Personal tools

Coexpression cluster:C4185

From FANTOM5_SSTAR

Revision as of 14:45, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4185_teratocarcinoma_iPS_H9_HES3GFP_NK_diffuse_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr2:219433617..219433629,+p5@RQCD1
Hg19::chr2:219433630..219433644,+p4@RQCD1
Hg19::chr2:219433648..219433655,+p6@RQCD1


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.47e-07254
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.64e-1394
nervous system2.64e-1394
central nervous system1.31e-1282
neural tube1.74e-1157
neural rod1.74e-1157
future spinal cord1.74e-1157
neural keel1.74e-1157
brain5.44e-1169
future brain5.44e-1169
regional part of brain3.49e-1059
neural plate1.79e-0986
presumptive neural plate1.79e-0986
regional part of forebrain4.02e-0941
forebrain4.02e-0941
future forebrain4.02e-0941
neurectoderm7.00e-0990
pre-chordal neural plate1.96e-0861
anterior neural tube2.57e-0842
gray matter1.03e-0734
brain grey matter1.03e-0734
telencephalon2.59e-0734
regional part of telencephalon3.82e-0733
tube8.40e-07194
Disease
Ontology termp-valuen
disease of cellular proliferation7.12e-22239
cancer8.33e-22235
cell type cancer7.80e-13143
organ system cancer3.86e-11137
carcinoma6.06e-11106
hematologic cancer2.53e-0751
immune system cancer2.53e-0751


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


No analysis results for this cluster

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.