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Coexpression cluster:C3947

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Full id: C3947_cerebellum_amygdala_parietal_middle_caudate_occipital_olfactory



Phase1 CAGE Peaks

Hg19::chr1:228604454..228604504,-p3@TRIM17
Hg19::chr1:228604544..228604568,-p1@TRIM17
Hg19::chr1:228604572..228604589,-p4@TRIM17


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
neural tube6.85e-3157
neural rod6.85e-3157
future spinal cord6.85e-3157
neural keel6.85e-3157
adult organism2.73e-29115
central nervous system3.83e-2982
regional part of nervous system6.90e-2994
nervous system6.90e-2994
neurectoderm4.50e-2890
regional part of brain4.99e-2859
neural plate7.25e-2886
presumptive neural plate7.25e-2886
brain5.24e-2669
future brain5.24e-2669
anterior neural tube6.45e-2442
regional part of forebrain1.19e-2341
forebrain1.19e-2341
future forebrain1.19e-2341
ectoderm3.80e-23173
presumptive ectoderm3.80e-23173
ectoderm-derived structure1.16e-22169
pre-chordal neural plate1.73e-2261
telencephalon2.34e-2234
gray matter2.40e-2234
brain grey matter2.40e-2234
cerebral hemisphere9.98e-2232
regional part of telencephalon1.26e-2133
anterior region of body1.66e-20129
craniocervical region1.66e-20129
head6.65e-20123
cerebral cortex1.44e-1625
pallium1.44e-1625
regional part of cerebral cortex4.24e-1522
neocortex1.39e-1320
organ part1.91e-11219
posterior neural tube4.21e-0815
chordal neural plate4.21e-0815
cell layer6.01e-08312
epithelium1.08e-07309
basal ganglion1.64e-079
nuclear complex of neuraxis1.64e-079
aggregate regional part of brain1.64e-079
collection of basal ganglia1.64e-079
cerebral subcortex1.64e-079
nucleus of brain3.11e-079
neural nucleus3.11e-079
segmental subdivision of hindbrain3.91e-0712
hindbrain3.91e-0712
presumptive hindbrain3.91e-0712


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)

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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.