Coexpression cluster:C2371

Full id: C2371_Renal_Lymphatic_Alveolar_migratory_Endothelial_heart_tongue

Phase1 CAGE Peaks

Hg19::chr16:3115299..3115312,+	p5@IL32
Hg19::chr16:3115324..3115364,+	p3@IL32
Hg19::chr16:3115386..3115412,+	p2@IL32
Hg19::chr16:3115418..3115429,+	p4@IL32

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
mesodermal cell	2.08e-22	119
lining cell	4.12e-14	57
barrier cell	4.12e-14	57
meso-epithelial cell	1.47e-13	44
embryonic cell	9.63e-13	248
endothelial cell of vascular tree	5.78e-12	24
endothelial cell	9.87e-12	35
kidney cell	4.35e-09	18
kidney epithelial cell	4.35e-09	18
contractile cell	1.04e-08	59
blood vessel endothelial cell	3.18e-08	18
embryonic blood vessel endothelial progenitor cell	3.18e-08	18
epithelial cell of nephron	3.98e-08	16
vascular associated smooth muscle cell	8.12e-08	32
muscle precursor cell	1.80e-07	57
myoblast	1.80e-07	57
multi-potent skeletal muscle stem cell	1.80e-07	57
muscle cell	2.23e-07	54
smooth muscle cell	7.17e-07	42
smooth muscle myoblast	7.17e-07	42

Uber Anatomy

Ontology term	p-value	n
epithelial tube	4.27e-31	118
unilaminar epithelium	1.60e-23	138
vessel	9.46e-23	69
splanchnic layer of lateral plate mesoderm	2.17e-20	84
trunk mesenchyme	2.73e-18	143
blood vessel	4.21e-18	60
epithelial tube open at both ends	4.21e-18	60
blood vasculature	4.21e-18	60
vascular cord	4.21e-18	60
anatomical conduit	5.18e-18	241
vasculature	1.18e-17	79
vascular system	1.18e-17	79
circulatory system	5.56e-17	113
cardiovascular system	2.92e-16	110
trunk	4.07e-15	216
mesenchyme	5.84e-15	238
entire embryonic mesenchyme	5.84e-15	238
epithelium	1.91e-14	309
cell layer	6.09e-14	312
anatomical cluster	1.35e-13	286
abdominal segment of trunk	2.47e-13	61
abdomen	2.47e-13	61
abdomen element	3.61e-13	55
abdominal segment element	3.61e-13	55
tube	5.17e-13	194
compound organ	3.13e-12	69
artery	1.38e-11	42
arterial blood vessel	1.38e-11	42
arterial system	1.38e-11	42
immaterial anatomical entity	1.08e-10	126
gut epithelium	2.96e-10	54
multi-tissue structure	4.49e-10	347
systemic artery	5.19e-10	33
systemic arterial system	5.19e-10	33
subdivision of trunk	8.01e-10	113
body cavity precursor	9.74e-10	63
renal system	3.09e-09	45
multilaminar epithelium	3.25e-09	82
muscle tissue	4.48e-09	63
musculature	4.48e-09	63
musculature of body	4.48e-09	63
urinary system structure	5.38e-09	44
intermediate mesoderm	6.05e-09	37
skeletal muscle tissue	9.68e-09	61
striated muscle tissue	9.68e-09	61
myotome	9.68e-09	61
parenchyma	1.20e-08	17
urogenital ridge	2.64e-08	20
endothelium	3.18e-08	18
blood vessel endothelium	3.18e-08	18
cardiovascular system endothelium	3.18e-08	18
intraembryonic coelom	3.59e-08	21
nephron epithelium	3.98e-08	16
nephron	3.98e-08	16
uriniferous tubule	3.98e-08	16
metanephric mesenchyme	3.98e-08	16
nephrogenic mesenchyme	3.98e-08	16
excretory tube	4.13e-08	17
mesonephric epithelium	4.13e-08	17
mesonephric tubule	4.13e-08	17
nephric duct	4.13e-08	17
kidney epithelium	4.13e-08	17
renal duct	4.13e-08	17
mesonephric duct	4.13e-08	17
pronephric duct	4.13e-08	17
anatomical cavity	5.10e-08	70
trunk region element	5.19e-08	107
endo-epithelium	5.19e-08	82
immune organ	6.56e-08	26
mesonephros	1.17e-07	18
pronephros	1.17e-07	18
nephrogenic cord	1.17e-07	18
pronephric mesoderm	1.17e-07	18
rostral part of nephrogenic cord	1.17e-07	18
presumptive pronephric mesoderm	1.17e-07	18
epithelium of foregut-midgut junction	1.31e-07	25
anatomical boundary	1.31e-07	25
hepatobiliary system	1.31e-07	25
foregut-midgut junction	1.31e-07	25

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
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00433879610928826
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.00030330482020104
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.00062616740431326
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185835582093101
HNF4A#3172	4	23.1322903629537	3.48990320893214e-06	0.000115452011795269
HNF4G#3174	4	28.7534225264468	1.46167379934821e-06	5.66230526447062e-05
HSF1#3297	4	164.290666666667	1.36534966436082e-09	1.22715794833201e-07
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.000742582809472487
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00391338674304788
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.0076751980600755
PPARGC1A#10891	4	350.051136363636	6.58479147384085e-11	7.28505335525915e-09
RXRA#6256	4	20.0746171391333	6.1537798808435e-06	0.00018211805524948
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795531792547084
SP1#6667	4	5.6983813781409	0.000948260606533398	0.0068370997228679
TCF12#6938	4	10.6344649021864	7.8163066689251e-05	0.00119977550293338
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279670653790952

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.