Coexpression cluster:C3937

Full id: C3937_Mesenchymal_Renal_Alveolar_Pericytes_Placental_Fibroblast_Osteoblast

Phase1 CAGE Peaks

Hg19::chr1:2126156..2126167,-	p3@C1orf86
Hg19::chr1:2126174..2126190,-	p2@C1orf86
Hg19::chr1:2126192..2126218,-	p1@C1orf86

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
embryonic cell	6.26e-24	250
non-terminally differentiated cell	1.24e-19	106
contractile cell	4.92e-14	59
mesodermal cell	1.65e-13	121
electrically responsive cell	1.83e-12	61
electrically active cell	1.83e-12	61
smooth muscle cell	2.44e-12	43
smooth muscle myoblast	2.44e-12	43
muscle precursor cell	3.67e-12	58
myoblast	3.67e-12	58
multi-potent skeletal muscle stem cell	3.67e-12	58
muscle cell	6.14e-12	55
somatic cell	1.39e-11	588
vascular associated smooth muscle cell	3.22e-10	32
animal cell	8.00e-10	679
eukaryotic cell	8.00e-10	679
ectodermal cell	3.61e-08	72
neurectodermal cell	4.04e-07	59
epithelial cell	5.04e-07	253

Uber Anatomy

Ontology term	p-value	n
mesenchyme	1.86e-17	160
entire embryonic mesenchyme	1.86e-17	160
organism subdivision	5.72e-16	264
trunk	7.65e-16	199
epithelial vesicle	5.32e-15	78
trunk mesenchyme	2.76e-14	122
multilaminar epithelium	8.39e-14	83
unilaminar epithelium	1.36e-13	148
somite	2.93e-12	71
presomitic mesoderm	2.93e-12	71
presumptive segmental plate	2.93e-12	71
dermomyotome	2.93e-12	71
trunk paraxial mesoderm	2.93e-12	71
dense mesenchyme tissue	3.79e-12	73
cell layer	4.99e-12	309
vasculature	9.68e-12	78
vascular system	9.68e-12	78
epithelium	9.73e-12	306
paraxial mesoderm	9.95e-12	72
presumptive paraxial mesoderm	9.95e-12	72
epithelial tube	1.15e-11	117
skeletal muscle tissue	5.83e-11	62
striated muscle tissue	5.83e-11	62
myotome	5.83e-11	62
muscle tissue	3.68e-10	64
musculature	3.68e-10	64
musculature of body	3.68e-10	64
epithelial tube open at both ends	2.62e-09	59
blood vessel	2.62e-09	59
blood vasculature	2.62e-09	59
vascular cord	2.62e-09	59
splanchnic layer of lateral plate mesoderm	4.08e-09	83
artery	7.71e-09	42
arterial blood vessel	7.71e-09	42
arterial system	7.71e-09	42
multi-tissue structure	8.29e-09	342
vessel	1.20e-08	68
subdivision of trunk	2.21e-07	112
urinary system structure	2.70e-07	47
anatomical cluster	3.45e-07	373
renal system	3.89e-07	48

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190154061320695
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279628509979683
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325580062886531
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322460017397447
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320855538659316
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462610434236759
ELK4#2005	3	16.235681658468	0.000233604395574599	0.002557916698408
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00762790431354461
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.015421170704018
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108775515227471
REST#5978	3	9.65002871612802	0.00111263624711459	0.0076807863713663
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.027698567532085
SP1#6667	3	5.6983813781409	0.00540396270171217	0.024672544725863
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109115142590216
THAP1#55145	3	31.3691446028513	3.23800758564397e-05	0.000647099644540893
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329638120935918
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140314616793219

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.