Coexpression cluster:C896

Full id: C896_retinoblastoma_iPS_acute_lymphoma_chronic_Burkitt_testicular

Phase1 CAGE Peaks

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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
Id	Short description

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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

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p.value	FDR	nGenes	nPathway	Name

p.value	FDR	nGenes	nPathway	Name
7.12e-8	4.51e-5	4	194	{POLR2A,195} (Static Module)
1.58e-6	4.99e-4	4	421	Gene Expression (Reactome)
3.49e-6	7.37e-4	3	134	mRNA processing (Wikipathways)
4.71e-6	7.45e-4	3	148	mRNA Processing (Reactome)

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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

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GO ID	GO name	FDR corrected p-value

GO ID	GO name	FDR corrected p-value
GO:0000096	sulfur amino acid metabolic process	1.59e-2
GO:0000097	sulfur amino acid biosynthetic process	1.34e-2
GO:0000105	histidine biosynthetic process	6.81e-3
GO:0000245	spliceosome assembly	1.61e-2
GO:0000375	RNA splicing, via transesterification reactions	2.71e-3
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	2.71e-3
GO:0000398	nuclear mRNA splicing, via spliceosome	2.71e-3
GO:0003697	single-stranded DNA binding	2.58e-2
GO:0003723	RNA binding	6.01e-3
GO:0003727	single-stranded RNA binding	1.34e-2

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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>

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Cell Type

Ontology term	p-value	n

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

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Disease

Ontology term	p-value	n

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

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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

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Novel motifs

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif46_CGNAGT	2.42
motif134_ATAAGAGAGGC	2.29
motif140_WTAAATAACG	2.00
motif23_CGCNAT	1.93
motif73_GAGCKMGC	1.91
motif106_KCGCANTC	1.85
motif128_NNGNATRCGWN	1.85
motif148_NTCSYSTYT	1.84
motif137_MAACAGAAGY	1.77
motif17_CGCTAN	1.73

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JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

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

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(#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

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This analysis result is provided for C0 - C305 clusters.