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Coexpression cluster:C753

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Full id: C753_Retinal_retina_eye_kidney_caudate_corpus_putamen



Phase1 CAGE Peaks

  Short description
Hg19::chr13:51913806..51913817,+ p2@SERPINE3
Hg19::chr13:51913819..51913838,+ p1@SERPINE3
Hg19::chr13:51913893..51913901,+ p@chr13:51913893..51913901
+
Hg19::chr13:51913997..51914020,+ p@chr13:51913997..51914020
+
Hg19::chr14:28081776..28081788,+ p1@LOC100505967
Hg19::chr14:28081790..28081795,+ p2@LOC100505967
Hg19::chr1:75180314..75180323,- p@chr1:75180314..75180323
-
Hg19::chr2:219610770..219610777,+ p19@TTLL4
Hg19::chr2:219610813..219610832,+ p8@TTLL4
Hg19::chr8:75898210..75898219,+ p11@CRISPLD1
Hg19::chr8:75898244..75898255,+ p7@CRISPLD1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0004835tubulin-tyrosine ligase activity0.0328891110651264



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
retinal pigment epithelial cell1.62e-603
visual pigment cell1.25e-454
pigment cell1.35e-1314
Uber Anatomy
Ontology termp-valuen
pigmented layer of retina1.62e-603
presumptive retinal pigmented epithelium1.62e-603
retina1.81e-536
photoreceptor array1.81e-536
posterior segment of eyeball1.81e-536
layer of retina1.25e-454
eye5.84e-2421
visual system5.84e-2421
sense organ5.35e-2124
sensory system5.35e-2124
entire sense organ system5.35e-2124
pigment epithelium of eye4.11e-1711
camera-type eye2.03e-1620
simple eye2.03e-1620
immature eye2.03e-1620
ocular region2.03e-1620
eyeball of camera-type eye2.03e-1620
optic cup2.03e-1620
optic vesicle2.03e-1620
eye primordium2.03e-1620
face5.77e-1522
pre-chordal neural plate1.72e-1161
neural plate1.74e-1182
presumptive neural plate1.74e-1182
neurectoderm6.03e-1186
ectodermal placode9.89e-1131
ecto-epithelium5.07e-09104
frontal cortex7.76e-083
medulla oblongata8.29e-083
myelencephalon8.29e-083
future myelencephalon8.29e-083
structure with developmental contribution from neural crest4.73e-07132
ectoderm-derived structure6.56e-07171
ectoderm6.56e-07171
presumptive ectoderm6.56e-07171
subdivision of head6.72e-0749


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.