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Coexpression cluster:C1918

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Full id: C1918_smooth_leiomyoma_bladder_Mesenchymal_cervix_esophagus_prostate



Phase1 CAGE Peaks

Hg19::chr3:123419560..123419573,-p26@MYLK
Hg19::chr3:123419588..123419611,-p15@MYLK
Hg19::chr3:123419651..123419676,-p8@MYLK
Hg19::chr3:123419683..123419705,-p17@MYLK
Hg19::chr3:123419964..123419975,-p13@MYLK


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 organism4.05e-50115
neural tube8.69e-2657
neural rod8.69e-2657
future spinal cord8.69e-2657
neural keel8.69e-2657
regional part of brain1.46e-2459
brain5.49e-2369
future brain5.49e-2369
central nervous system5.15e-2182
anterior neural tube2.17e-2042
regional part of forebrain8.66e-2041
forebrain8.66e-2041
future forebrain8.66e-2041
neural plate1.99e-1986
presumptive neural plate1.99e-1986
regional part of nervous system2.71e-1994
nervous system2.71e-1994
gray matter4.99e-1934
brain grey matter4.99e-1934
telencephalon7.93e-1934
regional part of telencephalon4.15e-1833
cerebral hemisphere1.24e-1732
neurectoderm1.38e-1790
head4.05e-15123
anterior region of body4.49e-15129
craniocervical region4.49e-15129
organism subdivision6.55e-15365
pre-chordal neural plate7.53e-1561
organ7.24e-13511
regional part of cerebral cortex1.20e-1222
cerebral cortex2.88e-1225
pallium2.88e-1225
ectoderm-derived structure1.35e-11169
neocortex4.58e-1120
ectoderm9.25e-11173
presumptive ectoderm9.25e-11173
anatomical cluster1.04e-10286
anatomical conduit2.04e-10241
organ part1.58e-09219
tube3.12e-09194
multi-tissue structure6.50e-09347
basal ganglion1.17e-089
nuclear complex of neuraxis1.17e-089
aggregate regional part of brain1.17e-089
collection of basal ganglia1.17e-089
cerebral subcortex1.17e-089
nucleus of brain1.24e-089
neural nucleus1.24e-089
multi-cellular organism3.11e-08659
epithelium4.15e-08309
cell layer5.76e-08312
anatomical system1.54e-07625
anatomical group1.95e-07626
reproductive structure2.10e-0759
reproductive system2.10e-0759
telencephalic nucleus5.19e-077
brainstem7.35e-078


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.