Personal tools

Coexpression cluster:C3215

From FANTOM5_SSTAR

Revision as of 15:59, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3215_parotid_mesothelioma_occipital_astrocytoma_amygdala_pituitary_frontal



Phase1 CAGE Peaks

Hg19::chr11:98891671..98891695,+p2@CNTN5
Hg19::chr11:98891735..98891753,+p1@CNTN5
Hg19::chr11:98891797..98891806,+p7@CNTN5


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>


Cell Type
Ontology termp-valuen
mesothelial cell4.40e-0719
Uber Anatomy
Ontology termp-valuen
neural tube5.12e-4956
neural rod5.12e-4956
future spinal cord5.12e-4956
neural keel5.12e-4956
regional part of nervous system2.31e-4753
regional part of brain2.31e-4753
central nervous system1.77e-4581
nervous system4.50e-4589
brain1.23e-4368
future brain1.23e-4368
regional part of forebrain3.46e-4241
forebrain3.46e-4241
anterior neural tube3.46e-4241
future forebrain3.46e-4241
cerebral hemisphere1.44e-3732
telencephalon3.35e-3734
brain grey matter7.39e-3734
gray matter7.39e-3734
neural plate9.02e-3682
presumptive neural plate9.02e-3682
regional part of cerebral cortex1.56e-3522
regional part of telencephalon1.59e-3432
neurectoderm2.05e-3386
neocortex1.79e-3220
pre-chordal neural plate6.02e-3261
cerebral cortex1.51e-3025
pallium1.51e-3025
adult organism1.03e-26114
ecto-epithelium2.10e-26104
structure with developmental contribution from neural crest2.15e-25132
ectoderm-derived structure1.61e-24171
ectoderm1.61e-24171
presumptive ectoderm1.61e-24171
organ system subdivision1.21e-21223
anatomical cluster8.87e-12373
gyrus2.52e-116
multi-tissue structure1.56e-10342
occipital lobe6.41e-105
limbic system8.69e-105
tube1.07e-09192
parietal lobe1.13e-095
temporal lobe1.52e-096
basal ganglion6.95e-099
nuclear complex of neuraxis6.95e-099
aggregate regional part of brain6.95e-099
collection of basal ganglia6.95e-099
cerebral subcortex6.95e-099
posterior neural tube1.34e-0815
chordal neural plate1.34e-0815
anatomical conduit3.56e-08240
neural nucleus5.92e-089
nucleus of brain5.92e-089
organ part1.24e-07218
epithelium2.25e-07306
corpus striatum2.28e-074
striatum2.28e-074
ventral part of telencephalon2.28e-074
future corpus striatum2.28e-074
cell layer3.72e-07309
segmental subdivision of hindbrain5.02e-0712
hindbrain5.02e-0712
presumptive hindbrain5.02e-0712


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
CTCF#1066435.360256373075030.0064925092527670.0278514406411621



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.