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Coexpression cluster:C4094

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Full id: C4094_Urothelial_Prostate_serous_Mallassezderived_Keratinocyte_Esophageal_Corneal



Phase1 CAGE Peaks

Hg19::chr22:31644309..31644350,+p3@LIMK2
Hg19::chr22:31644352..31644379,+p2@LIMK2
Hg19::chr22:31644394..31644405,+p4@LIMK2


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
organism subdivision1.38e-24365
ectoderm-derived structure2.00e-19169
ectoderm3.18e-18173
presumptive ectoderm3.18e-18173
multi-tissue structure3.84e-16347
head1.08e-15123
anterior region of body2.60e-15129
craniocervical region2.60e-15129
organ part3.32e-15219
multi-cellular organism4.03e-15659
cell layer4.58e-15312
epithelium4.94e-15309
neural plate3.26e-1286
presumptive neural plate3.26e-1286
embryo6.32e-12612
anatomical system7.06e-12625
embryonic structure1.01e-11605
developing anatomical structure1.01e-11605
anatomical group1.37e-11626
germ layer1.55e-11604
embryonic tissue1.55e-11604
presumptive structure1.55e-11604
epiblast (generic)1.55e-11604
neurectoderm6.62e-1190
neural tube1.83e-1057
neural rod1.83e-1057
future spinal cord1.83e-1057
neural keel1.83e-1057
regional part of brain2.62e-1059
organ5.69e-10511
pre-chordal neural plate8.83e-1061
anatomical cluster2.51e-09286
central nervous system6.53e-0982
brain1.15e-0869
future brain1.15e-0869
regional part of nervous system2.86e-0894
nervous system2.86e-0894
extraembryonic membrane5.27e-0814
membranous layer5.27e-0814
ectodermal placode1.51e-0729
multilaminar epithelium2.17e-0782
anatomical conduit3.17e-07241
organ segment3.76e-0797
organ component layer5.81e-0757
anterior neural tube5.99e-0742
regional part of forebrain6.41e-0741
forebrain6.41e-0741
future forebrain6.41e-0741
extraembryonic structure8.71e-0724


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
CEBPB#105137.971147625824820.001974187055288560.0115424129131323
SPI1#668838.204323508522730.001810593189410520.010920966913592
TRIM28#10155318.59052504526250.0001555969297255280.00197381121627649



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.