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Coexpression cluster:C636

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Full id: C636_thymus_skeletal_cerebellum_Hodgkin_temporal_duodenum_parietal



Phase1 CAGE Peaks

Hg19::chr3:35680783..35680788,+p29@ARPP21
Hg19::chr3:35680971..35680982,+p12@ARPP21
Hg19::chr3:35681007..35681023,+p2@ARPP21
Hg19::chr3:35681084..35681099,+p10@ARPP21
Hg19::chr3:35681110..35681124,+p14@ARPP21
Hg19::chr3:35681137..35681148,+p8@ARPP21
Hg19::chr3:35681164..35681173,+p13@ARPP21
Hg19::chr3:35681192..35681203,+p9@ARPP21
Hg19::chr3:35681221..35681234,+p5@ARPP21
Hg19::chr3:35681260..35681273,+p6@ARPP21
Hg19::chr3:35681346..35681369,+p11@ARPP21
Hg19::chr3:35683726..35683735,+p41@ARPP21
Hg19::chr3:35683816..35683839,+p7@ARPP21
Hg19::chr7:71802595..71802610,-p15@CALN1


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
central nervous system1.51e-4382
regional part of nervous system8.82e-4294
nervous system8.82e-4294
neural tube1.01e-4057
neural rod1.01e-4057
future spinal cord1.01e-4057
neural keel1.01e-4057
regional part of brain2.98e-3759
brain1.04e-3669
future brain1.04e-3669
regional part of forebrain1.51e-3441
forebrain1.51e-3441
future forebrain1.51e-3441
adult organism1.56e-33115
anterior neural tube2.56e-3342
neurectoderm3.33e-3390
neural plate7.86e-3286
presumptive neural plate7.86e-3286
telencephalon1.46e-3134
gray matter1.68e-3134
brain grey matter1.68e-3134
regional part of telencephalon1.40e-3033
cerebral hemisphere4.72e-3032
pre-chordal neural plate2.37e-2761
anterior region of body9.12e-25129
craniocervical region9.12e-25129
ectoderm1.76e-24173
presumptive ectoderm1.76e-24173
cerebral cortex7.46e-2425
pallium7.46e-2425
ectoderm-derived structure3.38e-23169
regional part of cerebral cortex6.78e-2322
head9.47e-23123
neocortex3.92e-2120
epithelium1.15e-11309
cell layer1.45e-11312
tube5.82e-11194
basal ganglion2.95e-099
nuclear complex of neuraxis2.95e-099
aggregate regional part of brain2.95e-099
collection of basal ganglia2.95e-099
cerebral subcortex2.95e-099
nucleus of brain4.94e-099
neural nucleus4.94e-099
multi-tissue structure5.28e-09347
organism subdivision1.00e-08365
temporal lobe1.15e-087
posterior neural tube1.19e-0815
chordal neural plate1.19e-0815
anatomical cluster1.39e-08286
anatomical conduit1.00e-07241
telencephalic nucleus1.98e-077
gyrus2.52e-076
segmental subdivision of nervous system4.76e-0713


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
SUZ12#23512310.73909590951350.002450333088738650.0137919880061857
ZNF263#10127105.87274402643624.43453169106043e-072.11285609161798e-05



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.