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Coexpression cluster:C2186

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Full id: C2186_liver_Hepatocyte_mature_left_vagina_skeletal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr12:112219753..112219770,+p@chr12:112219753..112219770
+
Hg19::chr19:35630316..35630339,+p9@FXYD1
Hg19::chr19:35630344..35630384,+p5@FXYD1
Hg19::chr19:35630385..35630392,+p17@FXYD1


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
fat cell9.07e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.72e-64114
neural tube2.16e-2556
neural rod2.16e-2556
future spinal cord2.16e-2556
neural keel2.16e-2556
regional part of nervous system8.80e-2353
regional part of brain8.80e-2353
regional part of forebrain1.33e-1841
forebrain1.33e-1841
anterior neural tube1.33e-1841
future forebrain1.33e-1841
neural plate2.21e-1882
presumptive neural plate2.21e-1882
central nervous system2.52e-1781
brain5.19e-1768
future brain5.19e-1768
neurectoderm7.53e-1786
brain grey matter2.73e-1634
gray matter2.73e-1634
telencephalon3.04e-1634
cerebral hemisphere1.39e-1432
regional part of telencephalon1.46e-1432
nervous system3.11e-1489
structure with developmental contribution from neural crest3.87e-14132
ecto-epithelium7.80e-14104
organ system subdivision1.77e-13223
organ1.54e-11503
regional part of cerebral cortex2.50e-1122
pre-chordal neural plate3.66e-1161
anatomical conduit9.86e-11240
tube4.07e-10192
neocortex6.76e-1020
multi-tissue structure1.94e-09342
cerebral cortex1.98e-0925
pallium1.98e-0925
neural nucleus2.77e-099
nucleus of brain2.77e-099
anatomical cluster5.43e-09373
basal ganglion5.74e-099
nuclear complex of neuraxis5.74e-099
aggregate regional part of brain5.74e-099
collection of basal ganglia5.74e-099
cerebral subcortex5.74e-099
posterior neural tube5.61e-0815
chordal neural plate5.61e-0815
ectoderm-derived structure6.04e-08171
ectoderm6.04e-08171
presumptive ectoderm6.04e-08171
multi-cellular organism1.04e-07656
anatomical system2.33e-07624
telencephalic nucleus2.34e-077
epithelium2.71e-07306
anatomical group2.75e-07625
brainstem4.27e-076
cell layer5.00e-07309


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
CEBPB#105135.978360719368610.007153832484726970.0297167731633283



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.