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Coexpression cluster:C2796

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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 cell3.77e-0825
neuronal stem cell2.66e-078
oligodendrocyte3.53e-077
macroglial cell3.53e-077
astrocyte3.53e-077
oligodendrocyte precursor cell3.53e-077
Uber Anatomy
Ontology termp-valuen
central nervous system3.14e-3482
regional part of nervous system2.62e-3294
nervous system2.62e-3294
neural plate1.12e-3086
presumptive neural plate1.12e-3086
neurectoderm7.73e-2990
neural tube7.20e-2757
neural rod7.20e-2757
future spinal cord7.20e-2757
neural keel7.20e-2757
brain2.61e-2569
future brain2.61e-2569
anterior region of body9.53e-25129
craniocervical region9.53e-25129
head5.35e-24123
regional part of brain6.35e-2459
ectoderm-derived structure9.26e-24169
ectoderm6.68e-23173
presumptive ectoderm6.68e-23173
adult organism3.27e-22115
pre-chordal neural plate1.94e-2161
anterior neural tube1.01e-1842
regional part of forebrain2.41e-1841
forebrain2.41e-1841
future forebrain2.41e-1841
gray matter3.08e-1534
brain grey matter3.08e-1534
telencephalon4.61e-1534
regional part of telencephalon1.70e-1433
cerebral hemisphere5.33e-1432
cerebral cortex9.19e-1225
pallium9.19e-1225
organism subdivision4.27e-10365
posterior neural tube2.21e-0915
chordal neural plate2.21e-0915
neocortex2.43e-0920
regional part of cerebral cortex2.71e-0922
pigment epithelium of eye9.16e-0911
organ1.93e-08511
tube4.43e-08194
anatomical cluster3.38e-07286
segmental subdivision of hindbrain5.00e-0712
hindbrain5.00e-0712
presumptive hindbrain5.00e-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
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.