Coexpression cluster:C896

Full id: C896_retinoblastoma_iPS_acute_lymphoma_chronic_Burkitt_testicular

Phase1 CAGE Peaks

Hg19::chr12:54674482..54674520,+	p1@HNRNPA1
Hg19::chr14:64855014..64855091,+	p1@MTHFD1
Hg19::chr18:19192235..19192337,+	p1@SNRPD1
Hg19::chr1:54303949..54303979,-	p1@TMEM48
Hg19::chr2:9563769..9563832,+	p1@CPSF3
Hg19::chr4:57301896..57301945,+	p3@PAICS
Hg19::chr4:57302399..57302441,+	p1@PAICS
Hg19::chr6:8102752..8102806,-	p1@EEF1E1
Hg19::chr8:4644826..4644848,+	p1@PAICSP4

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

---

p.value	FDR	nGenes	nPathway	Name
3.49156482482783e-06	0.000736720178038672	3	134	mRNA processing (Wikipathways):WP1863
1.57612000639245e-06	0.000498841982023211	4	421	Gene Expression (Reactome):REACT_71
4.7073957674912e-06	0.000744945380205483	3	148	mRNA Processing (Reactome):REACT_1675
7.12387426768043e-08	4.50941241144171e-05	4	194	{POLR2A,195} (Static Module):NA

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

---

GO ID	GO name	FDR corrected p-value
GO:0006397	mRNA processing	0.00271301856430786
GO:0016071	mRNA metabolic process	0.00271301856430786
GO:0044428	nuclear part	0.00271301856430786
GO:0000398	nuclear mRNA splicing, via spliceosome	0.00271301856430786
GO:0000375	RNA splicing, via transesterification reactions	0.00271301856430786
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.00271301856430786
GO:0051028	mRNA transport	0.00271301856430786
GO:0006396	RNA processing	0.00271301856430786
GO:0050658	RNA transport	0.00271301856430786
GO:0051236	establishment of RNA localization	0.00271301856430786
GO:0050657	nucleic acid transport	0.00271301856430786
GO:0006403	RNA localization	0.00271301856430786
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.00271301856430786
GO:0051292	nuclear pore complex assembly	0.00271301856430786
GO:0043517	positive regulation of DNA damage response, signal transduction by p53 class mediator	0.00271301856430786
GO:0043516	regulation of DNA damage response, signal transduction by p53 class mediator	0.00271301856430786
GO:0031081	nuclear pore distribution	0.00271301856430786
GO:0051664	nuclear pore localization	0.00271301856430786
GO:0046483	heterocycle metabolic process	0.00375888651171585
GO:0005681	spliceosome	0.00408093417500499
GO:0006999	nuclear pore organization and biogenesis	0.00465047824450652
GO:0006164	purine nucleotide biosynthetic process	0.00484923975527564
GO:0006163	purine nucleotide metabolic process	0.00505093545520049
GO:0006725	aromatic compound metabolic process	0.00505093545520049
GO:0004638	phosphoribosylaminoimidazole carboxylase activity	0.00505093545520049
GO:0004477	methenyltetrahydrofolate cyclohydrolase activity	0.00505093545520049
GO:0031503	protein complex localization	0.00505093545520049
GO:0004488	methylenetetrahydrofolate dehydrogenase (NADP+) activity	0.00505093545520049
GO:0009320	phosphoribosylaminoimidazole carboxylase complex	0.00505093545520049
GO:0003723	RNA binding	0.00601224402120285
GO:0004486	methylenetetrahydrofolate dehydrogenase activity	0.00610267470704545
GO:0004639	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity	0.00610267470704545
GO:0008380	RNA splicing	0.00641648721647463
GO:0044237	cellular metabolic process	0.00641648721647463
GO:0046040	IMP metabolic process	0.00641648721647463
GO:0006189	'de novo' IMP biosynthetic process	0.00641648721647463
GO:0016155	formyltetrahydrofolate dehydrogenase activity	0.00641648721647463
GO:0006188	IMP biosynthetic process	0.00641648721647463
GO:0044238	primary metabolic process	0.00641648721647463
GO:0009165	nucleotide biosynthetic process	0.00681108494481145
GO:0000105	histidine biosynthetic process	0.00681108494481145
GO:0009076	histidine family amino acid biosynthetic process	0.00681108494481145
GO:0019238	cyclohydrolase activity	0.00681108494481145
GO:0009113	purine base biosynthetic process	0.00742737510308045
GO:0017056	structural constituent of nuclear pore	0.00742737510308045
GO:0048584	positive regulation of response to stimulus	0.00742737510308045
GO:0006379	mRNA cleavage	0.00808909795120509
GO:0043231	intracellular membrane-bound organelle	0.00808909795120509
GO:0043227	membrane-bound organelle	0.00808909795120509
GO:0006378	mRNA polyadenylation	0.00878397215086816
GO:0009117	nucleotide metabolic process	0.00920670492014003
GO:0004329	formate-tetrahydrofolate ligase activity	0.00920670492014003
GO:0006144	purine base metabolic process	0.00920670492014003
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0101610744609576
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0101610744609576
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0101946355089543
GO:0043631	RNA polyadenylation	0.0103962941467483
GO:0009086	methionine biosynthetic process	0.0103962941467483
GO:0009077	histidine family amino acid catabolic process	0.0103962941467483
GO:0006548	histidine catabolic process	0.0103962941467483
GO:0051668	localization within membrane	0.0103962941467483
GO:0005634	nucleus	0.0104898718485841
GO:0031124	mRNA 3'-end processing	0.0106702538866237
GO:0046112	nucleobase biosynthetic process	0.0106702538866237
GO:0030330	DNA damage response, signal transduction by p53 class mediator	0.0120048467004822
GO:0009067	aspartate family amino acid biosynthetic process	0.0125607805918415
GO:0030530	heterogeneous nuclear ribonucleoprotein complex	0.0129073440839092
GO:0006555	methionine metabolic process	0.0129073440839092
GO:0031123	RNA 3'-end processing	0.0133568403480145
GO:0006547	histidine metabolic process	0.0133568403480145
GO:0009075	histidine family amino acid metabolic process	0.0133568403480145
GO:0000097	sulfur amino acid biosynthetic process	0.0133568403480145
GO:0003727	single-stranded RNA binding	0.0133568403480145
GO:0032991	macromolecular complex	0.0143517521129979
GO:0005654	nucleoplasm	0.0146921544393844
GO:0009112	nucleobase metabolic process	0.0147501284471468
GO:0009167	purine ribonucleoside monophosphate metabolic process	0.0147509141632119
GO:0009168	purine ribonucleoside monophosphate biosynthetic process	0.0147509141632119
GO:0030532	small nuclear ribonucleoprotein complex	0.0147509141632119
GO:0009127	purine nucleoside monophosphate biosynthetic process	0.0147509141632119
GO:0009126	purine nucleoside monophosphate metabolic process	0.0147509141632119
GO:0043229	intracellular organelle	0.0147509141632119
GO:0043226	organelle	0.0147509141632119
GO:0044249	cellular biosynthetic process	0.0153285431293036
GO:0005941	unlocalized protein complex	0.0153285431293036
GO:0044446	intracellular organelle part	0.0153285431293036
GO:0044422	organelle part	0.0153285431293036
GO:0009066	aspartate family amino acid metabolic process	0.0155011953877277
GO:0000096	sulfur amino acid metabolic process	0.0158730168833439
GO:0006405	RNA export from nucleus	0.0160580573782975
GO:0000245	spliceosome assembly	0.0160580573782975
GO:0009161	ribonucleoside monophosphate metabolic process	0.0172794177673077
GO:0009156	ribonucleoside monophosphate biosynthetic process	0.0172794177673077
GO:0016646	oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor	0.0176120875006243
GO:0016874	ligase activity	0.0177508126499261
GO:0048583	regulation of response to stimulus	0.0177508126499261
GO:0046148	pigment biosynthetic process	0.018313385097542
GO:0006997	nuclear organization and biogenesis	0.018313385097542
GO:0009124	nucleoside monophosphate biosynthetic process	0.018313385097542
GO:0009123	nucleoside monophosphate metabolic process	0.018313385097542
GO:0009396	folic acid and derivative biosynthetic process	0.018313385097542
GO:0031981	nuclear lumen	0.0187839884277303
GO:0042440	pigment metabolic process	0.0198410709876166
GO:0042770	DNA damage response, signal transduction	0.0201163796120492
GO:0051168	nuclear export	0.0201940384489898
GO:0006760	folic acid and derivative metabolic process	0.0201940384489898
GO:0044272	sulfur compound biosynthetic process	0.0204581691664226
GO:0065003	macromolecular complex assembly	0.0211608155288724
GO:0016814	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	0.0218602066024701
GO:0009058	biosynthetic process	0.0227569158174758
GO:0016645	oxidoreductase activity, acting on the CH-NH group of donors	0.0227745621898682
GO:0019748	secondary metabolic process	0.0230032491780804
GO:0022607	cellular component assembly	0.0232599132872617
GO:0016831	carboxy-lyase activity	0.0238725883458216
GO:0003697	single-stranded DNA binding	0.0257665731809479
GO:0046907	intracellular transport	0.0281202584035222
GO:0043623	cellular protein complex assembly	0.0283847522894954
GO:0065002	intracellular protein transport across a membrane	0.0283847522894954
GO:0044424	intracellular part	0.0288803720298249
GO:0010467	gene expression	0.0302607832292535
GO:0031974	membrane-enclosed lumen	0.0302607832292535
GO:0043233	organelle lumen	0.0302607832292535
GO:0005515	protein binding	0.0319526487732182
GO:0016830	carbon-carbon lyase activity	0.0319526487732182
GO:0033036	macromolecule localization	0.0319526487732182
GO:0008652	amino acid biosynthetic process	0.0323185505394083
GO:0006790	sulfur metabolic process	0.0325652914814427
GO:0005643	nuclear pore	0.0325652914814427
GO:0009063	amino acid catabolic process	0.0326856938226464
GO:0009310	amine catabolic process	0.0350222804975169
GO:0044270	nitrogen compound catabolic process	0.0353154754539087
GO:0051649	establishment of cellular localization	0.0353154754539087
GO:0046930	pore complex	0.0353154754539087
GO:0051170	nuclear import	0.0354101628056411
GO:0051641	cellular localization	0.0362188448013473
GO:0030529	ribonucleoprotein complex	0.0366795809431643
GO:0044453	nuclear membrane part	0.0391841976045881
GO:0016043	cellular component organization and biogenesis	0.040027704534505
GO:0009309	amine biosynthetic process	0.041374638916086
GO:0006752	group transfer coenzyme metabolic process	0.0475581868919423
GO:0022618	protein-RNA complex assembly	0.0475588805752745
GO:0044271	nitrogen compound biosynthetic process	0.0495576642363756
GO:0009152	purine ribonucleotide biosynthetic process	0.0495576642363756

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br><br>disease_data<br>

---

Cell Type

Ontology term	p-value	n
animal cell	3.05e-21	679
eukaryotic cell	3.05e-21	679
epithelial cell	1.07e-15	253
native cell	9.21e-15	722
embryonic cell	3.53e-08	250

Disease

Ontology term	p-value	n
disease of cellular proliferation	2.60e-54	239
cancer	2.82e-54	235
organ system cancer	8.23e-27	137
cell type cancer	3.65e-26	143
carcinoma	2.49e-22	106
hematologic cancer	4.15e-21	51
immune system cancer	4.15e-21	51
leukemia	4.55e-17	39
myeloid leukemia	3.40e-13	31

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

---

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
MA0003.1	0.818094
MA0004.1	1.06719
MA0006.1	0.265592
MA0007.1	0.397529
MA0009.1	0.870971
MA0014.1	0.367355
MA0017.1	0.301634
MA0019.1	0.558663
MA0024.1	3.019
MA0025.1	1.00397
MA0027.1	2.48103
MA0028.1	2.15039
MA0029.1	0.785955
MA0030.1	0.774581
MA0031.1	0.710608
MA0038.1	0.514558
MA0040.1	0.791764
MA0041.1	0.433167
MA0042.1	0.402577
MA0043.1	0.871285
MA0046.1	0.860127
MA0048.1	0.264106
MA0050.1	0.403421
MA0051.1	0.510444
MA0052.1	0.795605
MA0055.1	0.0199484
MA0056.1	0
MA0057.1	1.37904
MA0058.1	0.86817
MA0059.1	1.55919
MA0060.1	2.16206
MA0061.1	0.432181
MA0063.1	0
MA0066.1	0.514973
MA0067.1	1.18766
MA0068.1	0.109867
MA0069.1	0.856287
MA0070.1	0.845142
MA0071.1	0.47692
MA0072.1	0.840664
MA0073.1	3.19635e-05
MA0074.1	0.509711
MA0076.1	1.61616
MA0077.1	0.832987
MA0078.1	0.607575
MA0081.1	0.324031
MA0083.1	0.878452
MA0084.1	1.37471
MA0087.1	0.838229
MA0088.1	0.363555
MA0089.1	0
MA0090.1	0.931587
MA0091.1	0.417885
MA0092.1	0.381858
MA0093.1	1.35827
MA0095.1	0
MA0098.1	0
MA0100.1	0.528088
MA0101.1	0.746654
MA0103.1	0.257174
MA0105.1	0.229733
MA0106.1	0.554855
MA0107.1	0.205358
MA0108.2	0.707575
MA0109.1	0
MA0111.1	0.959847
MA0113.1	0.57094
MA0114.1	0.200901
MA0115.1	1.11137
MA0116.1	0.599942
MA0117.1	0.908433
MA0119.1	0.83188
MA0122.1	0.934245
MA0124.1	1.06995
MA0125.1	0.986127
MA0130.1	0
MA0131.1	1.51455
MA0132.1	0
MA0133.1	0
MA0135.1	0.90122
MA0136.1	0.521435
MA0139.1	1.90392
MA0140.1	0.474342
MA0141.1	0.322254
MA0142.1	0.679161
MA0143.1	0.571113
MA0144.1	0.552298
MA0145.1	0.177438
MA0146.1	0.51271
MA0147.1	1.7891
MA0148.1	0.439278
MA0149.1	0.464973
MA0062.2	1.95022
MA0035.2	0.473658
MA0039.2	0.679176
MA0138.2	0.608783
MA0002.2	0.152495
MA0137.2	0.28622
MA0104.2	1.50683
MA0047.2	0.542971
MA0112.2	0.674448
MA0065.2	0.0483532
MA0150.1	0.34802
MA0151.1	0
MA0152.1	0.480711
MA0153.1	0.969315
MA0154.1	0.488402
MA0155.1	0.156896
MA0156.1	0.288314
MA0157.1	0.652111
MA0158.1	0
MA0159.1	0.60858
MA0160.1	0.453945
MA0161.1	0
MA0162.1	0.294626
MA0163.1	0.101664
MA0164.1	0.583138
MA0080.2	0.268439
MA0018.2	1.36887
MA0099.2	0.481058
MA0079.2	0.48507
MA0102.2	1.41188
MA0258.1	0.532421
MA0259.1	1.82941
MA0442.1	0

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCLAF1#9774	4	9.62339893783193	0.000474887791394397	0.00433273399540835
BRCA1#672	4	8.97076917476612	0.000620269035673191	0.00514088388355467
CCNT2#905	5	3.52011198720146	0.00704556022641387	0.0293944499055822
CHD2#1106	6	6.89601522274457	5.28898897155739e-05	0.000897735607346794
E2F1#1869	8	4.3621237465594	2.18983367577486e-05	0.000480975897506311
E2F4#1874	6	8.44537354352296	1.64629101974599e-05	0.000380055233888707
E2F6#1876	7	3.90223223576463	0.000306742359949273	0.00316247436631216
ELF1#1997	7	3.31185396796142	0.000896020581017362	0.0066694813955436
EP300#2033	5	3.76330095901289	0.00524217846159075	0.024286380532763
ETS1#2113	6	6.48584061480156	7.51193928811803e-05	0.00116331469055718
GABPB1#2553	5	3.92649102010121	0.00433797609228731	0.0205858726418754
HEY1#23462	8	3.59120981609396	9.88548321897326e-05	0.00139216556351989
HMGN3#9324	5	4.54363762408366	0.00224461831902441	0.0128911571416327
IRF1#3659	6	5.09144250237593	0.000296360970332	0.00309392676734344
IRF3#3661	3	15.6606507371632	0.000735147872062502	0.00579326255265492
MAX#4149	6	4.30170367267141	0.000759756385172366	0.00596827356983954
MXI1#4601	7	7.74788904459056	3.07469224127045e-06	0.000103686723598981
MYC#4609	7	4.06177478902954	0.000235555679657337	0.00256797490894913
NFKB1#4790	6	3.65870894946256	0.00185064964860272	0.0109339819341755
NFYA#4800	3	6.14186023327684	0.0104816316305809	0.038817457744982
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479503904969054
NRF1#4899	6	8.14018629847394	2.03653511272495e-05	0.000451674858012065
PAX5#5079	5	3.70531418398768	0.00561655707771942	0.0253901053819823
POLR2A#5430	8	1.90884726805162	0.011661228959883	0.0425804870757715
REST#5978	4	4.28890165161245	0.00945702594596283	0.0356641269867268
RFX5#5993	4	5.35462703430893	0.00424944502767474	0.0202208761274523
SIN3A#25942	7	4.20691034307844	0.000186784365617447	0.00226017522427535
SP1#6667	8	5.0652278916808	6.82787133058497e-06	0.000198412925402049
SP2#6668	3	8.7178434979482	0.00394553175057863	0.0189438851829111
TAF1#6872	8	2.97159669844026	0.000423374995123481	0.00395924616007354
TAF7#6879	6	7.62204626994928	2.97588074999805e-05	0.000616418107197633
TBP#6908	8	3.29490727741901	0.000191885322027247	0.00231546056004664
TRIM28#10155	3	6.19684168175417	0.010227806502978	0.0380827082378878
USF1#7391	6	4.24099951813864	0.000822001744194416	0.00626041275883618
YY1#7528	7	3.81979947210855	0.000352967281214194	0.00353641115528868
ZBTB33#10009	4	14.0732111244361	0.00011021168021743	0.00153186021695877

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

---

This analysis result is provided for C0 - C305 clusters.