Personal tools

Coexpression cluster:C3464

From FANTOM5_SSTAR

Revision as of 16:24, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3464_Small_granulosa_Fibroblast_squamous_amygdala_thalamus_epidermoid



Phase1 CAGE Peaks

Hg19::chr14:94640633..94640667,+p1@PPP4R4
Hg19::chr14:94640671..94640694,+p2@PPP4R4
Hg19::chr14:94640699..94640709,+p3@PPP4R4


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
endo-epithelial cell7.06e-0743
Uber Anatomy
Ontology termp-valuen
neural tube1.12e-2057
neural rod1.12e-2057
future spinal cord1.12e-2057
neural keel1.12e-2057
head2.56e-18123
anterior region of body4.67e-18129
craniocervical region4.67e-18129
neural plate2.36e-1786
presumptive neural plate2.36e-1786
central nervous system3.96e-1782
regional part of brain9.90e-1759
brain2.16e-1669
future brain2.16e-1669
neurectoderm1.79e-1590
anterior neural tube2.06e-1542
regional part of forebrain3.79e-1541
forebrain3.79e-1541
future forebrain3.79e-1541
regional part of nervous system2.15e-1494
nervous system2.15e-1494
ectoderm-derived structure3.34e-14169
ectoderm4.15e-13173
presumptive ectoderm4.15e-13173
pre-chordal neural plate2.76e-1261
gray matter5.20e-1234
brain grey matter5.20e-1234
telencephalon9.79e-1234
regional part of telencephalon2.81e-1133
cerebral hemisphere2.82e-1132
organism subdivision3.57e-11365
adult organism4.47e-11115
organ5.48e-10511
regional part of cerebral cortex5.49e-1022
neocortex8.43e-0920
cerebral cortex4.96e-0825
pallium4.96e-0825


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
E2F1#186934.907389214879320.008460985347239390.0324456342456521
E2F6#187635.017155731697390.00791769806886330.0321332271941406
EGR1#195834.988179094810140.008056488137383440.0319818907818689
NRF1#4899312.21027944771090.0005492172401020010.00470277111904673
ZNF263#1012738.221841637010680.001799043925565870.0109149731928764



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.