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Coexpression cluster:C2749

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Full id: C2749_lung_smooth_uterus_cervix_vagina_ovary_kidney



Phase1 CAGE Peaks

Hg19::chr3:64670534..64670545,+p5@ADAMTS9-AS2
Hg19::chr3:64670551..64670629,+p2@ADAMTS9-AS2
Hg19::chr3:64670630..64670642,+p3@ADAMTS9-AS2
Hg19::chr3:64670757..64670798,+p1@ADAMTS9-AS2


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


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.33e-53114
neural tube1.54e-2856
neural rod1.54e-2856
future spinal cord1.54e-2856
neural keel1.54e-2856
regional part of nervous system2.02e-2653
regional part of brain2.02e-2653
neural plate1.67e-2582
presumptive neural plate1.67e-2582
neurectoderm1.14e-2386
regional part of forebrain8.36e-2341
forebrain8.36e-2341
anterior neural tube8.36e-2341
future forebrain8.36e-2341
structure with developmental contribution from neural crest1.29e-20132
brain1.27e-1968
future brain1.27e-1968
brain grey matter3.95e-1934
gray matter3.95e-1934
telencephalon8.44e-1934
pre-chordal neural plate1.11e-1861
central nervous system4.53e-1881
regional part of telencephalon9.46e-1832
cerebral hemisphere1.28e-1732
ecto-epithelium2.07e-17104
nervous system1.72e-1689
anatomical cluster8.55e-15373
regional part of cerebral cortex1.35e-1422
multi-tissue structure2.96e-14342
cerebral cortex1.23e-1325
pallium1.23e-1325
neocortex2.33e-1320
organ system subdivision4.08e-13223
ectoderm-derived structure6.56e-13171
ectoderm6.56e-13171
presumptive ectoderm6.56e-13171
multi-cellular organism4.35e-12656
anatomical conduit5.40e-12240
organ3.37e-11503
anatomical system1.08e-10624
anatomical group1.48e-10625
tube2.57e-09192
epithelium6.92e-09306
cell layer1.88e-08309
organ part3.78e-08218
neural nucleus5.02e-079
nucleus of brain5.02e-079
posterior neural tube5.30e-0715
chordal neural plate5.30e-0715
basal ganglion9.32e-079
nuclear complex of neuraxis9.32e-079
aggregate regional part of brain9.32e-079
collection of basal ganglia9.32e-079
cerebral subcortex9.32e-079


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#235348.99795530889440.0001525147711168630.00195130346449517
GATA2#2624412.7449317335543.78864877853583e-050.00072336871989306
MAX#414946.452555509007120.0005767613195645490.0048601238868809
REST#597849.650028716128020.0001152825614219170.00157344425409613
USF1#739146.361499277207960.0006105011399140830.00508656789401571



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.