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Coexpression cluster:C2796: Difference between revisions

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|tf_chipseq_enrich=STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123353121733342!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327034708332987!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114730868837488
|tf_chipseq_enrich=STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123353121733342!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000327034708332987!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114730868837488
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2796_Astrocyte_signet_Ciliary_small_Neural_anaplastic_Lens



Phase1 CAGE Peaks

Hg19::chr4:77356248..77356295,+p5@SHROOM3
Hg19::chr4:77356310..77356326,+p25@SHROOM3
Hg19::chr4:77356342..77356353,+p17@SHROOM3
Hg19::chr4:77356369..77356405,+p4@SHROOM3


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
neural cell9.78e-1225
oligodendrocyte8.86e-107
macroglial cell8.86e-107
astrocyte8.86e-107
oligodendrocyte precursor cell8.86e-107
neurectodermal cell1.26e-0959
neuronal stem cell8.39e-088
ectodermal cell1.27e-0772
glial cell (sensu Vertebrata)2.28e-0715
glial cell2.28e-0715
glioblast2.28e-0715
glioblast (sensu Vertebrata)2.28e-0715
Uber Anatomy
Ontology termp-valuen
central nervous system4.82e-2781
neural plate8.64e-2582
presumptive neural plate8.64e-2582
nervous system8.86e-2489
neurectoderm7.25e-2386
neural tube6.53e-2156
neural rod6.53e-2156
future spinal cord6.53e-2156
neural keel6.53e-2156
ectoderm-derived structure4.59e-19171
ectoderm4.59e-19171
presumptive ectoderm4.59e-19171
structure with developmental contribution from neural crest4.86e-19132
pre-chordal neural plate1.15e-1861
regional part of nervous system3.13e-1853
regional part of brain3.13e-1853
ecto-epithelium6.86e-18104
brain1.44e-1768
future brain1.44e-1768
adult organism1.52e-16114
brain grey matter1.15e-1434
gray matter1.15e-1434
cerebral hemisphere1.82e-1432
telencephalon1.95e-1434
regional part of forebrain1.98e-1441
forebrain1.98e-1441
anterior neural tube1.98e-1441
future forebrain1.98e-1441
regional part of telencephalon3.82e-1332
cerebral cortex1.02e-1225
pallium1.02e-1225
anatomical cluster3.40e-11373
organ system subdivision6.09e-11223
pigment epithelium of eye3.92e-1011
neocortex1.36e-0920
regional part of cerebral cortex1.66e-0922
posterior neural tube7.80e-0815
chordal neural plate7.80e-0815
organ1.94e-07503
atypical epithelium8.01e-074


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
STAT3#6774410.51946499715428.16377768286615e-050.00123353121733342
TFAP2A#7020416.5186343730451.34240829060362e-050.000327034708332987
TFAP2C#7022410.80922860986027.32289634782688e-050.00114730868837488



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.

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