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Coexpression cluster:C4322

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Full id: C4322_occipital_frontal_insula_medial_olfactory_aorta_serous



Phase1 CAGE Peaks

Hg19::chr3:24536253..24536328,-p1@THRB
Hg19::chr3:24536332..24536358,-p2@THRB
Hg19::chr3:24536516..24536545,-p6@THRB


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism8.88e-40114
neural tube6.21e-2356
neural rod6.21e-2356
future spinal cord6.21e-2356
neural keel6.21e-2356
regional part of forebrain9.08e-2241
forebrain9.08e-2241
anterior neural tube9.08e-2241
future forebrain9.08e-2241
regional part of nervous system2.35e-2153
regional part of brain2.35e-2153
organ system subdivision3.41e-21223
telencephalon6.12e-2034
brain grey matter1.42e-1934
gray matter1.42e-1934
cerebral hemisphere2.20e-1932
regional part of telencephalon7.46e-1932
regional part of cerebral cortex8.91e-1922
brain1.02e-1768
future brain1.02e-1768
neocortex2.28e-1720
central nervous system3.56e-1781
organ1.57e-15503
cerebral cortex4.17e-1525
pallium4.17e-1525
organ part5.81e-15218
multi-tissue structure8.02e-15342
neural plate1.32e-1482
presumptive neural plate1.32e-1482
nervous system8.03e-1489
neurectoderm7.33e-1386
structure with developmental contribution from neural crest7.37e-13132
pre-chordal neural plate1.41e-1261
ecto-epithelium2.34e-12104
ectoderm-derived structure1.97e-11171
ectoderm1.97e-11171
presumptive ectoderm1.97e-11171
endoderm-derived structure2.91e-11160
endoderm2.91e-11160
presumptive endoderm2.91e-11160
digestive system5.74e-11145
digestive tract5.74e-11145
primitive gut5.74e-11145
subdivision of digestive tract1.03e-09118
multi-cellular organism1.42e-09656
anatomical cluster3.27e-09373
anatomical system3.16e-08624
anatomical group4.31e-08625
basal ganglion9.65e-079
nuclear complex of neuraxis9.65e-079
aggregate regional part of brain9.65e-079
collection of basal ganglia9.65e-079
cerebral subcortex9.65e-079


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
CCNT2#90536.336201576962630.003930750035764890.0190639733902317
CTCF#1066435.360256373075030.0064925092527670.0280519267685642
E2F6#187635.017155731697390.00791769806886330.0323456471196563
TFAP2C#7022310.80922860986020.0007916746575753130.00617580740682015
ZNF263#1012738.221841637010680.001799043925565870.0109736215712051



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.