrocarbon receptor	www.broad.mit.e...
Broad V$E2F_03	View Gene Set	0.002261	171	0.04635	30	Genes with promoter regions [-2kb 2kb] around transcription start site containing motif TTTSGCGCGMNR. Motif does not match any known transcription factor	www.broad.mit.e...

Gene Set Collection: Broad.c4.CGN

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad MORF_AATF	View Gene Set	1.628e-17	179	6.951e-15	1	Neighborhood of AATF	www.broad.mit.e...
Broad MORF_BUB3	View Gene Set	6.953e-16	256	1.484e-13	2	Neighborhood of BUB3	www.broad.mit.e...
Broad MORF_HDAC2	View Gene Set	3.278e-13	256	3.831e-11	3	Neighborhood of HDAC2	www.broad.mit.e...
Broad MORF_EIF3S2	View Gene Set	3.589e-13	220	3.831e-11	3	Neighborhood of EIF3S2	www.broad.mit.e...
Broad MORF_RAD23A	View Gene Set	5.789e-13	316	4.944e-11	5	Neighborhood of RAD23A	www.broad.mit.e...
Broad MORF_PRKDC	View Gene Set	1.125e-12	173	8.009e-11	6	Neighborhood of PRKDC	www.broad.mit.e...
Broad MORF_FBL	View Gene Set	8.52e-12	121	5.197e-10	7	Neighborhood of FBL	www.broad.mit.e...
Broad MORF_PPP1CC	View Gene Set	8.642e-11	150	4.612e-09	8	Neighborhood of PPP1CC	www.broad.mit.e...
Broad MORF_RFC4	View Gene Set	4.493e-10	137	2.131e-08	9	Neighborhood of RFC4	www.broad.mit.e...
Broad MORF_DEAF1	View Gene Set	2.042e-09	54	8.72e-08	10	Neighborhood of DEAF1	www.broad.mit.e...
Broad MORF_DNMT1	View Gene Set	2.513e-09	105	9.755e-08	11	Neighborhood of DNMT1	www.broad.mit.e...
Broad MORF_RAD54L	View Gene Set	4.013e-09	94	1.428e-07	12	Neighborhood of RAD54L	www.broad.mit.e...
Broad GNF2_PA2G4	View Gene Set	7.81e-09	73	2.565e-07	13	Neighborhood of PA2G4	www.broad.mit.e...
Broad MORF_CDC16	View Gene Set	2.02e-08	67	5.751e-07	14	Neighborhood of CDC16	www.broad.mit.e...
Broad GNF2_RRM1	View Gene Set	1.903e-08	82	5.751e-07	14	Neighborhood of RRM1	www.broad.mit.e...
Broad GNF2_SMC4L1	View Gene Set	4.453e-08	75	1.188e-06	16	Neighborhood of SMC4L1	www.broad.mit.e...
Broad MORF_PCNA	View Gene Set	5.602e-08	71	1.407e-06	17	Neighborhood of PCNA	www.broad.mit.e...
Broad GNF2_RAN	View Gene Set	2.485e-07	78	5.894e-06	18	Neighborhood of RAN	www.broad.mit.e...
Broad MORF_PHB	View Gene Set	3.405e-07	112	7.653e-06	19	Neighborhood of PHB	www.broad.mit.e...
Broad MORF_CSNK2B	View Gene Set	4.534e-07	256	9.681e-06	20	Neighborhood of CSNK2B	www.broad.mit.e...
Broad MORF_UNG	View Gene Set	4.931e-07	65	1.003e-05	21	Neighborhood of UNG	www.broad.mit.e...
Broad GNF2_NS	View Gene Set	6.175e-07	35	1.198e-05	22	Neighborhood of NS	www.broad.mit.e...
Broad MORF_MSH2	View Gene Set	7.694e-07	52	1.428e-05	23	Neighborhood of MSH2	www.broad.mit.e...
Broad MORF_HAT1	View Gene Set	1.469e-06	155	2.614e-05	24	Neighborhood of HAT1	www.broad.mit.e...
Broad MORF_SMC1L1	View Gene Set	1.882e-06	47	3.215e-05	25	Neighborhood of SMC1L1	www.broad.mit.e...
Broad MORF_RRM1	View Gene Set	3.22e-06	90	5.095e-05	26	Neighborhood of RRM1	www.broad.mit.e...
Broad GCM_SMARCD1	View Gene Set	3.222e-06	101	5.095e-05	26	Neighborhood of SMARCD1	www.broad.mit.e...
Broad GNF2_APEX1	View Gene Set	3.776e-06	72	5.759e-05	28	Neighborhood of APEX1	www.broad.mit.e...
Broad MORF_FEN1	View Gene Set	4.952e-06	58	7.095e-05	29	Neighborhood of FEN1	www.broad.mit.e...
Broad GNF2_MCM5	View Gene Set	4.985e-06	51	7.095e-05	29	Neighborhood of MCM5	www.broad.mit.e...
Broad GNF2_MCM4	View Gene Set	8.035e-06	50	0.0001107	31	Neighborhood of MCM4	www.broad.mit.e...
Broad GCM_RING1	View Gene Set	8.5e-06	106	0.0001134	32	Neighborhood of RING1	www.broad.mit.e...
Broad MORF_BUB1B	View Gene Set	9.571e-06	61	0.0001238	33	Neighborhood of BUB1B	www.broad.mit.e...
Broad GNF2_RFC4	View Gene Set	1.229e-05	57	0.0001544	34	Neighborhood of RFC4	www.broad.mit.e...
Broad GNF2_PCNA	View Gene Set	1.331e-05	62	0.0001623	35	Neighborhood of PCNA	www.broad.mit.e...
Broad MORF_EIF4E	View Gene Set	1.397e-05	76	0.0001657	36	Neighborhood of EIF4E	www.broad.mit.e...
Broad MORF_ESPL1	View Gene Set	1.653e-05	58	0.0001907	37	Neighborhood of ESPL1	www.broad.mit.e...
Broad GCM_SMARCC1	View Gene Set	2.22e-05	33	0.0002495	38	Neighborhood of SMARCC1	www.broad.mit.e...
Broad GNF2_MLH1	View Gene Set	3.467e-05	36	0.0003796	39	Neighborhood of MLH1	www.broad.mit.e...
Broad MORF_DDB1	View Gene Set	3.966e-05	220	0.0004234	40	Neighborhood of DDB1	www.broad.mit.e...
Broad MORF_RPA2	View Gene Set	4.093e-05	170	0.0004255	41	Neighborhood of RPA2	www.broad.mit.e...
Broad MORF_EI24	View Gene Set	4.185e-05	136	0.0004255	41	Neighborhood of EI24	www.broad.mit.e...
Broad GNF2_MSH6	View Gene Set	4.387e-05	30	0.0004357	43	Neighborhood of MSH6	www.broad.mit.e...
Broad MORF_SOD1	View Gene Set	5.747e-05	247	0.0005577	44	Neighborhood of SOD1	www.broad.mit.e...
Broad GNF2_BUB1B	View Gene Set	6.478e-05	46	0.0006147	45	Neighborhood of BUB1B	www.broad.mit.e...
Broad MORF_USP5	View Gene Set	7.039e-05	46	0.0006534	46	Neighborhood of USP5	www.broad.mit.e...
Broad MORF_G22P1	View Gene Set	7.462e-05	145	0.000678	47	Neighborhood of G22P1	www.broad.mit.e...
Broad MORF_UBE2N	View Gene Set	8.484e-05	79	0.0007547	48	Neighborhood of UBE2N	www.broad.mit.e...
Broad GNF2_FEN1	View Gene Set	0.000106	49	0.0009099	49	Neighborhood of FEN1	www.broad.mit.e...
Broad GNF2_KPNB1	View Gene Set	0.0001065	52	0.0009099	49	Neighborhood of KPNB1	www.broad.mit.e...
Broad MORF_GSPT1	View Gene Set	0.000109	41	0.0009128	51	Neighborhood of GSPT1	www.broad.mit.e...
Broad MORF_PTPN11	View Gene Set	0.0001158	93	0.0009511	52	Neighborhood of PTPN11	www.broad.mit.e...
Broad GNF2_RFC3	View Gene Set	0.0001325	38	0.001067	53	Neighborhood of RFC3	www.broad.mit.e...
Broad MORF_XRCC5	View Gene Set	0.0001788	210	0.00139	54	Neighborhood of XRCC5	www.broad.mit.e...
Broad GNF2_CCNA2	View Gene Set	0.000179	62	0.00139	54	Neighborhood of CCNA2	www.broad.mit.e...
Broad GNF2_DENR	View Gene Set	0.0001892	39	0.001443	56	Neighborhood of DENR	www.broad.mit.e...
Broad MORF_DEK	View Gene Set	0.0001935	229	0.00145	57	Neighborhood of DEK	www.broad.mit.e...
Broad GNF2_RRM2	View Gene Set	0.0002442	36	0.001798	58	Neighborhood of RRM2	www.broad.mit.e...
Broad GCM_FANCC	View Gene Set	0.0003161	120	0.002265	59	Neighborhood of FANCC	www.broad.mit.e...
Broad GNF2_CENPF	View Gene Set	0.0003182	56	0.002265	59	Neighborhood of CENPF	www.broad.mit.e...
Broad GNF2_ESPL1	View Gene Set	0.0003453	35	0.002378	61	Neighborhood of ESPL1	www.broad.mit.e...
Broad GNF2_ELAC2	View Gene Set	0.0003412	32	0.002378	61	Neighborhood of ELAC2	www.broad.mit.e...
Broad GCM_HMGA2	View Gene Set	0.0003816	123	0.002586	63	Neighborhood of HMGA2	www.broad.mit.e...
Broad MORF_GMPS	View Gene Set	0.0004236	48	0.002783	64	Neighborhood of GMPS	www.broad.mit.e...
Broad GNF2_CKS1B	View Gene Set	0.0004194	36	0.002783	64	Neighborhood of CKS1B	www.broad.mit.e...
Broad GNF2_NPM1	View Gene Set	0.0004336	57	0.002805	66	Neighborhood of NPM1	www.broad.mit.e...
Broad MORF_RAN	View Gene Set	0.0004941	242	0.003147	67	Neighborhood of RAN	www.broad.mit.e...
Broad MORF_UBE2I	View Gene Set	0.0005012	208	0.003147	67	Neighborhood of UBE2I	www.broad.mit.e...
Broad MORF_CCNF	View Gene Set	0.0005173	65	0.003201	69	Neighborhood of CCNF	www.broad.mit.e...
Broad MORF_ANP32B	View Gene Set	0.000583	174	0.00341	70	Neighborhood of ANP32B	www.broad.mit.e...
Broad GCM_PRKCG	View Gene Set	0.0005732	60	0.00341	70	Neighborhood of PRKCG	www.broad.mit.e...
Broad GNF2_BUB1	View Gene Set	0.0005811	25	0.00341	70	Neighborhood of BUB1	www.broad.mit.e...
Broad GNF2_MSH2	View Gene Set	0.0005699	26	0.00341	70	Neighborhood of MSH2	www.broad.mit.e...
Broad MORF_GNB1	View Gene Set	0.000807	276	0.004595	74	Neighborhood of GNB1	www.broad.mit.e...
Broad GCM_BECN1	View Gene Set	0.0007968	59	0.004595	74	Neighborhood of BECN1	www.broad.mit.e...
Broad MORF_DAP3	View Gene Set	0.0008693	175	0.004884	76	Neighborhood of DAP3	www.broad.mit.e...
Broad MORF_BUB1	View Gene Set	0.0008823	49	0.004892	77	Neighborhood of BUB1	www.broad.mit.e...
Broad MORF_RBBP8	View Gene Set	0.001005	190	0.005503	78	Neighborhood of RBBP8	www.broad.mit.e...
Broad MORF_ERH	View Gene Set	0.001052	103	0.005688	79	Neighborhood of ERH	www.broad.mit.e...
Broad GCM_SUPT4H1	View Gene Set	0.001104	58	0.005895	80	Neighborhood of SUPT4H1	www.broad.mit.e...
Broad GNF2_CDC27	View Gene Set	0.001411	56	0.00744	81	Neighborhood of CDC27	www.broad.mit.e...
Broad MORF_REV3L	View Gene Set	0.001438	52	0.007486	82	Neighborhood of REV3L	www.broad.mit.e...
Broad GNF2_HAT1	View Gene Set	0.001506	45	0.007749	83	Neighborhood of HAT1	www.broad.mit.e...
Broad GNF2_ANP32B	View Gene Set	0.001558	29	0.007918	84	Neighborhood of ANP32B	www.broad.mit.e...
Broad GNF2_HMMR	View Gene Set	0.001648	43	0.008277	85	Neighborhood of HMMR	www.broad.mit.e...
Broad MORF_CDK2	View Gene Set	0.001691	63	0.008396	86	Neighborhood of CDK2	www.broad.mit.e...
Broad MORF_HDAC1	View Gene Set	0.001874	222	0.009196	87	Neighborhood of HDAC1	www.broad.mit.e...
Broad GNF2_SMC1L1	View Gene Set	0.001967	24	0.009545	88	Neighborhood of SMC1L1	www.broad.mit.e...
Broad GCM_AIP	View Gene Set	0.002037	36	0.009773	89	Neighborhood of AIP	www.broad.mit.e...
Broad GNF2_FBL	View Gene Set	0.00211	119	0.01001	90	Neighborhood of FBL	www.broad.mit.e...
Broad MORF_BNIP1	View Gene Set	0.002154	179	0.01011	91	Neighborhood of BNIP1	www.broad.mit.e...
Broad GCM_LTK	View Gene Set	0.002183	43	0.01013	92	Neighborhood of LTK	www.broad.mit.e...
Broad MORF_DDX11	View Gene Set	0.002283	138	0.01047	93	Neighborhood of DDX11	www.broad.mit.e...
Broad GNF2_CDC20	View Gene Set	0.002305	52	0.01047	93	Neighborhood of CDC20	www.broad.mit.e...
Broad MORF_PRKACA	View Gene Set	0.002421	104	0.01088	95	Neighborhood of PRKACA	www.broad.mit.e...
Broad GCM_BNIP1	View Gene Set	0.002501	71	0.01112	96	Neighborhood of BNIP1	www.broad.mit.e...
Broad GNF2_G22P1	View Gene Set	0.00254	29	0.01118	97	Neighborhood of G22P1	www.broad.mit.e...
Broad MORF_PRKAG1	View Gene Set	0.002845	202	0.0124	98	Neighborhood of PRKAG1	www.broad.mit.e...
Broad MORF_RAP1A	View Gene Set	0.00311	122	0.01341	99	Neighborhood of RAP1A	www.broad.mit.e...
Broad MORF_HEAB	View Gene Set	0.003793	71	0.01604	100	Neighborhood of HEAB	www.broad.mit.e...
Broad MORF_RUNX1	View Gene Set	0.003785	138	0.01604	100	Neighborhood of RUNX1	www.broad.mit.e...
Broad MORF_RPA1	View Gene Set	0.003978	55	0.01651	102	Neighborhood of RPA1	www.broad.mit.e...
Broad GNF2_CENPE	View Gene Set	0.003981	37	0.01651	102	Neighborhood of CENPE	www.broad.mit.e...
Broad MORF_FANCG	View Gene Set	0.004067	148	0.0167	104	Neighborhood of FANCG	www.broad.mit.e...
Broad GCM_ATM	View Gene Set	0.004256	24	0.01731	105	Neighborhood of ATM	www.broad.mit.e...
Broad MORF_FDXR	View Gene Set	0.004409	205	0.01776	106	Neighborhood of FDXR	www.broad.mit.e...
Broad MORF_RFC5	View Gene Set	0.005013	69	0.02	107	Neighborhood of RFC5	www.broad.mit.e...
Broad GNF2_DEK	View Gene Set	0.005142	45	0.02033	108	Neighborhood of DEK	www.broad.mit.e...
Broad GNF2_TDG	View Gene Set	0.005494	23	0.02152	109	Neighborhood of TDG	www.broad.mit.e...
Broad MORF_BCL2	View Gene Set	0.00602	202	0.02287	110	Neighborhood of BCL2	www.broad.mit.e...
Broad GCM_FCGR2B	View Gene Set	0.006053	37	0.02287	110	Neighborhood of FCGR2B	www.broad.mit.e...
Broad GCM_USP6	View Gene Set	0.005946	54	0.02287	110	Neighborhood of USP6	www.broad.mit.e...
Broad GNF2_CDC2	View Gene Set	0.006049	56	0.02287	110	Neighborhood of CDC2	www.broad.mit.e...
Broad MORF_NF1	View Gene Set	0.006259	158	0.02344	114	Neighborhood of NF1	www.broad.mit.e...
Broad GNF2_CKS2	View Gene Set	0.006452	45	0.02396	115	Neighborhood of CKS2	www.broad.mit.e...
Broad MORF_IL13	View Gene Set	0.006779	216	0.02495	116	Neighborhood of IL13	www.broad.mit.e...
Broad MORF_CUL1	View Gene Set	0.007302	62	0.02665	117	Neighborhood of CUL1	www.broad.mit.e...
Broad GCM_PTPRU	View Gene Set	0.007784	55	0.02817	118	Neighborhood of PTPRU	www.broad.mit.e...
Broad GCM_DENR	View Gene Set	0.008275	40	0.02969	119	Neighborhood of DENR	www.broad.mit.e...
Broad MORF_ACP1	View Gene Set	0.008516	178	0.0303	120	Neighborhood of ACP1	www.broad.mit.e...
Broad MORF_MAP2K2	View Gene Set	0.009313	123	0.03207	121	Neighborhood of MAP2K2	www.broad.mit.e...
Broad GCM_VAV1	View Gene Set	0.009303	46	0.03207	121	Neighborhood of VAV1	www.broad.mit.e...
Broad GNF2_CCNB2	View Gene Set	0.009261	53	0.03207	121	Neighborhood of CCNB2	www.broad.mit.e...
Broad GNF2_RBBP6	View Gene Set	0.009118	54	0.03207	121	Neighborhood of RBBP6	www.broad.mit.e...
Broad MORF_RFC1	View Gene Set	0.01	98	0.03416	125	Neighborhood of RFC1	www.broad.mit.e...
Broad MORF_BMI1	View Gene Set	0.01046	71	0.03544	126	Neighborhood of BMI1	www.broad.mit.e...
Broad GNF2_HDAC1	View Gene Set	0.0106	85	0.03565	127	Neighborhood of HDAC1	www.broad.mit.e...
Broad GCM_TEC	View Gene Set	0.01139	33	0.03801	128	Neighborhood of TEC	www.broad.mit.e...
Broad MORF_MSH3	View Gene Set	0.01182	226	0.03913	129	Neighborhood of MSH3	www.broad.mit.e...
Broad GCM_RAF1	View Gene Set	0.01201	34	0.03943	130	Neighborhood of RAF1	www.broad.mit.e...
Broad GNF2_H2AFX	View Gene Set	0.01211	28	0.03948	131	Neighborhood of H2AFX	www.broad.mit.e...
Broad MORF_JAK3	View Gene Set	0.01266	86	0.04096	132	Neighborhood of JAK3	www.broad.mit.e...
Broad GNF2_BUB3	View Gene Set	0.01361	22	0.04371	133	Neighborhood of BUB3	www.broad.mit.e...
Broad MORF_RAD21	View Gene Set	0.01381	157	0.04401	134	Neighborhood of RAD21	www.broad.mit.e...
Broad MORF_ATRX	View Gene Set	0.01404	185	0.04442	135	Neighborhood of ATRX	www.broad.mit.e...
Broad MORF_SS18	View Gene Set	0.0143	55	0.04491	136	Neighborhood of SS18	www.broad.mit.e...
Broad MORF_PPP1CA	View Gene Set	0.01519	145	0.04734	137	Neighborhood of PPP1CA	www.broad.mit.e...
Broad MORF_PPP5C	View Gene Set	0.01574	81	0.0487	138	Neighborhood of PPP5C	www.broad.mit.e...
Broad MORF_TERF1	View Gene Set	0.01591	57	0.04888	139	Neighborhood of TERF1	www.broad.mit.e...
Broad GNF2_XRCC5	View Gene Set	0.01622	61	0.04947	140	Neighborhood of XRCC5	www.broad.mit.e...
Broad MORF_ERCC2	View Gene Set	0.01644	91	0.04968	141	Neighborhood of ERCC2	www.broad.mit.e...
Broad GCM_PPP1CC	View Gene Set	0.01652	47	0.04968	141	Neighborhood of PPP1CC	www.broad.mit.e...

Gene Set Collection: Broad.c4.CM

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c5.BP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad module_17	View Gene Set	6.291e-10	351	2.856e-07	1	Genes in module_17	www.broad.mit.e...
Broad module_219	View Gene Set	7.686e-07	26	0.0001745	2	Genes in module_219	www.broad.mit.e...
Broad module_244	View Gene Set	5.344e-06	182	0.0008087	3	Genes in module_244	www.broad.mit.e...
Broad module_54	View Gene Set	1.228e-05	242	0.001115	4	Genes in module_54	www.broad.mit.e...
Broad module_61	View Gene Set	1.177e-05	50	0.001115	4	Genes in module_61	www.broad.mit.e...
Broad module_102	View Gene Set	2.157e-05	18	0.001632	6	Genes in module_102	www.broad.mit.e...
Broad module_16	View Gene Set	0.0001693	495	0.00854	7	Genes in module_16	www.broad.mit.e...
Broad module_35	View Gene Set	0.0001616	16	0.00854	7	Genes in module_35	www.broad.mit.e...
Broad module_183	View Gene Set	0.0001338	52	0.00854	7	Genes in module_183	www.broad.mit.e...
Broad module_57	View Gene Set	0.0004259	54	0.01934	10	Genes in module_57	www.broad.mit.e...
Broad module_110	View Gene Set	0.0004947	15	0.02042	11	Genes in module_110	www.broad.mit.e...
Broad module_337	View Gene Set	0.0006364	59	0.02408	12	Genes in module_337	www.broad.mit.e...
Broad module_126	View Gene Set	0.000712	173	0.02487	13	Genes in module_126	www.broad.mit.e...
Broad module_355	View Gene Set	0.00114	28	0.0348	14	Genes in module_355	www.broad.mit.e...
Broad module_392	View Gene Set	0.00115	18	0.0348	14	Genes in module_392	www.broad.mit.e...
Broad module_397	View Gene Set	0.001232	114	0.03497	16	Genes in module_397	www.broad.mit.e...
Broad module_77	View Gene Set	0.001321	28	0.03527	17	Genes in module_77	www.broad.mit.e...
Broad module_8	View Gene Set	0.001995	403	0.04604	18	Genes in module_8	www.broad.mit.e...
Broad module_18	View Gene Set	0.002076	434	0.04604	18	Genes in module_18	www.broad.mit.e...
Broad module_133	View Gene Set	0.002163	15	0.04604	18	Genes in module_133	www.broad.mit.e...
Broad module_203	View Gene Set	0.002231	16	0.04604	18	Genes in module_203	www.broad.mit.e...
Broad module_528	View Gene Set	0.002151	10	0.04604	18	Genes in module_528	www.broad.mit.e...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_METABOLIC_PROCESS	View Gene Set	5.982e-10	1197	4.935e-07	1	Genes annotated by the GO term GO:0006139. The chemical reactions and pathways involving nucleobases nucleosides nucleotides and nucleic acids.	www.broad.mit.e...
Broad RNA_PROCESSING	View Gene Set	1.013e-08	147	4.18e-06	2	Genes annotated by the GO term GO:0006396. Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.	www.broad.mit.e...
Broad RNA_SPLICING	View Gene Set	1.09e-07	73	2.996e-05	3	Genes annotated by the GO term GO:0008380. The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.	www.broad.mit.e...
Broad RNA_METABOLIC_PROCESS	View Gene Set	1.697e-07	801	3.501e-05	4	Genes annotated by the GO term GO:0016070. The chemical reactions and pathways involving RNA ribonucleic acid one of the two main type of nucleic acid consisting of a long unbranched macromolecule formed from ribonucleotides joined in 3' 5'-phosphodiester linkage.	www.broad.mit.e...
Broad COENZYME_METABOLIC_PROCESS	View Gene Set	4.741e-07	37	7.823e-05	5	Genes annotated by the GO term GO:0006732. The chemical reactions and pathways involving coenzymes any of various nonprotein organic cofactors that are required in addition to an enzyme and a substrate for an enzymatic reaction to proceed.	www.broad.mit.e...
Broad COFACTOR_METABOLIC_PROCESS	View Gene Set	4.019e-06	53	0.0005526	6	Genes annotated by the GO term GO:0051186. The chemical reactions and pathways involving a cofactor a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic such as the metal atoms zinc iron and copper in certain forms or organic in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.	www.broad.mit.e...
Broad RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY	View Gene Set	2.495e-05	74	0.002899	7	Genes annotated by the GO term GO:0022613. The cellular process by which a complex containing RNA and proteins is synthesized aggregates and bonds together.	www.broad.mit.e...
Broad RIBOSOME_BIOGENESIS_AND_ASSEMBLY	View Gene Set	2.811e-05	14	0.002899	7	Genes annotated by the GO term GO:0042254. The process of the formation of the constituents of the ribosome subunits their assembly and their transport to the sites of protein synthesis.	www.broad.mit.e...
Broad TRANSCRIPTION_FROM_RNA_POLYMERASE_III_PROMOTER	View Gene Set	4.565e-05	19	0.004185	9	Genes annotated by the GO term GO:0006383. The synthesis of RNA from a DNA template by RNA polymerase III (Pol III) originating at a Pol III-specific promoter.	www.broad.mit.e...
Broad NITROGEN_COMPOUND_METABOLIC_PROCESS	View Gene Set	9.201e-05	150	0.007591	10	Genes annotated by the GO term GO:0006807. The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds; includes nitrogen fixation nitrification denitrification assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.	www.broad.mit.e...
Broad AMINO_ACID_METABOLIC_PROCESS	View Gene Set	0.0001199	75	0.008993	11	Genes annotated by the GO term GO:0006520. The chemical reactions and pathways involving amino acids organic acids containing one or more amino substituents.	www.broad.mit.e...
Broad RRNA_PROCESSING	View Gene Set	0.0001558	11	0.01071	12	Genes annotated by the GO term GO:0006364. Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.	www.broad.mit.e...
Broad NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_NUCLEIC_ACID_TRANSPORT	View Gene Set	0.0001837	31	0.01166	13	Genes annotated by the GO term GO:0015931. The directed movement of nucleobases nucleosides nucleotides and nucleic acids into out of within or between cells.	www.broad.mit.e...
Broad MITOCHONDRION_ORGANIZATION_AND_BIOGENESIS	View Gene Set	0.0002366	47	0.01301	14	Genes annotated by the GO term GO:0007005. A process that is carried out at the cellular level which results in the formation arrangement of constituent parts or disassembly of a mitochondrion; includes mitochondrial morphology and distribution and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.	www.broad.mit.e...
Broad RRNA_METABOLIC_PROCESS	View Gene Set	0.0002239	12	0.01301	14	Genes annotated by the GO term GO:0016072. The chemical reactions and pathways involving rRNA ribosomal RNA a structural constituent of ribosomes.	www.broad.mit.e...
Broad AMINE_METABOLIC_PROCESS	View Gene Set	0.0002557	137	0.01319	16	Genes annotated by the GO term GO:0009308. The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary secondary or tertiary according to whether one two or three carbon atoms are attached to the nitrogen atom.	www.broad.mit.e...
Broad BIOPOLYMER_METABOLIC_PROCESS	View Gene Set	0.0003102	1623	0.01506	17	Genes annotated by the GO term GO:0043283. The chemical reactions and pathways involving biopolymers long repeating chains of monomers found in nature e.g. polysaccharides and proteins.	www.broad.mit.e...
Broad RNA_SPLICINGVIA_TRANSESTERIFICATION_REACTIONS	View Gene Set	0.0004851	27	0.02223	18	Genes annotated by the GO term GO:0000375. Splicing of RNA via a series of two transesterification reactions.	www.broad.mit.e...
Broad RNA_EXPORT_FROM_NUCLEUS	View Gene Set	0.0007555	20	0.03281	19	Genes annotated by the GO term GO:0006405. The directed movement of RNA from the nucleus to the cytoplasm.	www.broad.mit.e...
Broad AMINO_ACID_AND_DERIVATIVE_METABOLIC_PROCESS	View Gene Set	0.001068	98	0.04405	20	Genes annotated by the GO term GO:0006519. The chemical reactions and pathways involving amino acids organic acids containing one or more amino substituents and compounds derived from amino acids.	www.broad.mit.e...
Broad MITOCHONDRIAL_TRANSPORT	View Gene Set	0.001266	20	0.04974	21	Genes annotated by the GO term GO:0006839. Transport of substances into out of or within a mitochondrion.	www.broad.mit.e...

Gene Set Collection: Broad.c5.CC

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad NUCLEAR_PART	View Gene Set	3.755e-13	543	6.458e-11	1	Genes annotated by the GO term GO:0044428. Any constituent part of the nucleus a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.	www.broad.mit.e...
Broad MITOCHONDRION	View Gene Set	5.543e-13	335	6.458e-11	1	Genes annotated by the GO term GO:0005739. A semiautonomous self replicating organelle that occurs in varying numbers shapes and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.	www.broad.mit.e...
Broad MITOCHONDRIAL_PART	View Gene Set	2.418e-10	140	1.77e-08	3	Genes annotated by the GO term GO:0044429. Any constituent part of a mitochondrion a semiautonomous self replicating organelle that occurs in varying numbers shapes and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.	www.broad.mit.e...
Broad ORGANELLE_LUMEN	View Gene Set	3.799e-10	434	1.77e-08	3	Genes annotated by the GO term GO:0043233. The volume enclosed by the membranes of a particular organelle e.g. endoplasmic reticulum lumen or the space between the two lipid bilayers of a double membrane surrounding an organelle e.g. nuclear membrane lumen.	www.broad.mit.e...
Broad MEMBRANE_ENCLOSED_LUMEN	View Gene Set	3.799e-10	434	1.77e-08	3	Genes annotated by the GO term GO:0031974. The enclosed volume within a sealed membrane or between two sealed membranes.	www.broad.mit.e...
Broad MITOCHONDRIAL_MEMBRANE	View Gene Set	6.077e-09	85	2.36e-07	6	Genes annotated by the GO term GO:0031966. Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.	www.broad.mit.e...
Broad NUCLEAR_LUMEN	View Gene Set	2.43e-08	365	7.555e-07	7	Genes annotated by the GO term GO:0031981. The volume enclosed by the nuclear inner membrane.	www.broad.mit.e...
Broad MITOCHONDRIAL_ENVELOPE	View Gene Set	2.594e-08	95	7.555e-07	7	Genes annotated by the GO term GO:0005740. The double lipid bilayer enclosing the mitochondrion and separating its contents from the cell cytoplasm; includes the intermembrane space.	www.broad.mit.e...
Broad NUCLEOLUS	View Gene Set	8.694e-08	116	2.251e-06	9	Genes annotated by the GO term GO:0005730. A small dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein is not bounded by a limiting membrane and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA the processing of this RNA into 5.8S 18S and 28S components of ribosomal RNA and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.	www.broad.mit.e...
Broad ENVELOPE	View Gene Set	1.579e-07	165	3.344e-06	10	Genes annotated by the GO term GO:0031975. A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers and may include a cell wall layer also includes the space between layers.	www.broad.mit.e...
Broad ORGANELLE_ENVELOPE	View Gene Set	1.579e-07	165	3.344e-06	10	Genes annotated by the GO term GO:0031967. A double membrane structure enclosing an organelle including two lipid bilayers and the region between them. In some cases an organelle envelope may have more than two membranes.	www.broad.mit.e...
Broad NUCLEUS	View Gene Set	2.695e-07	1353	5.232e-06	12	Genes annotated by the GO term GO:0005634. A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells the nucleus contains all of the cell's chromosomes except the organellar chromosomes and is the site of RNA synthesis and processing. In some species or in specialized cell types RNA metabolism or DNA replication may be absent.	www.broad.mit.e...
Broad MITOCHONDRIAL_INNER_MEMBRANE	View Gene Set	4.974e-07	66	8.914e-06	13	Genes annotated by the GO term GO:0005743. The inner i.e. lumen-facing lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.	www.broad.mit.e...
Broad ORGANELLE_INNER_MEMBRANE	View Gene Set	6.315e-07	74	1.051e-05	14	Genes annotated by the GO term GO:0019866. The inner i.e. lumen-facing lipid bilayer of an organelle envelope; usually highly selective to most ions and metabolites.	www.broad.mit.e...
Broad NUCLEOLAR_PART	View Gene Set	1.681e-06	16	2.611e-05	15	Genes annotated by the GO term GO:0044452. Any constituent part of a nucleolus a small dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein is not bounded by a limiting membrane and is not seen during mitosis.	www.broad.mit.e...
Broad INTRACELLULAR_ORGANELLE_PART	View Gene Set	1.916e-06	1144	2.791e-05	16	Genes annotated by the GO term GO:0044446. A constituent part of an intracellular organelle an organized structure of distinctive morphology and function occurring within the cell. Includes constituent parts of the nucleus mitochondria plastids vacuoles vesicles ribosomes and the cytoskeleton but excludes the plasma membrane.	www.broad.mit.e...
Broad ORGANELLE_PART	View Gene Set	3.004e-06	1149	4.118e-05	17	Genes annotated by the GO term GO:0044422. Any constituent part of an organelle an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus mitochondria plastids vacuoles vesicles ribosomes and the cytoskeleton but excludes the plasma membrane.	www.broad.mit.e...
Broad RIBONUCLEOPROTEIN_COMPLEX	View Gene Set	6.159e-06	129	7.972e-05	18	Genes annotated by the GO term GO:0030529. A macromolecular complex containing both protein and RNA molecules.	www.broad.mit.e...
Broad MITOCHONDRIAL_MEMBRANE_PART	View Gene Set	2.502e-05	52	0.0003069	19	Genes annotated by the GO term GO:0044455. Any constituent part of the mitochondrial membrane either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.	www.broad.mit.e...
Broad MITOCHONDRIAL_OUTER_MEMBRANE	View Gene Set	0.0001379	18	0.001607	20	Genes annotated by the GO term GO:0005741. The outer i.e. cytoplasm-facing lipid bilayer of the mitochondrial envelope.	www.broad.mit.e...
Broad OUTER_MEMBRANE	View Gene Set	0.0001466	25	0.001626	21	Genes annotated by the GO term GO:0019867. The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.	www.broad.mit.e...
Broad ORGANELLE_OUTER_MEMBRANE	View Gene Set	0.0001563	24	0.001656	22	Genes annotated by the GO term GO:0031968. The outer i.e. cytoplasm-facing lipid bilayer of an organelle envelope.	www.broad.mit.e...
Broad NUCLEOPLASM	View Gene Set	0.0005105	266	0.005171	23	Genes annotated by the GO term GO:0005654. That part of the nuclear content other than the chromosomes or the nucleolus.	www.broad.mit.e...
Broad MITOCHONDRIAL_MATRIX	View Gene Set	0.0005866	46	0.005437	24	Genes annotated by the GO term GO:0005759. The gel-like material with considerable fine structure that lies in the matrix space or lumen of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and in some organisms the enzymes concerned with fatty-acid oxidation.	www.broad.mit.e...
Broad MITOCHONDRIAL_LUMEN	View Gene Set	0.0005866	46	0.005437	24	Genes annotated by the GO term GO:0031980. The volume enclosed by the mitochondrial inner membrane.	www.broad.mit.e...
Broad MACROMOLECULAR_COMPLEX	View Gene Set	0.0006067	914	0.005437	24	Genes annotated by the GO term GO:0032991. A stable assembly of two or more macromolecules i.e. proteins nucleic acids carbohydrates or lipids in which the constituent parts function together.	www.broad.mit.e...
Broad NADH_DEHYDROGENASE_COMPLEX	View Gene Set	0.0007921	15	0.006364	27	Genes annotated by the GO term GO:0030964. An integral membrane complex that possesses NADH oxidoreductase activity. The complex is one of the components of the electron transport chain. It catalyses the transfer of a pair of electrons from NADH to a quinone.	www.broad.mit.e...
Broad MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_I	View Gene Set	0.0007921	15	0.006364	27	Genes annotated by the GO term GO:0005747. A part of the respiratory chain located in the mitochondrion. It contains about 25 different polypeptide subunits including NADH dehydrogenase (ubiquinone) flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III) and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone.	www.broad.mit.e...
Broad RESPIRATORY_CHAIN_COMPLEX_I	View Gene Set	0.0007921	15	0.006364	27	Genes annotated by the GO term GO:0045271. Respiratory chain complex I is an enzyme of the respiratory chain. It consists of at least 34 polypeptide chains and is L-shaped with a horizontal arm lying in the membrane and a vertical arm that projects into the matrix. The electrons of NADH enter the chain at this complex.	www.broad.mit.e...
Broad NUCLEAR_CHROMOSOME	View Gene Set	0.001175	53	0.009022	30	Genes annotated by the GO term GO:0000228. A chromosome found in the nucleus of a eukaryotic cell.	www.broad.mit.e...
Broad NUCLEOPLASM_PART	View Gene Set	0.0012	202	0.009022	30	Genes annotated by the GO term GO:0044451. Any constituent part of the nucleoplasm that part of the nuclear content other than the chromosomes or the nucleolus.	www.broad.mit.e...
Broad ORGANELLAR_RIBOSOME	View Gene Set	0.003183	22	0.02247	32	Genes annotated by the GO term GO:0000313. A ribosome contained within a subcellular organelle.	www.broad.mit.e...
Broad MITOCHONDRIAL_RIBOSOME	View Gene Set	0.003183	22	0.02247	32	Genes annotated by the GO term GO:0005761. A ribosome found in the mitochondrion of a eukaryotic cell; contains a characteristic set of proteins distinct from those of cytosolic ribosomes.	www.broad.mit.e...
Broad MITOCHONDRIAL_RESPIRATORY_CHAIN	View Gene Set	0.00358	24	0.02453	34	Genes annotated by the GO term GO:0005746. The protein complexes that form the mitochondrial electron transport system (the respiratory chain). Complexes I III and IV can transport protons if embedded in an oriented membrane such as an intact mitochondrial inner membrane.	www.broad.mit.e...
Broad SMALL_NUCLEAR_RIBONUCLEOPROTEIN_COMPLEX	View Gene Set	0.004378	20	0.02834	35	Genes annotated by the GO term GO:0030532. A complex composed of RNA of the small nuclear RNA (snRNA) class and protein found in the nucleus of a eukaryotic cell. These are typically named after the snRNA(s) they contain e.g. U1 snRNP or U4/U6 snRNP. Many but not all of these complexes are involved in splicing of nuclear mRNAs.	www.broad.mit.e...
Broad RIBOSOMAL_SUBUNIT	View Gene Set	0.004362	20	0.02834	35	Genes annotated by the GO term GO:0033279. Either of the two ribonucleoprotein complexes that associate to form a ribosome.	www.broad.mit.e...
Broad CHROMATIN	View Gene Set	0.004534	35	0.02855	37	Genes annotated by the GO term GO:0000785. The ordered and organized complex of DNA and protein that forms the chromosome.	www.broad.mit.e...
Broad NUCLEAR_MEMBRANE	View Gene Set	0.005006	48	0.0307	38	Genes annotated by the GO term GO:0031965. Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.	www.broad.mit.e...
Broad DNA_DIRECTED_RNA_POLYMERASE_COMPLEX	View Gene Set	0.006943	16	0.03852	39	Genes annotated by the GO term GO:0000428. A protein complex that possesses DNA-directed RNA polymerase activity.	www.broad.mit.e...
Broad RNA_POLYMERASE_COMPLEX	View Gene Set	0.006943	16	0.03852	39	Genes annotated by the GO term GO:0030880. Any complex that possesses RNA polymerase activity; generally comprises a catalytic subunit and one or more additional subunits.	www.broad.mit.e...
Broad NUCLEAR_DNA_DIRECTED_RNA_POLYMERASE_COMPLEX	View Gene Set	0.006943	16	0.03852	39	Genes annotated by the GO term GO:0055029. A protein complex located in the nucleus that possesses DNA-directed RNA polymerase activity.	www.broad.mit.e...
Broad NUCLEAR_CHROMOSOME_PART	View Gene Set	0.006491	33	0.03852	39	Genes annotated by the GO term GO:0044454. Any constituent part of a nuclear chromosome a chromosome found in the nucleus of a eukaryotic cell.	www.broad.mit.e...
Broad ORGANELLAR_SMALL_RIBOSOMAL_SUBUNIT	View Gene Set	0.007502	11	0.03884	43	Genes annotated by the GO term GO:0000314. The smaller of the two subunits of an organellar ribosome.	www.broad.mit.e...
Broad MITOCHONDRIAL_SMALL_RIBOSOMAL_SUBUNIT	View Gene Set	0.007502	11	0.03884	43	Genes annotated by the GO term GO:0005763. The smaller of the two subunits of a mitochondrial ribosome.	www.broad.mit.e...
Broad SMALL_RIBOSOMAL_SUBUNIT	View Gene Set	0.007502	11	0.03884	43	Genes annotated by the GO term GO:0015935. The smaller of the two subunits of a ribosome.	www.broad.mit.e...
Broad CONDENSED_NUCLEAR_CHROMOSOME	View Gene Set	0.00978	17	0.04848	46	Genes annotated by the GO term GO:0000794. A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure that remains in the nucleus.	www.broad.mit.e...
Broad DNA_DIRECTED_RNA_POLYMERASEII_HOLOENZYME	View Gene Set	0.009615	65	0.04848	46	Genes annotated by the GO term GO:0016591. Large protein complex composed of the RNA polymerase core complex and a variety of other proteins including transcription factor complexes TFIIA D E F and H which are required for promoter recognition and the Mediator subcomplex. Catalyzes the synthesis of eukaryotic pre-mRNA.	www.broad.mit.e...

Gene Set Collection: Broad.c5.MF

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: PMID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Broad LIGASE_ACTIVITY_FORMING_CARBON_OXYGEN_BONDS	View Gene Set	6.261e-05	14	0.02479	1	Genes annotated by the GO term GO:0016875. Catalysis of the ligation of two substances via a carbon-oxygen bond with concomitant breakage of a diphosphate linkage usually in a nucleoside triphosphate.	www.broad.mit.e...
Broad NUCLEOTIDYLTRANSFERASE_ACTIVITY	View Gene Set	0.0001527	47	0.02608	2	Genes annotated by the GO term GO:0016779. Catalysis of the transfer of a nucleotidyl group to a reactant.	www.broad.mit.e...
Broad TRANSLATION_FACTOR_ACTIVITY_NUCLEIC_ACID_BINDING	View Gene Set	0.0001976	39	0.02608	2	Genes annotated by the GO term GO:0008135. Functions during translation by binding nucleic acids during polypeptide synthesis at the ribosome.	www.broad.mit.e...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
PMID 12429849	View Gene Set	2.596e-26	106	6.509e-23	1	Functional proteomic analysis of human nucleolus.	www.ncbi.nlm.ni...
PMID 15635413	View Gene Set	1.096e-19	421	1.373e-16	2	Nucleolar proteome dynamics.	www.ncbi.nlm.ni...
PMID 11790298	View Gene Set	5.08e-16	208	3.582e-13	3	Directed proteomic analysis of the human nucleolus.	www.ncbi.nlm.ni...
PMID 12706105	View Gene Set	5.715e-16	182	3.582e-13	3	Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.	www.ncbi.nlm.ni...
PMID 17643375	View Gene Set	5.405e-14	391	2.71e-11	5	Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme.	www.ncbi.nlm.ni...
PMID 15302935	View Gene Set	1.802e-13	773	7.529e-11	6	Large-scale characterization of HeLa cell nuclear phosphoproteins.	www.ncbi.nlm.ni...
PMID 11543634	View Gene Set	7.912e-13	58	2.834e-10	7	The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders.	www.ncbi.nlm.ni...
PMID 11080476	View Gene Set	2.521e-09	87	7.9e-07	8	Acetylation of HIV-1 Tat by CBP/P300 increases transcription of integrated HIV-1 genome and enhances binding to core histones.	www.ncbi.nlm.ni...
PMID 11991638	View Gene Set	1.03e-08	74	2.869e-06	9	Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis.	www.ncbi.nlm.ni...
PMID 20085707	View Gene Set	1.431e-08	42	3.588e-06	10	Aire's partners in the molecular control of immunological tolerance.	www.ncbi.nlm.ni...
PMID 12408966	View Gene Set	1.803e-08	76	4.108e-06	11	The human and mouse replication-dependent histone genes.	www.ncbi.nlm.ni...
PMID 14657027	View Gene Set	4.102e-08	74	8.569e-06	12	Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter.	www.ncbi.nlm.ni...
PMID 9566873	View Gene Set	6.031e-08	74	1.163e-05	13	Transcriptional activation of the integrated chromatin-associated human immunodeficiency virus type 1 promoter.	www.ncbi.nlm.ni...
PMID 12226669	View Gene Set	8.953e-08	108	1.496e-05	14	Comprehensive proteomic analysis of the human spliceosome.	www.ncbi.nlm.ni...
PMID 9439656	View Gene Set	8.637e-08	55	1.496e-05	14	The human histone gene cluster at the D6S105 locus.	www.ncbi.nlm.ni...
PMID 11689053	View Gene Set	1.14e-07	70	1.787e-05	16	Enhancement of the p300 HAT activity by HIV-1 Tat on chromatin DNA.	www.ncbi.nlm.ni...
PMID 11279123	View Gene Set	1.668e-07	31	2.46e-05	17	The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present.	www.ncbi.nlm.ni...
PMID 16283522	View Gene Set	7.657e-07	18	0.000101	18	Inhibition of core histones acetylation by carcinogenic nickel(II).	www.ncbi.nlm.ni...
PMID 16713563	View Gene Set	7.532e-07	19	0.000101	18	Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.	www.ncbi.nlm.ni...
PMID 16319397	View Gene Set	9.338e-07	20	0.0001171	20	Characterization of histone H2A and H2B variants and their post-translational modifications by mass spectrometry.	www.ncbi.nlm.ni...
PMID 14559993	View Gene Set	1.348e-06	51	0.0001609	21	Regulation of alternative splicing by SRrp86 and its interacting proteins.	www.ncbi.nlm.ni...
PMID 11551941	View Gene Set	2.616e-06	26	0.0002981	22	The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present.	www.ncbi.nlm.ni...
PMID 16964243	View Gene Set	3.105e-06	504	0.0003384	23	A probability-based approach for high-throughput protein phosphorylation analysis and site localization.	www.ncbi.nlm.ni...
PMID 12757711	View Gene Set	4.484e-06	18	0.0004684	24	Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase.	www.ncbi.nlm.ni...
PMID 12391170	View Gene Set	5.707e-06	18	0.0005723	25	Characterization of human RNA polymerase III identifies orthologues for Saccharomyces cerevisiae RNA polymerase III subunits.	www.ncbi.nlm.ni...
PMID 1403646	View Gene Set	6.632e-06	17	0.0006395	26	The human immunodeficiency virus tat protein increases the transcription of human Alu repeated sequences by increasing the activity of the cellular transcription factor TFIIIC.	www.ncbi.nlm.ni...
PMID 10064132	View Gene Set	1.384e-05	14	0.001285	27	The human H2A and H2B histone gene complement.	www.ncbi.nlm.ni...
PMID 9119399	View Gene Set	1.797e-05	35	0.001609	28	Human histone gene organization: nonregular arrangement within a large cluster.	www.ncbi.nlm.ni...
PMID 18162579	View Gene Set	1.938e-05	22	0.001675	29	Identification of novel human Cdt1-binding proteins by a proteomics approach: proteolytic regulation by APC/CCdh1.	www.ncbi.nlm.ni...
PMID 15130578	View Gene Set	2.163e-05	22	0.001808	30	Why do cells need an assembly machine for RNA-protein complexes?	www.ncbi.nlm.ni...
PMID 16307923	View Gene Set	2.818e-05	23	0.002228	31	Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation.	www.ncbi.nlm.ni...
PMID 17148452	View Gene Set	2.844e-05	87	0.002228	31	Characterization of the interactome of the human MutL homologues MLH1 PMS1 and PMS2.	www.ncbi.nlm.ni...
PMID 16627869	View Gene Set	3.011e-05	17	0.002288	33	Quantitative proteomic analysis of post-translational modifications of human histones.	www.ncbi.nlm.ni...
PMID 15823041	View Gene Set	5.174e-05	13	0.003706	34	Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes.	www.ncbi.nlm.ni...
PMID 16565220	View Gene Set	5.168e-05	210	0.003706	34	Phosphoproteome analysis of the human mitotic spindle.	www.ncbi.nlm.ni...
PMID 15231747	View Gene Set	6.187e-05	212	0.004309	36	A protein interaction framework for human mRNA degradation.	www.ncbi.nlm.ni...
PMID 11714285	View Gene Set	7.421e-05	11	0.004327	37	The appended C-domain of human methionyl-tRNA synthetase has a tRNA-sequestering function.	www.ncbi.nlm.ni...
PMID 16055448	View Gene Set	7.421e-05	11	0.004327	37	The C-terminal appended domain of human cytosolic leucyl-tRNA synthetase is indispensable in its interaction with arginyl-tRNA synthetase in the multi-tRNA synthetase complex.	www.ncbi.nlm.ni...
PMID 8052601	View Gene Set	7.421e-05	11	0.004327	37	Human cytoplasmic isoleucyl-tRNA synthetase: selective divergence of the anticodon-binding domain and acquisition of a new structural unit.	www.ncbi.nlm.ni...
PMID 8078941	View Gene Set	7.421e-05	11	0.004327	37	Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer.	www.ncbi.nlm.ni...
PMID 8188258	View Gene Set	7.421e-05	11	0.004327	37	The human EPRS locus (formerly the QARS locus): a gene encoding a class I and a class II aminoacyl-tRNA synthetase.	www.ncbi.nlm.ni...
PMID 8449960	View Gene Set	7.421e-05	11	0.004327	37	Expression of human aspartyl-tRNA synthetase in Escherichia coli. Functional analysis of the N-terminal putative amphiphilic helix.	www.ncbi.nlm.ni...
PMID 9278442	View Gene Set	7.421e-05	11	0.004327	37	Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant.	www.ncbi.nlm.ni...
PMID 15226435	View Gene Set	9.205e-05	10	0.005245	44	Multiple protein-protein interactions by RNA polymerase I-associated factor PAF49 and role of PAF49 in rRNA transcription.	www.ncbi.nlm.ni...
PMID 12171929	View Gene Set	0.0001065	31	0.005935	45	A proteomics approach to identify proliferating cell nuclear antigen (PCNA)-binding proteins in human cell lysates. Identification of the human CHL12/RFCs2-5 complex as a novel PCNA-binding protein.	www.ncbi.nlm.ni...
PMID 16916647	View Gene Set	0.0001391	76	0.007581	46	Substrate and functional diversity of lysine acetylation revealed by a proteomics survey.	www.ncbi.nlm.ni...
PMID 11402041	View Gene Set	0.0001586	16	0.008282	47	Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28 S small subunit.	www.ncbi.nlm.ni...
PMID 18063578	View Gene Set	0.0001585	31	0.008282	47	The layered structure of human mitochondrial DNA nucleoids.	www.ncbi.nlm.ni...
PMID 1574589	View Gene Set	0.0001627	11	0.008327	49	De novo purine nucleotide biosynthesis.	www.ncbi.nlm.ni...
PMID 14983052	View Gene Set	0.0001726	391	0.008485	50	The human olfactory receptor gene family.	www.ncbi.nlm.ni...
PMID 15196461	View Gene Set	0.0001704	11	0.008485	50	The highly conserved and multifunctional NuA4 HAT complex.	www.ncbi.nlm.ni...
PMID 15960975	View Gene Set	0.0001999	28	0.009638	52	Physical association and coordinate function of the H3 K4 methyltransferase MLL1 and the H4 K16 acetyltransferase MOF.	www.ncbi.nlm.ni...
PMID 9222609	View Gene Set	0.0002112	10	0.00999	53	A pathway of multi-chaperone interactions common to diverse regulatory proteins: estrogen receptor Fes tyrosine kinase heat shock transcription factor Hsf1 and the aryl hydrocarbon receptor.	www.ncbi.nlm.ni...
PMID 15078818	View Gene Set	0.0002241	11	0.01021	54	Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo.	www.ncbi.nlm.ni...
PMID 16702407	View Gene Set	0.0002241	11	0.01021	54	DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A.	www.ncbi.nlm.ni...
PMID 11279069	View Gene Set	0.0002459	15	0.01101	56	Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria.	www.ncbi.nlm.ni...
PMID 11812149	View Gene Set	0.0002663	13	0.01171	57	Protein-protein interactions of hCsl4p with other human exosome subunits.	www.ncbi.nlm.ni...
PMID 12837248	View Gene Set	0.000358	22	0.01547	58	The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome.	www.ncbi.nlm.ni...
PMID 11719186	View Gene Set	0.0003888	17	0.01652	59	AU binding proteins recruit the exosome to degrade ARE-containing mRNAs.	www.ncbi.nlm.ni...
PMID 15461802	View Gene Set	0.0004028	293	0.01683	60	A genome annotation-driven approach to cloning the human ORFeome.	www.ncbi.nlm.ni...
PMID 11157797	View Gene Set	0.0004746	76	0.01919	61	Sequence structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16.	www.ncbi.nlm.ni...
PMID 15782174	View Gene Set	0.0004741	31	0.01919	61	Identifying and quantifying in vivo methylation sites by heavy methyl SILAC.	www.ncbi.nlm.ni...
PMID 12419256	View Gene Set	0.0005064	12	0.01984	63	Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring.	www.ncbi.nlm.ni...
PMID 9878398	View Gene Set	0.0005009	13	0.01984	63	Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein.	www.ncbi.nlm.ni...
PMID 12045100	View Gene Set	0.0005273	18	0.02034	65	DNA replication in eukaryotic cells.	www.ncbi.nlm.ni...
PMID 9731529	View Gene Set	0.0005425	24	0.02061	66	Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex.	www.ncbi.nlm.ni...
PMID 19710015	View Gene Set	0.0005852	48	0.0219	67	The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor.	www.ncbi.nlm.ni...
PMID 11110791	View Gene Set	0.0006861	12	0.0253	68	Three novel components of the human exosome.	www.ncbi.nlm.ni...
PMID 8724849	View Gene Set	0.000909	41	0.03303	69	Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1.	www.ncbi.nlm.ni...
PMID 15010469	View Gene Set	0.0009223	15	0.03303	70	Phosphorylation of histone H2A inhibits transcription on chromatin templates.	www.ncbi.nlm.ni...
PMID 10591208	View Gene Set	0.0009836	299	0.03473	71	The DNA sequence of human chromosome 22.	www.ncbi.nlm.ni...
PMID 19915574	View Gene Set	0.0011	14	0.0383	72	Common variants at five new loci associated with early-onset inflammatory bowel disease.	www.ncbi.nlm.ni...
PMID 10373521	View Gene Set	0.001137	13	0.03901	73	Transcriptional cofactor CA150 regulates RNA polymerase II elongation in a TATA-box-dependent manner.	www.ncbi.nlm.ni...
PMID 10725406	View Gene Set	0.001152	13	0.03901	73	BRCA1 interaction with RNA polymerase II reveals a role for hRPB2 and hRPB10alpha in activated transcription.	www.ncbi.nlm.ni...
PMID 15647280	View Gene Set	0.001213	17	0.04053	75	The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes.	www.ncbi.nlm.ni...
PMID 11076961	View Gene Set	0.00123	14	0.04059	76	Characterization of vertebrate cohesin complexes and their regulation in prophase.	www.ncbi.nlm.ni...
PMID 12788944	View Gene Set	0.001262	11	0.04075	77	The association of the human PM/Scl-75 autoantigen with the exosome is dependent on a newly identified N terminus.	www.ncbi.nlm.ni...
PMID 7638159	View Gene Set	0.001268	13	0.04075	77	Specific binding of RNA polymerase II to the human immunodeficiency virus trans-activating region RNA is regulated by cellular cofactors and Tat.	www.ncbi.nlm.ni...
PMID 11095689	View Gene Set	0.001303	17	0.04136	79	The human homolog of Saccharomyces cerevisiae Mcm10 interacts with replication factors and dissociates from nuclease-resistant nuclear structures in G(2) phase.	www.ncbi.nlm.ni...
PMID 10698937	View Gene Set	0.001329	13	0.04165	80	TIP30 has an intrinsic kinase activity required for up-regulation of a subset of apoptotic genes.	www.ncbi.nlm.ni...
PMID 15644312	View Gene Set	0.00141	10	0.04364	81	Dissection of the mitochondrial import and assembly pathway for human Tom40.	www.ncbi.nlm.ni...
PMID 12611891	View Gene Set	0.001443	40	0.04368	82	The subunit composition of the human NADH dehydrogenase obtained by rapid one-step immunopurification.	www.ncbi.nlm.ni...
PMID 7788527	View Gene Set	0.001446	42	0.04368	82	Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1.	www.ncbi.nlm.ni...
PMID 9878551	View Gene Set	0.001479	34	0.04414	84	cDNA of eight nuclear encoded subunits of NADH:ubiquinone oxidoreductase: human complex I cDNA characterization completed.	www.ncbi.nlm.ni...
PMID 10601273	View Gene Set	0.001521	21	0.04486	85	Nuclear import of hepatic glucokinase depends upon glucokinase regulatory protein whereas export is due to a nuclear export signal sequence in glucokinase.	www.ncbi.nlm.ni...
PMID 16387653	View Gene Set	0.001543	42	0.04497	86	ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation.	www.ncbi.nlm.ni...
PMID 8590280	View Gene Set	0.001572	41	0.0453	87	Prediction of the coding sequences of unidentified human genes. IV. The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1.	www.ncbi.nlm.ni...
PMID 9409616	View Gene Set	0.001711	17	0.04873	88	Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase.	www.ncbi.nlm.ni...

Gene Set Collection: ChromosomalTiles5Mb

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Prosite

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Enzyme

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.BioGRID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.HPRD

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.anyDB

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.humancyc

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.nci-nature

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.reactome

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null chr17_80-85Mb	View Gene Set	1.208e-07	37	0.0001346	1	Genomic tile: chr17 ; 80000001-85000001 Mb	genome.ucsc.edu...
Null chr17_0-5Mb	View Gene Set	5.433e-07	65	0.0003026	2	Genomic tile: chr17 ; 1-5000001 Mb	genome.ucsc.edu...
Null chr17_77.5-82.5Mb	View Gene Set	1.012e-06	54	0.000376	3	Genomic tile: chr17 ; 77500001-82500001 Mb	genome.ucsc.edu...
Null chr9_132.5-137.5Mb	View Gene Set	1.441e-05	53	0.004014	4	Genomic tile: chr9 ; 132500001-137500001 Mb	genome.ucsc.edu...
Null chr16_0-5Mb	View Gene Set	4.239e-05	113	0.009444	5	Genomic tile: chr16 ; 1-5000001 Mb	genome.ucsc.edu...
Null chr9_127.5-132.5Mb	View Gene Set	0.0001298	38	0.02066	6	Genomic tile: chr9 ; 127500001-132500001 Mb	genome.ucsc.edu...
Null chr9_130-135Mb	View Gene Set	0.0001298	40	0.02066	6	Genomic tile: chr9 ; 130000001-135000001 Mb	genome.ucsc.edu...
Null chr22_40-45Mb	View Gene Set	0.0003117	51	0.03859	8	Genomic tile: chr22 ; 40000001-45000001 Mb	genome.ucsc.edu...
Null chr7_0-5Mb	View Gene Set	0.0002835	24	0.03859	8	Genomic tile: chr7 ; 1-5000001 Mb	genome.ucsc.edu...
Null chr16_67.5-72.5Mb	View Gene Set	0.0005546	51	0.04698	10	Genomic tile: chr16 ; 67500001-72500001 Mb	genome.ucsc.edu...
Null chr16_85-90Mb	View Gene Set	0.0004397	43	0.04698	10	Genomic tile: chr16 ; 85000001-90000001 Mb	genome.ucsc.edu...
Null chr19_0-5Mb	View Gene Set	0.000531	105	0.04698	10	Genomic tile: chr19 ; 1-5000001 Mb	genome.ucsc.edu...
Null chr1_10-15Mb	View Gene Set	0.0004795	37	0.04698	10	Genomic tile: chr1 ; 10000001-15000001 Mb	genome.ucsc.edu...
Null chr3_45-50Mb	View Gene Set	0.0005904	72	0.04698	10	Genomic tile: chr3 ; 45000001-50000001 Mb	genome.ucsc.edu...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null PS00357	View Gene Set	3.935e-08	19	1.446e-05	1	HISTONE_H2B	expasy.org/pros...
Null PS51194	View Gene Set	2.912e-08	113	1.446e-05	1	HELICASE_CTER	expasy.org/pros...
Null PS51192	View Gene Set	2.195e-07	112	5.378e-05	3	HELICASE_ATP_BIND_1	expasy.org/pros...
Null PS51195	View Gene Set	1.892e-06	37	0.0003477	4	Q_MOTIF	expasy.org/pros...
Null PS50102	View Gene Set	1.682e-05	229	0.002472	5	RRM	expasy.org/pros...
Null PS00047	View Gene Set	2.854e-05	14	0.003496	6	HISTONE_H4	expasy.org/pros...
Null PS00039	View Gene Set	0.0001922	27	0.02018	7	DEAD_ATP_HELICASE	expasy.org/pros...
Null PS00178	View Gene Set	0.0003616	15	0.03322	8	AA_TRNA_LIGASE_I	expasy.org/pros...
Null PS50833	View Gene Set	0.0004105	7	0.03353	9	BRIX	expasy.org/pros...
Null PS00847	View Gene Set	0.0004914	6	0.03612	10	MCM_1	expasy.org/pros...
Null PS00469	View Gene Set	0.0005513	6	0.03684	11	NDP_KINASES	expasy.org/pros...
Null PS00690	View Gene Set	0.0007293	24	0.04467	12	DEAH_ATP_HELICASE	expasy.org/pros...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null EC:1.6.5.3	View Gene Set	0.0007036	43	0.0471	1	NADH dehydrogenase (ubiquinone)	expasy.org/enzy...
Null EC:1.6.99.3	View Gene Set	0.0008942	35	0.0471	1	NADH dehydrogenase	expasy.org/enzy...
Null EC:2.7.7.6	View Gene Set	0.0007374	17	0.0471	1	DNA-directed RNA polymerase	expasy.org/enzy...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null ppi.155871	View Gene Set	1.076e-16	236	2.472e-13	1	Protein-protein-interaction for 155871	www.ncbi.nlm.ni...
Null ppi.RPA1	View Gene Set	2.85e-06	23	0.003273	2	Protein-protein-interaction for RPA1	www.ncbi.nlm.ni...
Null ppi.TAF10	View Gene Set	6.391e-06	27	0.004893	3	Protein-protein-interaction for TAF10	www.ncbi.nlm.ni...
Null ppi.SRRM1	View Gene Set	1.388e-05	64	0.006098	4	Protein-protein-interaction for SRRM1	www.ncbi.nlm.ni...
Null ppi.USP39	View Gene Set	1.879e-05	15	0.006098	4	Protein-protein-interaction for USP39	www.ncbi.nlm.ni...
Null ppi.USP36	View Gene Set	1.66e-05	17	0.006098	4	Protein-protein-interaction for USP36	www.ncbi.nlm.ni...
Null ppi.RPA2	View Gene Set	1.764e-05	24	0.006098	4	Protein-protein-interaction for RPA2	www.ncbi.nlm.ni...
Null ppi.RPAP3	View Gene Set	2.124e-05	29	0.006098	4	Protein-protein-interaction for RPAP3	www.ncbi.nlm.ni...
Null ppi.POLR1A	View Gene Set	4.208e-05	11	0.009133	9	Protein-protein-interaction for POLR1A	www.ncbi.nlm.ni...
Null ppi.MEPCE	View Gene Set	4.374e-05	147	0.009133	9	Protein-protein-interaction for MEPCE	www.ncbi.nlm.ni...
Null ppi.CDT1	View Gene Set	4.329e-05	37	0.009133	9	Protein-protein-interaction for CDT1	www.ncbi.nlm.ni...
Null ppi.SRRM2	View Gene Set	4.895e-05	101	0.009371	12	Protein-protein-interaction for SRRM2	www.ncbi.nlm.ni...
Null ppi.POLR3C	View Gene Set	5.833e-05	10	0.01031	13	Protein-protein-interaction for POLR3C	www.ncbi.nlm.ni...
Null ppi.SSRP1	View Gene Set	6.959e-05	15	0.01142	14	Protein-protein-interaction for SSRP1	www.ncbi.nlm.ni...
Null ppi.USP42	View Gene Set	0.0001076	24	0.01612	15	Protein-protein-interaction for USP42	www.ncbi.nlm.ni...
Null ppi.MED26	View Gene Set	0.0001123	22	0.01612	15	Protein-protein-interaction for MED26	www.ncbi.nlm.ni...
Null ppi.RNPS1	View Gene Set	0.0002288	38	0.03092	17	Protein-protein-interaction for RNPS1	www.ncbi.nlm.ni...
Null ppi.DMAP1	View Gene Set	0.0003533	13	0.04058	18	Protein-protein-interaction for DMAP1	www.ncbi.nlm.ni...
Null ppi.GTF3C3	View Gene Set	0.0003275	11	0.04058	18	Protein-protein-interaction for GTF3C3	www.ncbi.nlm.ni...
Null ppi.POLR1C	View Gene Set	0.0003376	6	0.04058	18	Protein-protein-interaction for POLR1C	www.ncbi.nlm.ni...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null ppi.SFRS12	View Gene Set	2.959e-06	49	0.007025	1	Protein-protein-interaction for SFRS12	www.ncbi.nlm.ni...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null ppi.155871	View Gene Set	2.137e-17	251	7.681e-14	1	Protein-protein-interaction for 155871	www.ncbi.nlm.ni...
Null ppi.SFRS12	View Gene Set	1.959e-06	50	0.002347	2	Protein-protein-interaction for SFRS12	www.ncbi.nlm.ni...
Null ppi.TAF10	View Gene Set	1.404e-06	29	0.002347	2	Protein-protein-interaction for TAF10	www.ncbi.nlm.ni...
Null ppi.RPA1	View Gene Set	4.924e-06	24	0.004424	4	Protein-protein-interaction for RPA1	www.ncbi.nlm.ni...
Null ppi.SSRP1	View Gene Set	1.327e-05	21	0.009537	5	Protein-protein-interaction for SSRP1	www.ncbi.nlm.ni...
Null ppi.USP36	View Gene Set	1.66e-05	17	0.009945	6	Protein-protein-interaction for USP36	www.ncbi.nlm.ni...
Null ppi.SRRM1	View Gene Set	2.909e-05	66	0.01494	7	Protein-protein-interaction for SRRM1	www.ncbi.nlm.ni...
Null ppi.SRRM2	View Gene Set	4.895e-05	101	0.01759	8	Protein-protein-interaction for SRRM2	www.ncbi.nlm.ni...
Null ppi.POLR1A	View Gene Set	4.444e-05	13	0.01759	8	Protein-protein-interaction for POLR1A	www.ncbi.nlm.ni...
Null ppi.MEPCE	View Gene Set	4.374e-05	147	0.01759	8	Protein-protein-interaction for MEPCE	www.ncbi.nlm.ni...
Null ppi.POLR3C	View Gene Set	5.833e-05	10	0.01906	11	Protein-protein-interaction for POLR3C	www.ncbi.nlm.ni...
Null ppi.RPA2	View Gene Set	8.621e-05	25	0.02383	12	Protein-protein-interaction for RPA2	www.ncbi.nlm.ni...
Null ppi.RPAP3	View Gene Set	8.493e-05	30	0.02383	12	Protein-protein-interaction for RPAP3	www.ncbi.nlm.ni...
Null ppi.WRN	View Gene Set	9.355e-05	21	0.02402	14	Protein-protein-interaction for WRN	www.ncbi.nlm.ni...
Null ppi.USP42	View Gene Set	0.0001076	24	0.02577	15	Protein-protein-interaction for USP42	www.ncbi.nlm.ni...
Null ppi.CDT1	View Gene Set	0.0001185	42	0.02661	16	Protein-protein-interaction for CDT1	www.ncbi.nlm.ni...
Null ppi.USP39	View Gene Set	0.0001342	16	0.02838	17	Protein-protein-interaction for USP39	www.ncbi.nlm.ni...
Null ppi.GTF3C3	View Gene Set	0.0001467	12	0.02928	18	Protein-protein-interaction for GTF3C3	www.ncbi.nlm.ni...
Null ppi.ING3	View Gene Set	0.0001581	12	0.02991	19	Protein-protein-interaction for ING3	www.ncbi.nlm.ni...
Null ppi.COPS4	View Gene Set	0.000183	17	0.03289	20	Protein-protein-interaction for COPS4	www.ncbi.nlm.ni...
Null ppi.MED26	View Gene Set	0.0002558	23	0.04378	21	Protein-protein-interaction for MED26	www.ncbi.nlm.ni...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null purine nucleotides de novo biosynthesis II	View Gene Set	0.0001627	11	0.04231	1	HUMANCYC - purine nucleotides de novo biosynthesis II gene set	www.pathwaycomm...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null Validated targets of C-MYC transcriptional activation	View Gene Set	2.33e-09	80	4.333e-07	1	NCI_NATURE - Validated targets of C-MYC transcriptional activation gene set	www.pathwaycomm...

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null Processing of Capped Intron-Containing Pre-mRNA	View Gene Set	3.281e-09	138	3.664e-06	1	REACTOME - Processing of Capped Intron-Containing Pre-mRNA gene set	www.pathwaycomm...
Null mRNA Processing	View Gene Set	2.098e-08	158	1.172e-05	2	REACTOME - mRNA Processing gene set	www.pathwaycomm...
Null Formation and Maturation of mRNA Transcript	View Gene Set	3.513e-08	185	1.308e-05	3	REACTOME - Formation and Maturation of mRNA Transcript gene set	www.pathwaycomm...
Null Gene Expression	View Gene Set	7.338e-08	381	2.049e-05	4	REACTOME - Gene Expression gene set	www.pathwaycomm...
Null mRNA Splicing - Major Pathway	View Gene Set	1.802e-07	107	3.354e-05	5	REACTOME - mRNA Splicing - Major Pathway gene set	www.pathwaycomm...
Null mRNA Splicing	View Gene Set	1.802e-07	107	3.354e-05	5	REACTOME - mRNA Splicing gene set	www.pathwaycomm...
Null Transcription	View Gene Set	4.033e-07	178	6.435e-05	7	REACTOME - Transcription gene set	www.pathwaycomm...
Null tRNA Aminoacylation	View Gene Set	1.403e-06	42	0.0001958	8	REACTOME - tRNA Aminoacylation gene set	www.pathwaycomm...
Null snRNP Assembly	View Gene Set	2.449e-06	50	0.0002735	9	REACTOME - snRNP Assembly gene set	www.pathwaycomm...
Null Metabolism of non-coding RNA	View Gene Set	2.449e-06	50	0.0002735	9	REACTOME - Metabolism of non-coding RNA gene set	www.pathwaycomm...
Null RNA Polymerase III Transcription Initiation From Type 2 Promoter	View Gene Set	4.424e-06	20	0.0004118	11	REACTOME - RNA Polymerase III Transcription Initiation From Type 2 Promoter gene set	www.pathwaycomm...
Null RNA Polymerase III Transcription Initiation From Type 1 Promoter	View Gene Set	4.424e-06	21	0.0004118	11	REACTOME - RNA Polymerase III Transcription Initiation From Type 1 Promoter gene set	www.pathwaycomm...
Null Transport of Mature Transcript to Cytoplasm	View Gene Set	1.287e-05	55	0.001106	13	REACTOME - Transport of Mature Transcript to Cytoplasm gene set	www.pathwaycomm...
Null Transport of Mature mRNA derived from an Intron-Containing Transcript	View Gene Set	1.731e-05	51	0.001381	14	REACTOME - Transport of Mature mRNA derived from an Intron-Containing Transcript gene set	www.pathwaycomm...
Null RNA Polymerase I RNA Polymerase III and Mitochondrial Transcription	View Gene Set	2.06e-05	93	0.001534	15	REACTOME - RNA Polymerase I RNA Polymerase III and Mitochondrial Transcription gene set	www.pathwaycomm... RNA Polymerase ... and Mitochondri...
Null RNA Polymerase III Transcription Initiation	View Gene Set	3.758e-05	29	0.002623	16	REACTOME - RNA Polymerase III Transcription Initiation gene set	www.pathwaycomm...
Null Telomere Maintenance	View Gene Set	6.825e-05	49	0.004485	17	REACTOME - Telomere Maintenance gene set	www.pathwaycomm...
Null mRNA Splicing - Minor Pathway	View Gene Set	8.715e-05	42	0.005123	18	REACTOME - mRNA Splicing - Minor Pathway gene set	www.pathwaycomm...
Null Metabolism of RNA	View Gene Set	8.454e-05	174	0.005123	18	REACTOME - Metabolism of RNA gene set	www.pathwaycomm...
Null Cytosolic tRNA aminoacylation	View Gene Set	0.0001419	24	0.00755	20	REACTOME - Cytosolic tRNA aminoacylation gene set	www.pathwaycomm...
Null Pyrimidine biosynthesis	View Gene Set	0.0001415	6	0.00755	20	REACTOME - Pyrimidine biosynthesis gene set	www.pathwaycomm...
Null Mitochondrial tRNA aminoacylation	View Gene Set	0.0002553	21	0.01296	22	REACTOME - Mitochondrial tRNA aminoacylation gene set	www.pathwaycomm...
Null RNA Polymerase III Transcription	View Gene Set	0.0004096	34	0.01906	23	REACTOME - RNA Polymerase III Transcription gene set	www.pathwaycomm...
Null RNA Polymerase III Abortive And Retractive Initiation	View Gene Set	0.0004096	34	0.01906	23	REACTOME - RNA Polymerase III Abortive And Retractive Initiation gene set	www.pathwaycomm...
Null Transport of Mature mRNA Derived from an Intronless Transcript	View Gene Set	0.0004769	35	0.02049	25	REACTOME - Transport of Mature mRNA Derived from an Intronless Transcript gene set	www.pathwaycomm...
Null Transport of Mature mRNAs Derived from Intronless Transcripts	View Gene Set	0.0004626	36	0.02049	25	REACTOME - Transport of Mature mRNAs Derived from Intronless Transcripts gene set	www.pathwaycomm...
Null Late Phase of HIV Life Cycle	View Gene Set	0.0005056	92	0.02056	27	REACTOME - Late Phase of HIV Life Cycle gene set	www.pathwaycomm...
Null Interactions of Rev with host cellular proteins	View Gene Set	0.0005154	33	0.02056	27	REACTOME - Interactions of Rev with host cellular proteins gene set	www.pathwaycomm...
Null Transport of the SLBP independent Mature mRNA	View Gene Set	0.0006294	32	0.0213	29	REACTOME - Transport of the SLBP independent Mature mRNA gene set	www.pathwaycomm...
Null Transport of the SLBP Dependant Mature mRNA	View Gene Set	0.0006126	33	0.0213	29	REACTOME - Transport of the SLBP Dependant Mature mRNA gene set	www.pathwaycomm...
Null Metabolism of nucleotides	View Gene Set	0.0006159	66	0.0213	29	REACTOME - Metabolism of nucleotides gene set	www.pathwaycomm...
Null Deadenylation-dependent mRNA decay	View Gene Set	0.0005957	46	0.0213	29	REACTOME - Deadenylation-dependent mRNA decay gene set	www.pathwaycomm...
Null Olfactory Signaling Pathway	View Gene Set	0.0006255	370	0.0213	29	REACTOME - Olfactory Signaling Pathway gene set	www.pathwaycomm...
Null Meiotic Recombination	View Gene Set	0.0006498	42	0.02135	34	REACTOME - Meiotic Recombination gene set	www.pathwaycomm...
Null Interactions of Vpr with host cellular proteins	View Gene Set	0.0007227	34	0.02306	35	REACTOME - Interactions of Vpr with host cellular proteins gene set	www.pathwaycomm...
Null HIV Life Cycle	View Gene Set	0.000848	103	0.02596	36	REACTOME - HIV Life Cycle gene set	www.pathwaycomm...
Null Nuclear import of Rev protein	View Gene Set	0.0008626	30	0.02596	36	REACTOME - Nuclear import of Rev protein gene set	www.pathwaycomm...
Null Cell Cycle Mitotic	View Gene Set	0.000883	312	0.02596	36	REACTOME - Cell Cycle Mitotic gene set	www.pathwaycomm... Mitotic&format=...
Null Rev-mediated nuclear export of HIV-1 RNA	View Gene Set	0.0009808	32	0.02809	39	REACTOME - Rev-mediated nuclear export of HIV-1 RNA gene set	www.pathwaycomm...
Null Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins.	View Gene Set	0.001058	91	0.02956	40	REACTOME - Respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins. gene set	www.pathwaycomm... ATP synthesis b... and heat produc...
Null Telomere Extension By Telomerase	View Gene Set	0.001168	6	0.03182	41	REACTOME - Telomere Extension By Telomerase gene set	www.pathwaycomm...
Null RNA Polymerase III Transcription Initiation From Type 3 Promoter	View Gene Set	0.001359	22	0.0353	42	REACTOME - RNA Polymerase III Transcription Initiation From Type 3 Promoter gene set	www.pathwaycomm...
Null RNA Polymerase II Transcription	View Gene Set	0.001352	101	0.0353	42	REACTOME - RNA Polymerase II Transcription gene set	www.pathwaycomm...
Null mRNA Decay by 3' to 5' Exoribonuclease	View Gene Set	0.001533	11	0.03891	44	REACTOME - mRNA Decay by 3' to 5' Exoribonuclease gene set	www.pathwaycomm...
Null RNA Polymerase III Chain Elongation	View Gene Set	0.001587	12	0.0394	45	REACTOME - RNA Polymerase III Chain Elongation gene set	www.pathwaycomm...
Null Chromosome Maintenance	View Gene Set	0.001683	69	0.04086	46	REACTOME - Chromosome Maintenance gene set	www.pathwaycomm...
Null Export of Viral Ribonucleoproteins from Nucleus	View Gene Set	0.001795	31	0.04267	47	REACTOME - Export of Viral Ribonucleoproteins from Nucleus gene set	www.pathwaycomm...
Null Respiratory electron transport	View Gene Set	0.002177	76	0.04962	48	REACTOME - Respiratory electron transport gene set	www.pathwaycomm...
Null Metabolism of carbohydrates	View Gene Set	0.002138	93	0.04962	48	REACTOME - Metabolism of carbohydrates gene set	www.pathwaycomm...

Gene Set Collection: mirbase.targets

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Name	GeneSetDescription	Value	Gene Set Size	Corrected Value	Ranking	Description	URL
Null hsa-miR-874	View Gene Set	1.024e-07	722	7.282e-05	1	microRNA targets for hsa-miR-874 from mirbase.targets	www.mirbase.org...
Null hsa-miR-146b-3p	View Gene Set	6.811e-07	695	0.0002421	2	microRNA targets for hsa-miR-146b-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-615-5p	View Gene Set	1.744e-06	848	0.0004133	3	microRNA targets for hsa-miR-615-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-486-3p	View Gene Set	4.378e-06	773	0.0007782	4	microRNA targets for hsa-miR-486-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-939	View Gene Set	8.407e-06	667	0.001195	5	microRNA targets for hsa-miR-939 from mirbase.targets	www.mirbase.org...
Null hsa-miR-331-3p	View Gene Set	1.031e-05	712	0.001221	6	microRNA targets for hsa-miR-331-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-941	View Gene Set	1.344e-05	590	0.001365	7	microRNA targets for hsa-miR-941 from mirbase.targets	www.mirbase.org...
Null hsa-miR-671-3p	View Gene Set	2.355e-05	767	0.002093	8	microRNA targets for hsa-miR-671-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-504	View Gene Set	4.53e-05	621	0.003579	9	microRNA targets for hsa-miR-504 from mirbase.targets	www.mirbase.org...
Null hsa-miR-324-3p	View Gene Set	6.95e-05	788	0.004775	10	microRNA targets for hsa-miR-324-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-328	View Gene Set	9.068e-05	685	0.004775	10	microRNA targets for hsa-miR-328 from mirbase.targets	www.mirbase.org...
Null hsa-miR-484	View Gene Set	8.418e-05	733	0.004775	10	microRNA targets for hsa-miR-484 from mirbase.targets	www.mirbase.org...
Null hsa-miR-634	View Gene Set	7.486e-05	714	0.004775	10	microRNA targets for hsa-miR-634 from mirbase.targets	www.mirbase.org...
Null hsa-miR-654-5p	View Gene Set	9.402e-05	718	0.004775	10	microRNA targets for hsa-miR-654-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-652	View Gene Set	0.0001026	662	0.004865	15	microRNA targets for hsa-miR-652 from mirbase.targets	www.mirbase.org...
Null hsa-miR-503	View Gene Set	0.0001128	748	0.005014	16	microRNA targets for hsa-miR-503 from mirbase.targets	www.mirbase.org...
Null hsa-miR-565	View Gene Set	0.0001282	689	0.005046	17	microRNA targets for hsa-miR-565 from mirbase.targets	www.mirbase.org...
Null hsa-miR-658	View Gene Set	0.0001349	660	0.005046	17	microRNA targets for hsa-miR-658 from mirbase.targets	www.mirbase.org...
Null hsa-miR-886-5p	View Gene Set	0.0001289	793	0.005046	17	microRNA targets for hsa-miR-886-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-125a-5p	View Gene Set	0.0001741	817	0.006189	20	microRNA targets for hsa-miR-125a-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-185*	View Gene Set	0.00023	506	0.007111	21	microRNA targets for hsa-miR-185* from mirbase.targets	www.mirbase.org...
Null hsa-miR-339-3p	View Gene Set	0.0002214	797	0.007111	21	microRNA targets for hsa-miR-339-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-611	View Gene Set	0.000217	671	0.007111	21	microRNA targets for hsa-miR-611 from mirbase.targets	www.mirbase.org...
Null hsa-miR-220b	View Gene Set	0.000321	852	0.009511	24	microRNA targets for hsa-miR-220b from mirbase.targets	www.mirbase.org...
Null hsa-miR-214	View Gene Set	0.0003373	797	0.009594	25	microRNA targets for hsa-miR-214 from mirbase.targets	www.mirbase.org...
Null hsa-miR-296-3p	View Gene Set	0.000363	905	0.009927	26	microRNA targets for hsa-miR-296-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-492	View Gene Set	0.0003801	625	0.01001	27	microRNA targets for hsa-miR-492 from mirbase.targets	www.mirbase.org...
Null hsa-miR-615-3p	View Gene Set	0.0004276	757	0.01086	28	microRNA targets for hsa-miR-615-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-612	View Gene Set	0.0004532	685	0.01111	29	microRNA targets for hsa-miR-612 from mirbase.targets	www.mirbase.org...
Null hsa-miR-940	View Gene Set	0.0005513	660	0.01307	30	microRNA targets for hsa-miR-940 from mirbase.targets	www.mirbase.org...
Null hsa-miR-99b	View Gene Set	0.0005723	708	0.01313	31	microRNA targets for hsa-miR-99b from mirbase.targets	www.mirbase.org...
Null hsa-miR-516a-3p	View Gene Set	0.0006343	780	0.01367	32	microRNA targets for hsa-miR-516a-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-646	View Gene Set	0.0006283	745	0.01367	32	microRNA targets for hsa-miR-646 from mirbase.targets	www.mirbase.org...
Null hsa-miR-637	View Gene Set	0.0007819	672	0.01588	34	microRNA targets for hsa-miR-637 from mirbase.targets	www.mirbase.org...
Null hsa-miR-671-5p	View Gene Set	0.0007601	813	0.01588	34	microRNA targets for hsa-miR-671-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-196a*	View Gene Set	0.0008635	526	0.01705	36	microRNA targets for hsa-miR-196a* from mirbase.targets	www.mirbase.org...
Null hsa-miR-134	View Gene Set	0.001005	703	0.01722	37	microRNA targets for hsa-miR-134 from mirbase.targets	www.mirbase.org...
Null hsa-miR-214*	View Gene Set	0.0009954	434	0.01722	37	microRNA targets for hsa-miR-214* from mirbase.targets	www.mirbase.org...
Null hsa-miR-220c	View Gene Set	0.0009539	831	0.01722	37	microRNA targets for hsa-miR-220c from mirbase.targets	www.mirbase.org...
Null hsa-miR-30b*	View Gene Set	0.001042	655	0.01722	37	microRNA targets for hsa-miR-30b* from mirbase.targets	www.mirbase.org...
Null hsa-miR-34a	View Gene Set	0.0009194	917	0.01722	37	microRNA targets for hsa-miR-34a from mirbase.targets	www.mirbase.org...
Null hsa-miR-650	View Gene Set	0.001036	693	0.01722	37	microRNA targets for hsa-miR-650 from mirbase.targets	www.mirbase.org...
Null hsa-miR-937	View Gene Set	0.001034	654	0.01722	37	microRNA targets for hsa-miR-937 from mirbase.targets	www.mirbase.org...
Null hsa-miR-886-3p	View Gene Set	0.0011	745	0.01778	44	microRNA targets for hsa-miR-886-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-923	View Gene Set	0.00119	690	0.0188	45	microRNA targets for hsa-miR-923 from mirbase.targets	www.mirbase.org...
Null hsa-miR-330-5p	View Gene Set	0.001302	728	0.02013	46	microRNA targets for hsa-miR-330-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-518a-3p	View Gene Set	0.001409	925	0.02045	47	microRNA targets for hsa-miR-518a-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-572	View Gene Set	0.001396	602	0.02045	47	microRNA targets for hsa-miR-572 from mirbase.targets	www.mirbase.org...
Null hsa-miR-635	View Gene Set	0.001382	648	0.02045	47	microRNA targets for hsa-miR-635 from mirbase.targets	www.mirbase.org...
Null hsa-miR-663	View Gene Set	0.001555	743	0.02212	50	microRNA targets for hsa-miR-663 from mirbase.targets	www.mirbase.org...
Null hsa-miR-92b*	View Gene Set	0.001623	648	0.02263	51	microRNA targets for hsa-miR-92b* from mirbase.targets	www.mirbase.org...
Null hsa-miR-596	View Gene Set	0.001699	644	0.02299	52	microRNA targets for hsa-miR-596 from mirbase.targets	www.mirbase.org...
Null hsa-miR-887	View Gene Set	0.001714	709	0.02299	52	microRNA targets for hsa-miR-887 from mirbase.targets	www.mirbase.org...
Null hsa-miR-604	View Gene Set	0.001772	691	0.02333	54	microRNA targets for hsa-miR-604 from mirbase.targets	www.mirbase.org...
Null hsa-miR-661	View Gene Set	0.001832	575	0.02369	55	microRNA targets for hsa-miR-661 from mirbase.targets	www.mirbase.org...
Null hsa-miR-566	View Gene Set	0.002086	787	0.02648	56	microRNA targets for hsa-miR-566 from mirbase.targets	www.mirbase.org...
Null hsa-miR-361-3p	View Gene Set	0.002141	634	0.02671	57	microRNA targets for hsa-miR-361-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-510	View Gene Set	0.002184	639	0.02678	58	microRNA targets for hsa-miR-510 from mirbase.targets	www.mirbase.org...
Null hsa-miR-326	View Gene Set	0.002227	650	0.02684	59	microRNA targets for hsa-miR-326 from mirbase.targets	www.mirbase.org...
Null hsa-miR-345	View Gene Set	0.002329	696	0.02759	60	microRNA targets for hsa-miR-345 from mirbase.targets	www.mirbase.org...
Null hsa-miR-502-5p	View Gene Set	0.002584	730	0.03011	61	microRNA targets for hsa-miR-502-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-185	View Gene Set	0.002822	607	0.03184	62	microRNA targets for hsa-miR-185 from mirbase.targets	www.mirbase.org...
Null hsa-miR-323-5p	View Gene Set	0.002779	763	0.03184	62	microRNA targets for hsa-miR-323-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-296-5p	View Gene Set	0.002955	755	0.03283	64	microRNA targets for hsa-miR-296-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-631	View Gene Set	0.003196	714	0.03496	65	microRNA targets for hsa-miR-631 from mirbase.targets	www.mirbase.org...
Null hsa-miR-92a-2*	View Gene Set	0.003487	654	0.03757	66	microRNA targets for hsa-miR-92a-2* from mirbase.targets	www.mirbase.org...
Null hsa-miR-608	View Gene Set	0.00367	729	0.03895	67	microRNA targets for hsa-miR-608 from mirbase.targets	www.mirbase.org...
Null hsa-miR-632	View Gene Set	0.00374	690	0.03911	68	microRNA targets for hsa-miR-632 from mirbase.targets	www.mirbase.org...
Null hsa-miR-453	View Gene Set	0.003837	702	0.03953	69	microRNA targets for hsa-miR-453 from mirbase.targets	www.mirbase.org...
Null hsa-miR-554	View Gene Set	0.004003	708	0.04028	70	microRNA targets for hsa-miR-554 from mirbase.targets	www.mirbase.org...
Null hsa-miR-662	View Gene Set	0.004023	663	0.04028	70	microRNA targets for hsa-miR-662 from mirbase.targets	www.mirbase.org...
Null hsa-miR-769-3p	View Gene Set	0.004093	823	0.04042	72	microRNA targets for hsa-miR-769-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-210	View Gene Set	0.004227	703	0.04117	73	microRNA targets for hsa-miR-210 from mirbase.targets	www.mirbase.org...
Null hsa-miR-766	View Gene Set	0.004581	517	0.04402	74	microRNA targets for hsa-miR-766 from mirbase.targets	www.mirbase.org...
Null hsa-miR-602	View Gene Set	0.004723	710	0.04419	75	microRNA targets for hsa-miR-602 from mirbase.targets	www.mirbase.org...
Null hsa-miR-621	View Gene Set	0.004696	713	0.04419	75	microRNA targets for hsa-miR-621 from mirbase.targets	www.mirbase.org...
Null hsa-miR-424	View Gene Set	0.004997	772	0.04614	77	microRNA targets for hsa-miR-424 from mirbase.targets	www.mirbase.org...
Null hsa-miR-346	View Gene Set	0.005166	568	0.04652	78	microRNA targets for hsa-miR-346 from mirbase.targets	www.mirbase.org...
Null hsa-miR-485-5p	View Gene Set	0.005169	556	0.04652	78	microRNA targets for hsa-miR-485-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-551a	View Gene Set	0.005293	676	0.04704	80	microRNA targets for hsa-miR-551a from mirbase.targets	www.mirbase.org...
Null hsa-miR-339-5p	View Gene Set	0.00542	659	0.04757	81	microRNA targets for hsa-miR-339-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-770-5p	View Gene Set	0.005537	702	0.04793	82	microRNA targets for hsa-miR-770-5p from mirbase.targets	www.mirbase.org...
Null hsa-miR-885-3p	View Gene Set	0.005595	799	0.04793	82	microRNA targets for hsa-miR-885-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-181a-2*	View Gene Set	0.005691	742	0.04817	84	microRNA targets for hsa-miR-181a-2* from mirbase.targets	www.mirbase.org...
Null hsa-miR-125a-3p	View Gene Set	0.005796	829	0.04848	85	microRNA targets for hsa-miR-125a-3p from mirbase.targets	www.mirbase.org...
Null hsa-miR-486-5p	View Gene Set	0.005985	729	0.04948	86	microRNA targets for hsa-miR-486-5p from mirbase.targets	www.mirbase.org...

Results

AFA results for: tSAHAda2PC3

Gene Set Collection: KEGG

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: GO

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c1.CYTOBAND

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CGP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CP.BIOCARTA

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CP.KEGG

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c2.CP.REACTOME

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c3.TFT

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c4.CGN

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c4.CM

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c5.BP

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c5.CC

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Broad.c5.MF

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: PMID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ChromosomalTiles5Mb

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Prosite

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: Enzyme

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.BioGRID

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.HPRD

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: ppi.anyDB

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.humancyc

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.nci-nature

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: pathwayCommons.reactome

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: mirbase.targets

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down

Gene Set Collection: tfbsK3Z3

Arguments: refPop=all, featureType=featureNames, colname=WilcoxDOWN, ranks.only=TRUE, absolute=FALSE, alternative=down