Coexpression cluster:C4185

Full id: C4185_teratocarcinoma_iPS_H9_HES3GFP_NK_diffuse_rhabdomyosarcoma

Phase1 CAGE Peaks

Hg19::chr2:219433617..219433629,+	p5@RQCD1
Hg19::chr2:219433630..219433644,+	p4@RQCD1
Hg19::chr2:219433648..219433655,+	p6@RQCD1

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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No results for this coexpression

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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No GOStat results

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>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.47e-07	254

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.64e-13	94
nervous system	2.64e-13	94
central nervous system	1.31e-12	82
neural tube	1.74e-11	57
neural rod	1.74e-11	57
future spinal cord	1.74e-11	57
neural keel	1.74e-11	57
brain	5.44e-11	69
future brain	5.44e-11	69
regional part of brain	3.49e-10	59
neural plate	1.79e-09	86
presumptive neural plate	1.79e-09	86
regional part of forebrain	4.02e-09	41
forebrain	4.02e-09	41
future forebrain	4.02e-09	41
neurectoderm	7.00e-09	90
pre-chordal neural plate	1.96e-08	61
anterior neural tube	2.57e-08	42
gray matter	1.03e-07	34
brain grey matter	1.03e-07	34
telencephalon	2.59e-07	34
regional part of telencephalon	3.82e-07	33
tube	8.40e-07	194

Disease

Ontology term	p-value	n
disease of cellular proliferation	7.12e-22	239
cancer	8.33e-22	235
cell type cancer	7.80e-13	143
organ system cancer	3.86e-11	137
carcinoma	6.06e-11	106
hematologic cancer	2.53e-07	51
immune system cancer	2.53e-07	51

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

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
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527521955279884
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115469378285888
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00661620413372918
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326241175766202
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437876935166973
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0323115219058305
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321394791665466
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463498118732279
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167807693197313
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154453279345084
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123021199919439
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000758044797795969
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128386344926055
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186980113972223
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295201055197772
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270146400754794
NR2C2#7182	3	32.6146109052409	2.88098172333076e-05	0.000605527973843714
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472096290856073
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.017327450118898
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00883614392425589
REST#5978	3	9.65002871612802	0.00111263624711459	0.00769248093554883
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165459540846042
SETDB1#9869	3	40.3200261780105	1.52461559299059e-05	0.000359515303491407
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277474802396341
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239970281354778
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247092710741262
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00544298446687264
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330131868355406
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140539732494796

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.