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Revision as of 05:48, 21 May 2012

Full id: C4449_brain_temporal_occipital_cerebellum_duodenum_Neurons_parietal

Phase1 CAGE Peaks

  Short description
Hg19::chr5:111092930..111092941,- p7@C5orf13
Hg19::chr5:111093123..111093136,- p6@C5orf13
Hg19::chr5:111093169..111093178,- p8@C5orf13

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

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

No GOStat results

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 Type
Ontology termp-valuen
non-terminally differentiated cell2.14e-08180
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.83e-2594
nervous system1.83e-2594
central nervous system7.21e-2582
future brain1.55e-2069
neural tube1.21e-1757
neural rod1.21e-1757
future spinal cord1.21e-1757
neural keel1.21e-1757
regional part of brain1.79e-1759
presumptive ectoderm1.06e-16173
ectoderm-derived structure2.02e-16169
neural plate7.46e-1686
presumptive neural plate7.46e-1686
cerebral hemisphere9.29e-1432
regional part of forebrain9.65e-1441
future forebrain9.65e-1441
cerebral cortex1.10e-1325
regional part of cerebral cortex4.81e-1322
regional part of telencephalon6.70e-1333
gray matter6.75e-1334
brain grey matter6.75e-1334
anterior neural tube9.10e-1342
anterior region of body1.01e-12129
craniocervical region1.01e-12129
pre-chordal neural plate1.16e-1161
organism subdivision1.47e-10365
multi-cellular organism1.61e-10659
cell layer3.38e-10312
anatomical conduit1.11e-07241
anatomical cluster1.51e-07286

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

Jaspar motifs

Novel motifs

JASPAR motifs



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


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.

link to data source

This analysis result is provided for C0 - C305 clusters.