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Coexpression cluster:C4775

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Full id: C4775_cerebellum_Mast_pancreas_seminal_optic_neuroectodermal_breast



Phase1 CAGE Peaks

Hg19::chr8:81786422..81786435,-p@chr8:81786422..81786435
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Hg19::chr8:81786444..81786482,-p@chr8:81786444..81786482
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Hg19::chr8:81786483..81786524,-p@chr8:81786483..81786524
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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 organism5.74e-41114
neural tube1.95e-2656
neural rod1.95e-2656
future spinal cord1.95e-2656
neural keel1.95e-2656
regional part of nervous system1.37e-2453
regional part of brain1.37e-2453
neurectoderm1.17e-2286
organ system subdivision1.44e-21223
nervous system2.00e-2189
central nervous system2.00e-2181
neural plate1.84e-2082
presumptive neural plate1.84e-2082
brain6.81e-2068
future brain6.81e-2068
regional part of forebrain6.08e-1941
forebrain6.08e-1941
anterior neural tube6.08e-1941
future forebrain6.08e-1941
brain grey matter1.37e-1634
gray matter1.37e-1634
telencephalon1.62e-1634
ectoderm-derived structure4.68e-16171
ectoderm4.68e-16171
presumptive ectoderm4.68e-16171
ecto-epithelium2.27e-15104
regional part of telencephalon3.19e-1532
cerebral hemisphere4.22e-1532
pre-chordal neural plate7.94e-1461
cerebral cortex6.46e-1325
pallium6.46e-1325
regional part of cerebral cortex1.36e-1222
anatomical cluster9.71e-12373
structure with developmental contribution from neural crest1.30e-11132
neocortex1.43e-1120
organ3.50e-11503
organ part7.10e-11218
multi-cellular organism1.01e-09656
posterior neural tube1.11e-0815
chordal neural plate1.11e-0815
multi-tissue structure3.80e-08342
anatomical conduit7.54e-08240
tube9.99e-08192
segmental subdivision of nervous system1.05e-0713
embryo4.23e-07592
anatomical system4.96e-07624
segmental subdivision of hindbrain6.36e-0712
hindbrain6.36e-0712
presumptive hindbrain6.36e-0712
anatomical group6.42e-07625
embryonic structure8.32e-07564


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
CTCF#1066435.360256373075030.0064925092527670.0281555941473128
E2F1#186934.907389214879320.008460985347239390.0328033576613087
FOXA1#3169311.08141974938550.000734755275698670.0058457458854798
GATA3#2625327.2365163572064.94721007899563e-050.000855150071897095
MYC#460935.22228187160940.007020843755740150.0296298501234794
NANOG#79923329.24477848101273.99627955670032e-050.000741854675830475
SP1#666735.69838137814090.005403962701712170.0248070177400605
TCF7L2#6934310.77017656313730.0008003181298398380.00617862397710991
TRIM28#10155318.59052504526250.0001555969297255280.00198175460287858



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.