Coexpression cluster:C3424

Full id: C3424_skeletal_tongue_diaphragm_mesenchymal_Fibroblast_basal_smooth

Phase1 CAGE Peaks

Hg19::chr14:35183771..35183784,-	p4@CFL2
Hg19::chr14:35183785..35183826,-	p1@CFL2
Hg19::chr14:35183837..35183867,-	p2@CFL2

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
non-terminally differentiated cell	6.94e-22	180
fibroblast	1.65e-13	75
muscle precursor cell	6.66e-10	57
myoblast	6.66e-10	57
multi-potent skeletal muscle stem cell	6.66e-10	57
muscle cell	9.07e-09	54
contractile cell	5.00e-08	59
skin fibroblast	5.04e-08	23
electrically responsive cell	1.87e-07	60
electrically active cell	1.87e-07	60
mesodermal cell	5.10e-07	119

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.51e-26	365
multi-tissue structure	6.28e-22	347
cell layer	1.89e-19	312
epithelium	9.55e-19	309
somite	3.15e-17	83
paraxial mesoderm	3.15e-17	83
presomitic mesoderm	3.15e-17	83
presumptive segmental plate	3.15e-17	83
trunk paraxial mesoderm	3.15e-17	83
presumptive paraxial mesoderm	3.15e-17	83
anatomical cluster	5.77e-16	286
trunk mesenchyme	1.76e-15	143
dermomyotome	2.52e-14	70
multi-cellular organism	1.03e-13	659
anatomical conduit	1.94e-13	241
trunk	1.31e-12	216
muscle tissue	2.75e-12	63
musculature	2.75e-12	63
musculature of body	2.75e-12	63
adult organism	5.48e-12	115
skeletal muscle tissue	5.75e-12	61
striated muscle tissue	5.75e-12	61
myotome	5.75e-12	61
tube	1.61e-11	194
anatomical system	1.71e-11	625
anatomical group	2.59e-11	626
regional part of nervous system	2.62e-11	94
nervous system	2.62e-11	94
multilaminar epithelium	4.35e-11	82
ectoderm-derived structure	3.71e-10	169
neural tube	5.39e-10	57
neural rod	5.39e-10	57
future spinal cord	5.39e-10	57
neural keel	5.39e-10	57
mesenchyme	6.45e-10	238
entire embryonic mesenchyme	6.45e-10	238
ectoderm	6.70e-10	173
presumptive ectoderm	6.70e-10	173
regional part of brain	8.64e-10	59
head	9.13e-10	123
brain	9.38e-10	69
future brain	9.38e-10	69
central nervous system	1.21e-09	82
neural plate	1.60e-09	86
presumptive neural plate	1.60e-09	86
unilaminar epithelium	3.48e-09	138
neurectoderm	4.47e-09	90
anterior region of body	6.52e-09	129
craniocervical region	6.52e-09	129
embryonic structure	6.68e-08	605
developing anatomical structure	6.68e-08	605
germ layer	7.98e-08	604
embryonic tissue	7.98e-08	604
presumptive structure	7.98e-08	604
epiblast (generic)	7.98e-08	604
organ part	9.67e-08	219
embryo	1.68e-07	612
surface structure	2.78e-07	95
regional part of forebrain	8.70e-07	41
forebrain	8.70e-07	41
future forebrain	8.70e-07	41

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	0.0012945627072275
BHLHE40#8553	3	44.8718135469774	1.10603738662898e-05	0.000284165900669481
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189600777288587
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0324337254057748
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321232409530733
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00913676838216309
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319721687342854
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039055087134443
HNF4G#3174	3	28.7534225264468	4.20470658818262e-05	0.000755826766545963
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156425350839758
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0186129553216269
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293793533538643
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000736227625017155
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.0016503637066485
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275931793293246
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054168223584188
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247726703532623
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00614094693720351
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0189882185738748
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00420986073271625
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328593795916181
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242327309288737
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00388318191205693

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.