Personal tools

Coexpression cluster:C3703

From FANTOM5_SSTAR

Revision as of 16:17, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3703_acute_medial_parietal_heart_pineal_cerebellum_occipital



Phase1 CAGE Peaks

Hg19::chr17:80708343..80708408,+p@chr17:80708343..80708408
+
Hg19::chr17:80708453..80708483,+p@chr17:80708453..80708483
+
Hg19::chr17:80708511..80708535,+p@chr17:80708511..80708535
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism5.53e-32114
nervous system1.56e-2989
neural tube3.27e-2956
neural rod3.27e-2956
future spinal cord3.27e-2956
neural keel3.27e-2956
central nervous system1.91e-2881
organ system subdivision4.11e-28223
regional part of nervous system1.38e-2753
regional part of brain1.38e-2753
brain1.54e-2668
future brain1.54e-2668
neurectoderm2.07e-2586
neural plate1.99e-2482
presumptive neural plate1.99e-2482
regional part of forebrain6.51e-2341
forebrain6.51e-2341
anterior neural tube6.51e-2341
future forebrain6.51e-2341
anatomical cluster6.01e-22373
ectoderm-derived structure4.56e-20171
ectoderm4.56e-20171
presumptive ectoderm4.56e-20171
brain grey matter3.28e-1934
gray matter3.28e-1934
telencephalon4.93e-1934
ecto-epithelium5.83e-19104
pre-chordal neural plate9.09e-1961
regional part of telencephalon5.92e-1832
cerebral hemisphere8.14e-1832
multi-tissue structure3.24e-15342
anatomical conduit9.71e-15240
regional part of cerebral cortex1.47e-1422
cerebral cortex7.48e-1425
pallium7.48e-1425
neocortex2.51e-1320
tube5.59e-13192
structure with developmental contribution from neural crest8.31e-13132
multi-cellular organism4.74e-11656
epithelium3.14e-10306
cell layer6.54e-10309
organ1.35e-08503
embryo2.61e-08592
organ part3.32e-08218
posterior neural tube1.68e-0715
chordal neural plate1.68e-0715
anatomical system5.07e-07624
basal ganglion6.52e-079
nuclear complex of neuraxis6.52e-079
aggregate regional part of brain6.52e-079
collection of basal ganglia6.52e-079
cerebral subcortex6.52e-079
anatomical group6.77e-07625
neural nucleus7.19e-079
nucleus of brain7.19e-079
Disease
Ontology termp-valuen
cell type cancer8.95e-08143


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
SETDB1#9869340.32002617801051.52461559299059e-050.000358543859302734



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.