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Coexpression cluster:C4483: Difference between revisions

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|tf_chipseq_enrich=NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739882007839435!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376049060423331!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197717334756106
|tf_chipseq_enrich=NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739882007839435!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376049060423331!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197717334756106
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}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4483_caudate_Fibroblast_acute_putamen_pituitary_mesenchymal_occipital



Phase1 CAGE Peaks

Hg19::chr5:163723701..163723725,+p2@ENST00000517508
Hg19::chr5:163723738..163723786,+p1@ENST00000517508
Hg19::chr5:163723787..163723799,+p3@ENST00000517508


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>

Uber Anatomy
Ontology termp-valuen
regional part of forebrain1.03e-3541
forebrain1.03e-3541
anterior neural tube1.03e-3541
future forebrain1.03e-3541
cerebral hemisphere1.12e-3532
brain grey matter1.33e-3534
gray matter1.33e-3534
telencephalon2.03e-3534
regional part of nervous system5.12e-3353
regional part of brain5.12e-3353
regional part of telencephalon6.57e-3332
neural tube1.14e-3256
neural rod1.14e-3256
future spinal cord1.14e-3256
neural keel1.14e-3256
neocortex1.46e-2920
regional part of cerebral cortex4.56e-2922
cerebral cortex2.36e-2725
pallium2.36e-2725
brain2.17e-2468
future brain2.17e-2468
neural plate2.65e-2482
presumptive neural plate2.65e-2482
pre-chordal neural plate6.04e-2461
neurectoderm1.30e-2286
nervous system9.84e-2289
central nervous system2.19e-2181
structure with developmental contribution from neural crest7.15e-19132
ecto-epithelium1.15e-16104
tube3.56e-14192
adult organism5.22e-14114
gyrus6.20e-126
epithelium1.09e-10306
cell layer2.05e-10309
parietal lobe2.07e-105
occipital lobe2.95e-105
anatomical conduit3.17e-10240
neural nucleus1.30e-099
nucleus of brain1.30e-099
corpus striatum4.52e-094
striatum4.52e-094
ventral part of telencephalon4.52e-094
future corpus striatum4.52e-094
ectoderm-derived structure4.67e-09171
ectoderm4.67e-09171
presumptive ectoderm4.67e-09171
cavity lining3.23e-0812
serous membrane3.23e-0812
artery wall5.50e-084
tunica adventitia of artery5.50e-084
adventitia5.50e-084
tunica adventitia of blood vessel5.50e-084
aorta tunica adventitia5.50e-084
aorta wall5.50e-084
anatomical cluster1.33e-07373
multi-tissue structure1.64e-07342
caudate-putamen2.74e-073
dorsal striatum2.74e-073
basal ganglion3.81e-079
nuclear complex of neuraxis3.81e-079
aggregate regional part of brain3.81e-079
collection of basal ganglia3.81e-079
cerebral subcortex3.81e-079
telencephalic nucleus4.78e-077
frontal cortex6.06e-073
organ system subdivision9.15e-07223


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
NANOG#79923329.24477848101273.99627955670032e-050.000739882007839435
SRF#6722313.79717826216780.0003806615025800190.00376049060423331
TRIM28#10155318.59052504526250.0001555969297255280.00197717334756106



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.

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