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Coexpression cluster:C4511

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Full id: C4511_occipital_ductus_parietal_temporal_aorta_spinal_pituitary



Phase1 CAGE Peaks

Hg19::chr5:63461487..63461525,+p3@RNF180
Hg19::chr5:63461526..63461560,+p2@RNF180
Hg19::chr5:63461642..63461722,+p1@RNF180


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 organism4.71e-55114
neural tube5.81e-3656
neural rod5.81e-3656
future spinal cord5.81e-3656
neural keel5.81e-3656
central nervous system1.00e-3581
nervous system1.31e-3389
regional part of nervous system1.31e-3353
regional part of brain1.31e-3353
neural plate7.02e-3182
presumptive neural plate7.02e-3182
brain9.43e-3168
future brain9.43e-3168
regional part of forebrain1.37e-2841
forebrain1.37e-2841
anterior neural tube1.37e-2841
future forebrain1.37e-2841
neurectoderm6.31e-2886
ecto-epithelium6.37e-27104
structure with developmental contribution from neural crest4.80e-24132
brain grey matter7.35e-2434
gray matter7.35e-2434
telencephalon1.76e-2334
pre-chordal neural plate6.66e-2361
regional part of telencephalon2.56e-2232
cerebral hemisphere2.74e-2232
anatomical cluster9.89e-21373
ectoderm-derived structure1.19e-20171
ectoderm1.19e-20171
presumptive ectoderm1.19e-20171
organ system subdivision1.43e-18223
cerebral cortex2.84e-1725
pallium2.84e-1725
anatomical conduit5.82e-16240
regional part of cerebral cortex6.13e-1622
tube1.59e-15192
multi-tissue structure4.07e-15342
neocortex1.52e-1420
epithelium2.48e-13306
cell layer5.23e-13309
multi-cellular organism5.45e-10656
embryo2.36e-09592
developing anatomical structure1.01e-08581
anatomical system1.09e-08624
anatomical group1.47e-08625
posterior neural tube1.53e-0815
chordal neural plate1.53e-0815
organ2.84e-08503
neural nucleus4.59e-089
nucleus of brain4.59e-089
embryonic structure1.02e-07564
basal ganglion1.23e-079
nuclear complex of neuraxis1.23e-079
aggregate regional part of brain1.23e-079
collection of basal ganglia1.23e-079
cerebral subcortex1.23e-079
segmental subdivision of nervous system3.49e-0713
germ layer3.56e-07560
germ layer / neural crest3.56e-07560
embryonic tissue3.56e-07560
presumptive structure3.56e-07560
germ layer / neural crest derived structure3.56e-07560
epiblast (generic)3.56e-07560


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#186934.907389214879320.008460985347239390.0327207601525711



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.