Personal tools

Coexpression cluster:C1252

From FANTOM5_SSTAR

Revision as of 11:02, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1252_aorta_heart_Mesothelial_neuroblastoma_Endothelial_rhabdomyosarcoma_bladder



Phase1 CAGE Peaks

Hg19::chr1:163114878..163114901,-p4@RGS5
Hg19::chr1:163115879..163115899,-p@chr1:163115879..163115899
-
Hg19::chr1:163116681..163116700,-p@chr1:163116681..163116700
-
Hg19::chr1:163116725..163116737,-p@chr1:163116725..163116737
-
Hg19::chr1:163116929..163116952,-p@chr1:163116929..163116952
-
Hg19::chr1:163116977..163117007,-p@chr1:163116977..163117007
-
Hg19::chr1:163172695..163172712,-p1@RGS5


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 organism1.68e-64114
neural tube1.81e-2156
neural rod1.81e-2156
future spinal cord1.81e-2156
neural keel1.81e-2156
regional part of nervous system5.35e-2053
regional part of brain5.35e-2053
structure with developmental contribution from neural crest6.48e-20132
central nervous system3.80e-1981
neural plate2.43e-1882
presumptive neural plate2.43e-1882
brain6.66e-1868
future brain6.66e-1868
nervous system2.27e-1789
neurectoderm5.80e-1786
regional part of forebrain1.11e-1441
forebrain1.11e-1441
anterior neural tube1.11e-1441
future forebrain1.11e-1441
anatomical cluster1.59e-14373
ecto-epithelium5.57e-14104
tube3.87e-13192
brain grey matter5.62e-1334
gray matter5.62e-1334
telencephalon1.18e-1234
anatomical conduit1.17e-11240
organ system subdivision1.43e-11223
regional part of telencephalon3.67e-1132
cerebral hemisphere4.96e-1132
multi-tissue structure2.68e-10342
regional part of cerebral cortex1.19e-0922
ectoderm-derived structure1.20e-09171
ectoderm1.20e-09171
presumptive ectoderm1.20e-09171
pre-chordal neural plate1.50e-0961
neocortex3.03e-0920
epithelium1.40e-08306
brainstem1.91e-086
cell layer2.49e-08309
embryo2.55e-08592
embryonic structure3.63e-08564
posterior neural tube3.75e-0815
chordal neural plate3.75e-0815
cerebral cortex3.84e-0825
pallium3.84e-0825
germ layer6.72e-08560
germ layer / neural crest6.72e-08560
embryonic tissue6.72e-08560
presumptive structure6.72e-08560
germ layer / neural crest derived structure6.72e-08560
epiblast (generic)6.72e-08560
developing anatomical structure1.30e-07581
multi-cellular organism1.58e-07656
neural nucleus9.03e-079
nucleus of brain9.03e-079
segmental subdivision of hindbrain9.87e-0712
hindbrain9.87e-0712
presumptive hindbrain9.87e-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
EP300#203343.870823843556110.01142567586684480.0418638142666784
FOS#235345.141688747939660.004042095865678250.0193505890225326
GATA2#262459.103522666824285.45256227113712e-050.000923998297964124
JUN#372547.150188109906480.001171328177707770.00795916353621484



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.