Coexpression cluster:C2443

Full id: C2443_Mesenchymal_Hepatic_Alveolar_Smooth_Astrocyte_Renal_Hair

Phase1 CAGE Peaks

Hg19::chr17:79479822..79479830,-	p1@ACTG1
Hg19::chr19:1026566..1026648,+	p1@CNN2
Hg19::chr19:2096259..2096342,-	p1@MOB3A
Hg19::chr7:143078379..143078454,+	p1@ZYX

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
0.000145853209864357	0.0307750272813793	2	200	Focal adhesion (KEGG):04510
8.75676438203826e-05	0.0307750272813793	2	155	Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289
0.000128870835041632	0.0307750272813793	2	188	Focal Adhesion (Wikipathways):WP306

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:0005911	intercellular junction	0.00105713136868672
GO:0030054	cell junction	0.00326156077542858
GO:0005913	cell-cell adherens junction	0.0104577467891468
GO:0031032	actomyosin structure organization and biogenesis	0.0126684703362576
GO:0005856	cytoskeleton	0.0142566507029949
GO:0005912	adherens junction	0.0217068263005428
GO:0044459	plasma membrane part	0.0264873599816309
GO:0043232	intracellular non-membrane-bound organelle	0.0336456441217229
GO:0043228	non-membrane-bound organelle	0.0336456441217229
GO:0005516	calmodulin binding	0.0339637806473224
GO:0005886	plasma membrane	0.0470180521288173
GO:0030036	actin cytoskeleton organization and biogenesis	0.048091021929576
GO:0030029	actin filament-based process	0.048091021929576

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
somatic cell	7.15e-44	588
animal cell	2.50e-28	679
eukaryotic cell	2.50e-28	679
mesodermal cell	2.09e-24	121
native cell	5.32e-24	722
contractile cell	4.80e-19	59
embryonic cell	3.20e-18	250
muscle precursor cell	5.50e-17	58
myoblast	5.50e-17	58
multi-potent skeletal muscle stem cell	5.50e-17	58
muscle cell	8.88e-17	55
smooth muscle cell	1.40e-15	43
smooth muscle myoblast	1.40e-15	43
somatic stem cell	1.43e-15	433
multi fate stem cell	1.87e-15	427
stem cell	7.20e-15	441
electrically responsive cell	1.80e-14	61
electrically active cell	1.80e-14	61
non-terminally differentiated cell	1.00e-12	106
vascular associated smooth muscle cell	2.64e-12	32
fibroblast	2.97e-12	76
meso-epithelial cell	5.36e-09	45
endothelial cell	7.01e-09	36
lining cell	8.67e-08	58
barrier cell	8.67e-08	58
blood vessel endothelial cell	2.25e-07	18
embryonic blood vessel endothelial progenitor cell	2.25e-07	18
endothelial cell of vascular tree	4.03e-07	24

Uber Anatomy

Ontology term	p-value	n
cardiovascular system	2.58e-22	109
mesoderm	1.20e-21	315
mesoderm-derived structure	1.20e-21	315
presumptive mesoderm	1.20e-21	315
vasculature	2.02e-21	78
vascular system	2.02e-21	78
circulatory system	1.43e-20	112
epithelial vesicle	4.83e-19	78
multilaminar epithelium	2.80e-17	83
vessel	1.95e-16	68
epithelial tube open at both ends	3.62e-16	59
blood vessel	3.62e-16	59
blood vasculature	3.62e-16	59
vascular cord	3.62e-16	59
somite	4.22e-16	71
presomitic mesoderm	4.22e-16	71
presumptive segmental plate	4.22e-16	71
dermomyotome	4.22e-16	71
trunk paraxial mesoderm	4.22e-16	71
lateral plate mesoderm	4.88e-16	203
splanchnic layer of lateral plate mesoderm	1.46e-15	83
dense mesenchyme tissue	1.91e-15	73
paraxial mesoderm	2.74e-15	72
presumptive paraxial mesoderm	2.74e-15	72
unilaminar epithelium	1.84e-14	148
skeletal muscle tissue	2.55e-14	62
striated muscle tissue	2.55e-14	62
myotome	2.55e-14	62
artery	5.41e-14	42
arterial blood vessel	5.41e-14	42
arterial system	5.41e-14	42
epithelial tube	1.40e-13	117
muscle tissue	1.48e-13	64
musculature	1.48e-13	64
musculature of body	1.48e-13	64
musculoskeletal system	2.82e-13	167
trunk mesenchyme	1.63e-11	122
mesenchyme	4.57e-11	160
entire embryonic mesenchyme	4.57e-11	160
organism subdivision	8.97e-10	264
systemic artery	1.32e-09	33
systemic arterial system	1.32e-09	33
trunk	2.66e-08	199
blood vessel endothelium	2.25e-07	18
endothelium	2.25e-07	18
cardiovascular system endothelium	2.25e-07	18
ectodermal placode	3.20e-07	31
surface structure	5.17e-07	99
simple squamous epithelium	9.02e-07	22

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	4	6.33620157696263	0.000620310058721564	0.00512090445204501
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00996776538292784
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.016087814057464
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418904907853015
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186003136596958
HMGN3#9324	3	6.13391079251294	0.00664069668332472	0.0282942118517359
JUND#3727	3	5.24599795640327	0.0104343275174842	0.038687543723322
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434917092686171
RXRA#6256	3	15.05596285435	0.000475830799730358	0.0043390633801658
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00796154761844302
SRF#6722	3	10.3478836966259	0.00143989377840126	0.00923773366438045
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322135864517627
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140323139116104
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244140178575391
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483025400891027
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00346399343823706

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.