Coexpression cluster:C4400

Full id: C4400_Fibroblast_Preadipocyte_mesodermal_Small_Keratinocyte_Gingival_basal

Phase1 CAGE Peaks

Hg19::chr4:187647702..187647734,-	p4@FAT1
Hg19::chr4:187647737..187647763,-	p3@FAT1
Hg19::chr4:187647773..187647864,-	p1@FAT1

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><br>

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Cell Type

Ontology term	p-value	n
endo-epithelial cell	2.68e-12	43
non-terminally differentiated cell	3.30e-11	180
endodermal cell	2.01e-10	59
embryonic cell	4.49e-10	248
epithelial cell	1.11e-08	254
respiratory epithelial cell	8.61e-07	13
fibroblast	9.45e-07	75

Uber Anatomy

Ontology term	p-value	n
organism subdivision	7.09e-21	365
multi-tissue structure	1.04e-14	347
surface structure	3.76e-14	95
endoderm-derived structure	1.69e-12	169
endoderm	1.69e-12	169
presumptive endoderm	1.69e-12	169
trunk	9.62e-12	216
multi-cellular organism	1.98e-11	659
digestive system	1.79e-10	155
digestive tract	1.79e-10	155
primitive gut	1.79e-10	155
mesenchyme	1.85e-10	238
entire embryonic mesenchyme	1.85e-10	238
organ	2.40e-09	511
anatomical system	3.94e-09	625
anatomical group	6.95e-09	626
skin of body	5.12e-08	40
integument	9.42e-08	45
integumental system	9.42e-08	45
subdivision of head	6.55e-07	48
trunk mesenchyme	7.61e-07	143

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
ATF3#467	3	22.4631745260087	8.81932387510763e-05	0.001299677389858
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000527741893556006
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190737166280374
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662177645613266
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000130173318697991
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280670215592422
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326892885720751
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0321861970996936
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168067925237789
FOSL2#2355	3	16.9302006045617	0.000206016205317162	0.00243781174565138
JUN#3725	3	12.5128291923363	0.000510331399272625	0.004456023828161
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157312390152696
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00666806588238158
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165778345356343
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277790154488974
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247493624190544
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631045956837498
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616267972884634
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617857641327964
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330639496865854
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140682679760182

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.