Personal tools

Coexpression cluster:C761

From FANTOM5_SSTAR

Revision as of 14:27, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C761_myeloma_CD14_small_CD4_colon_duodenum_lymph



Phase1 CAGE Peaks

Hg19::chr16:79631335..79631361,-p@chr16:79631335..79631361
-
Hg19::chr16:79631939..79631952,-p@chr16:79631939..79631952
-
Hg19::chr16:79632143..79632166,-p@chr16:79632143..79632166
-
Hg19::chr16:79632343..79632358,-p@chr16:79632343..79632358
-
Hg19::chr16:79632381..79632430,-p@chr16:79632381..79632430
-
Hg19::chr16:79632532..79632560,-p@chr16:79632532..79632560
-
Hg19::chr16:79633883..79633892,-p6@MAF
Hg19::chr16:79633894..79633954,-p3@MAF
Hg19::chr16:79634581..79634592,-p4@MAF
Hg19::chr16:79634595..79634620,-p2@MAF
Hg19::chr16:79634624..79634642,-p1@MAF


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 organism5.44e-34114
neural tube1.95e-1356
neural rod1.95e-1356
future spinal cord1.95e-1356
neural keel1.95e-1356
neural plate1.81e-1282
presumptive neural plate1.81e-1282
regional part of nervous system3.76e-1253
regional part of brain3.76e-1253
neurectoderm2.17e-1186
central nervous system2.27e-1181
regional part of forebrain9.51e-1141
forebrain9.51e-1141
anterior neural tube9.51e-1141
future forebrain9.51e-1141
ecto-epithelium1.02e-10104
brain3.57e-1068
future brain3.57e-1068
brain grey matter4.12e-1034
gray matter4.12e-1034
telencephalon4.59e-1034
regional part of telencephalon1.42e-0932
pre-chordal neural plate2.57e-0961
cerebral hemisphere3.25e-0932
regional part of cerebral cortex9.69e-0922
nervous system2.21e-0889
organ4.51e-08503
organ system subdivision5.14e-08223
neocortex6.23e-0820
cerebral cortex6.66e-0825
pallium6.66e-0825
structure with developmental contribution from neural crest3.44e-07132
ectoderm-derived structure3.69e-07171
ectoderm3.69e-07171
presumptive ectoderm3.69e-07171


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
CTBP2#1488317.10463645618040.0006070928651993480.0050682791165911



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.