Personal tools

Coexpression cluster:C2071

From FANTOM5_SSTAR

Revision as of 15:16, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2071_Dendritic_Endothelial_Renal_Hepatic_immature_Lymphatic_brain



Phase1 CAGE Peaks

Hg19::chr10:72238517..72238595,+p1@KIAA1274
Hg19::chr10:72238698..72238712,+p4@KIAA1274
Hg19::chr10:72238717..72238746,+p2@KIAA1274
Hg19::chr10:72238747..72238760,+p3@KIAA1274


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>


Uber Anatomy
Ontology termp-valuen
adult organism1.60e-25114
neurectoderm2.34e-2286
neural plate5.81e-2282
presumptive neural plate5.81e-2282
neural tube5.41e-2056
neural rod5.41e-2056
future spinal cord5.41e-2056
neural keel5.41e-2056
central nervous system2.33e-1981
regional part of nervous system6.86e-1953
regional part of brain6.86e-1953
nervous system5.41e-1889
brain3.38e-1668
future brain3.38e-1668
pre-chordal neural plate1.56e-1561
anatomical cluster2.52e-15373
regional part of forebrain7.81e-1441
forebrain7.81e-1441
anterior neural tube7.81e-1441
future forebrain7.81e-1441
structure with developmental contribution from neural crest1.54e-13132
ecto-epithelium3.11e-13104
blood vessel endothelium3.78e-1318
endothelium3.78e-1318
cardiovascular system endothelium3.78e-1318
tube4.16e-12192
telencephalon4.51e-1234
brain grey matter1.04e-1134
gray matter1.04e-1134
simple squamous epithelium1.52e-1122
anatomical conduit2.32e-11240
cerebral hemisphere3.94e-1132
regional part of telencephalon4.68e-1132
squamous epithelium6.29e-1025
ectoderm-derived structure1.89e-09171
ectoderm1.89e-09171
presumptive ectoderm1.89e-09171
organ system subdivision1.42e-08223
cerebral cortex1.27e-0725
pallium1.27e-0725
posterior neural tube1.61e-0715
chordal neural plate1.61e-0715
cell layer2.35e-07309
epithelium6.06e-07306
organ part6.08e-07218


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
EBF1#187948.9064668465690.00015887907472010.00199317377593904
EGR1#195844.988179094810140.001615011500076050.0101242608677337
MYC#460945.22228187160940.001344309395272740.00885458683986436
PBX3#5090421.91451268674414.33289161192893e-060.000135892752870344
ZBTB7A#5134147.35190930787590.000342223540015990.0034582955293401
ZNF263#1012748.221841637010680.0002187871180958320.00248045026344014



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.