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Coexpression cluster:C1272

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Full id: C1272_medulloblastoma_neuroblastoma_colon_Osteoblast_normal_Ciliary_pons



Phase1 CAGE Peaks

Hg19::chr4:151502879..151502889,-p8@LRBA
Hg19::chr4:151502911..151502924,-p5@LRBA
Hg19::chr4:151502958..151502978,-p6@LRBA
Hg19::chr4:151503105..151503132,+p2@MAB21L2
Hg19::chr4:151503215..151503245,+p4@MAB21L2
Hg19::chr4:151503507..151503518,+p6@MAB21L2
Hg19::chr4:151513323..151513325,+p@chr4:151513323..151513325
+


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
pigment epithelium of eye4.96e-1411
eye8.41e-1220
face3.56e-1121
visual system5.23e-1121
anterior region of body5.96e-11129
craniocervical region5.96e-11129
sense organ6.48e-1123
camera-type eye7.56e-1119
simple eye7.56e-1119
ocular region7.56e-1119
optic cup7.56e-1119
eye primordium7.56e-1119
optic vesicle7.56e-1119
sensory system3.01e-1024
entire sense organ system3.01e-1024
subdivision of head3.89e-1048
ectoderm-derived structure4.19e-10169
ectoderm6.06e-10173
presumptive ectoderm6.06e-10173
head7.71e-10123
neural plate8.12e-0986
presumptive neural plate8.12e-0986
regional part of nervous system1.13e-0894
nervous system1.13e-0894
neurectoderm1.61e-0890
anterior segment of eyeball1.27e-0714
large intestine2.45e-0711
colon3.66e-079
multi-tissue structure7.86e-07347


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
EP300#203354.838529804445140.001132708190785470.00775781433126394
YY1#752853.507979107038470.005072570672808980.0236168958852308



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.