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Coexpression cluster:C1887

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Full id: C1887_lung_Endothelial_adipose_heart_spleen_Hepatocyte_penis



Phase1 CAGE Peaks

Hg19::chr2:197226832..197226859,-p4@HECW2
Hg19::chr7:22259789..22259809,-p7@RAPGEF5
Hg19::chr7:22259826..22259838,-p11@RAPGEF5
Hg19::chr7:22259845..22259864,-p5@RAPGEF5
Hg19::chr7:22259867..22259876,-p13@RAPGEF5


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


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


GO IDGO nameFDR corrected p-value
GO:0017034Rap guanyl-nucleotide exchange factor activity0.00565162999117592
GO:0030742GTP-dependent protein binding0.015539923662318



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>


Uber Anatomy
Ontology termp-valuen
adult organism1.99e-53115
anatomical conduit6.44e-40241
tube1.69e-37194
anatomical cluster3.62e-36286
splanchnic layer of lateral plate mesoderm9.36e-2584
vessel2.30e-2469
epithelium7.79e-23309
cell layer3.63e-22312
neural tube3.32e-2157
neural rod3.32e-2157
future spinal cord3.32e-2157
neural keel3.32e-2157
vasculature6.29e-2179
vascular system6.29e-2179
blood vessel1.94e-2060
epithelial tube open at both ends1.94e-2060
blood vasculature1.94e-2060
vascular cord1.94e-2060
epithelial tube4.23e-20118
circulatory system6.88e-20113
cardiovascular system3.03e-18110
regional part of brain4.12e-1759
anterior neural tube1.99e-1642
endothelium2.47e-1618
blood vessel endothelium2.47e-1618
cardiovascular system endothelium2.47e-1618
neural plate8.44e-1686
presumptive neural plate8.44e-1686
regional part of forebrain1.01e-1541
forebrain1.01e-1541
future forebrain1.01e-1541
multi-cellular organism3.10e-15659
anatomical system1.39e-14625
central nervous system1.52e-1482
anatomical group1.88e-14626
neurectoderm2.74e-1490
brain1.25e-1369
future brain1.25e-1369
simple squamous epithelium3.13e-1322
regional part of nervous system1.00e-1294
nervous system1.00e-1294
gray matter1.09e-1234
brain grey matter1.09e-1234
telencephalon1.81e-1234
regional part of telencephalon4.93e-1233
squamous epithelium1.07e-1125
cerebral hemisphere2.04e-1132
multi-tissue structure2.45e-11347
neocortex7.64e-1120
artery8.62e-1142
arterial blood vessel8.62e-1142
arterial system8.62e-1142
regional part of cerebral cortex1.51e-1022
embryo4.32e-10612
organism subdivision1.01e-09365
pre-chordal neural plate1.31e-0961
embryonic structure1.38e-09605
developing anatomical structure1.38e-09605
germ layer3.35e-09604
embryonic tissue3.35e-09604
presumptive structure3.35e-09604
epiblast (generic)3.35e-09604
primary circulatory organ6.65e-0927
endothelial tube9.02e-099
arterial system endothelium9.02e-099
endothelium of artery9.02e-099
cerebral cortex1.44e-0825
pallium1.44e-0825
unilaminar epithelium1.55e-08138
compound organ5.41e-0869
anterior region of body8.59e-08129
craniocervical region8.59e-08129
lymphoid system1.80e-0710
systemic artery2.06e-0733
systemic arterial system2.06e-0733
heart3.81e-0724
primitive heart tube3.81e-0724
primary heart field3.81e-0724
anterior lateral plate mesoderm3.81e-0724
heart tube3.81e-0724
heart primordium3.81e-0724
cardiac mesoderm3.81e-0724
cardiogenic plate3.81e-0724
heart rudiment3.81e-0724
ectoderm-derived structure4.78e-07169
head6.78e-07123


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


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


No analysis results for this cluster

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


This analysis result is provided for C0 - C305 clusters.