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Coexpression cluster:C2678

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Full id: C2678_lung_Endothelial_Lymphatic_mature_migratory_adipose_Mast



Phase1 CAGE Peaks

Hg19::chr2:188312865..188312876,-p3@CALCRL
Hg19::chr2:188312971..188312987,-p1@CALCRL
Hg19::chr2:188312993..188313033,-p2@CALCRL
Hg19::chr4:101439242..101439256,-p5@EMCN


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:0001635calcitonin gene-related polypeptide receptor activity0.00276698457553279
GO:0004948calcitonin receptor activity0.00553372479694806
GO:0048661positive regulation of smooth muscle cell proliferation0.00737786532194403
GO:0048660regulation of smooth muscle cell proliferation0.00774607439651214
GO:0048659smooth muscle cell proliferation0.00774607439651214
GO:0033002muscle cell proliferation0.00922070262497986
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0138269813688443
GO:0001633secretin-like receptor activity0.0138269813688443
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.023612775104622
GO:0019933cAMP-mediated signaling0.023612775104622
GO:0007507heart development0.023612775104622
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0259208404334235
GO:0019935cyclic-nucleotide-mediated signaling0.0259208404334235
GO:0005886plasma membrane0.0423490121090567
GO:0008284positive regulation of cell proliferation0.0428337292268629
GO:0019932second-messenger-mediated signaling0.0461648561898207



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 organism2.48e-29115
multi-cellular organism1.64e-16659
anatomical conduit6.92e-16241
tube3.82e-15194
anatomical system1.96e-14625
anatomical group4.27e-14626
circulatory system5.78e-14113
embryo2.07e-13612
lateral plate mesoderm3.06e-13216
cardiovascular system4.13e-13110
embryonic structure4.35e-13605
developing anatomical structure4.35e-13605
neural tube4.75e-1357
neural rod4.75e-1357
future spinal cord4.75e-1357
neural keel4.75e-1357
splanchnic layer of lateral plate mesoderm8.09e-1384
vasculature1.03e-1279
vascular system1.03e-1279
germ layer1.06e-12604
embryonic tissue1.06e-12604
presumptive structure1.06e-12604
epiblast (generic)1.06e-12604
anatomical cluster1.14e-12286
regional part of brain1.66e-1259
vessel2.36e-1269
endothelium3.41e-1218
blood vessel endothelium3.41e-1218
cardiovascular system endothelium3.41e-1218
central nervous system3.09e-1182
blood vessel1.32e-1060
epithelial tube open at both ends1.32e-1060
blood vasculature1.32e-1060
vascular cord1.32e-1060
neurectoderm2.96e-1090
brain3.14e-1069
future brain3.14e-1069
neural plate8.89e-1086
presumptive neural plate8.89e-1086
simple squamous epithelium1.95e-0922
regional part of nervous system7.57e-0994
nervous system7.57e-0994
anterior neural tube1.32e-0842
tissue1.36e-08787
squamous epithelium3.22e-0825
regional part of forebrain3.64e-0841
forebrain3.64e-0841
future forebrain3.64e-0841
cell layer3.89e-08312
epithelium8.25e-08309
gray matter4.81e-0734
brain grey matter4.81e-0734
primary circulatory organ5.84e-0727
immune system5.92e-07115
epithelial tube6.01e-07118


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235336.74846648167080.005032452776317940.0234730175296266
GATA2#2624412.7449317335543.78864877853583e-050.000722576131814288
JUN#372539.384621894252250.001918994502030470.0112873319890494
RAD21#588537.766275421592250.0033411193858720.0172701394477152
SETDB1#9869330.24001963350795.98509618524166e-050.000985149661923489
SMC3#9126311.28369963369960.001115802366868050.00765759517632624
TRIM28#10155313.94289378394690.0005972858184258420.00499479010253635
WRNIP1#56897382.36497326203212.99417904077464e-060.00010146303206991



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.