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Coexpression cluster:C4515

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Full id: C4515_mesodermal_astrocytoma_Mesenchymal_Lens_Multipotent_osteoclastoma_bone



Phase1 CAGE Peaks

Hg19::chr5:71475449..71475460,+p45@MAP1B
Hg19::chr5:71475473..71475487,+p40@MAP1B
Hg19::chr5:71475488..71475517,+p13@MAP1B


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
non-terminally differentiated cell2.08e-21180
fibroblast5.50e-1375
skin fibroblast3.39e-1123
Uber Anatomy
Ontology termp-valuen
neural tube3.97e-2657
neural rod3.97e-2657
future spinal cord3.97e-2657
neural keel3.97e-2657
central nervous system7.81e-2682
neural plate9.84e-2586
presumptive neural plate9.84e-2586
regional part of nervous system1.01e-2394
nervous system1.01e-2394
neurectoderm2.85e-2290
brain3.48e-2269
future brain3.48e-2269
regional part of brain5.75e-2259
anterior neural tube2.38e-2042
regional part of forebrain6.28e-2041
forebrain6.28e-2041
future forebrain6.28e-2041
head1.61e-19123
anterior region of body1.99e-18129
craniocervical region1.99e-18129
ectoderm-derived structure3.81e-18169
pre-chordal neural plate3.93e-1861
gray matter9.24e-1834
brain grey matter9.24e-1834
telencephalon1.37e-1734
regional part of telencephalon3.59e-1733
organism subdivision4.81e-17365
ectoderm7.67e-17173
presumptive ectoderm7.67e-17173
cerebral hemisphere3.20e-1632
adult organism2.35e-14115
cerebral cortex2.66e-1225
pallium2.66e-1225
multi-tissue structure2.97e-10347
regional part of cerebral cortex4.33e-1022
neocortex7.38e-0920
epithelium1.49e-08309
anatomical cluster1.62e-08286
tube1.75e-08194
multi-cellular organism2.70e-08659
cell layer4.24e-08312
skin of body7.96e-0840
integument1.92e-0745
integumental system1.92e-0745
basal ganglion4.31e-079
nuclear complex of neuraxis4.31e-079
aggregate regional part of brain4.31e-079
collection of basal ganglia4.31e-079
cerebral subcortex4.31e-079
nucleus of brain4.57e-079
neural nucleus4.57e-079
posterior neural tube5.49e-0715
chordal neural plate5.49e-0715


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
CEBPB#105137.971147625824820.001974187055288560.0115650730237425



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.