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Coexpression cluster:C1288

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Full id: C1288_kidney_neuroectodermal_uterus_Mast_skin_rhabdomyosarcoma_ductus



Phase1 CAGE Peaks

Hg19::chr9:14909966..14909990,-p1@FREM1
Hg19::chr9:14909994..14910006,-p6@FREM1
Hg19::chr9:14910193..14910208,-p4@FREM1
Hg19::chr9:14910219..14910242,-p5@FREM1
Hg19::chr9:14910342..14910355,-p12@FREM1
Hg19::chr9:14910387..14910398,-p10@FREM1
Hg19::chr9:14910420..14910434,-p2@FREM1


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
adult organism8.70e-51115
neural tube2.40e-2157
neural rod2.40e-2157
future spinal cord2.40e-2157
neural keel2.40e-2157
central nervous system5.13e-2182
regional part of nervous system1.60e-1994
nervous system1.60e-1994
neurectoderm4.54e-1890
regional part of brain1.22e-1759
neural plate3.42e-1686
presumptive neural plate3.42e-1686
brain1.85e-1569
future brain1.85e-1569
regional part of forebrain3.35e-1441
forebrain3.35e-1441
future forebrain3.35e-1441
anterior neural tube1.22e-1342
telencephalon1.13e-1234
gray matter2.38e-1234
brain grey matter2.38e-1234
ectoderm2.84e-12173
presumptive ectoderm2.84e-12173
regional part of cerebral cortex3.02e-1222
regional part of telencephalon4.62e-1233
cerebral hemisphere1.93e-1132
ectoderm-derived structure6.28e-11169
neocortex7.08e-1120
cerebral cortex4.04e-1025
pallium4.04e-1025
anterior region of body4.09e-10129
craniocervical region4.09e-10129
posterior neural tube2.42e-0915
chordal neural plate2.42e-0915
head8.21e-09123
pre-chordal neural plate1.33e-0861
multi-tissue structure2.25e-07347
tube2.75e-07194
segmental subdivision of hindbrain5.20e-0712
hindbrain5.20e-0712
presumptive hindbrain5.20e-0712
anatomical conduit7.98e-07241


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
FOXA1#3169711.08141974938554.86782131208363e-083.14792811153376e-06
FOXA2#3170724.63046375266521.81353313360781e-101.89403586940866e-08
TRIM28#10155718.59052504526251.300439693691e-091.1759014819861e-07



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.