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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


uberon_data


Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.38e-3594
nervous system4.38e-3594
central nervous system1.70e-3282
neural tube1.68e-3157
neural rod1.68e-3157
future spinal cord1.68e-3157
neural keel1.68e-3157
neural plate2.42e-2786
presumptive neural plate2.42e-2786
brain2.10e-2669
future brain2.10e-2669
regional part of brain3.29e-2659
neurectoderm6.07e-2690
regional part of forebrain1.38e-2541
forebrain1.38e-2541
future forebrain1.38e-2541
anterior neural tube1.27e-2442
adult organism6.49e-24115
telencephalon4.97e-2234
gray matter5.26e-2234
brain grey matter5.26e-2234
regional part of telencephalon3.32e-2133
pre-chordal neural plate1.22e-2061
cerebral hemisphere3.30e-2032
ectoderm-derived structure6.77e-17169
ectoderm2.14e-16173
presumptive ectoderm2.14e-16173
head1.56e-15123
anterior region of body7.08e-15129
craniocervical region7.08e-15129
cerebral cortex4.98e-1425
pallium4.98e-1425
neocortex4.28e-1320
regional part of cerebral cortex5.64e-1322
organism subdivision1.73e-12365
tube6.39e-10194
nucleus of brain6.46e-109
neural nucleus6.46e-109
basal ganglion9.29e-109
nuclear complex of neuraxis9.29e-109
aggregate regional part of brain9.29e-109
collection of basal ganglia9.29e-109
cerebral subcortex9.29e-109
multi-cellular organism1.63e-09659
epithelium1.74e-09309
cell layer4.16e-09312
organ5.43e-09511
anatomical system3.30e-08625
embryo3.77e-08612
telencephalic nucleus4.01e-087
anatomical group4.13e-08626
posterior neural tube5.09e-0815
chordal neural plate5.09e-0815
anatomical conduit8.49e-08241
embryonic structure5.46e-07605
developing anatomical structure5.46e-07605
brainstem7.82e-078
multi-tissue structure7.97e-07347


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.