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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural
|full_id=C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural
|id=C4276
|id=C4276

Revision as of 17:20, 12 September 2012


Full id: C4276_duodenum_occipital_parietal_aorta_temporal_heart_Neural



Phase1 CAGE Peaks

Hg19::chr3:123752181..123752201,+p5@KALRN
Hg19::chr3:123752204..123752234,+p2@KALRN
Hg19::chr3:123752240..123752247,+p15@KALRN


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 nervous system8.85e-3694
nervous system8.85e-3694
central nervous system4.93e-3482
adult organism2.21e-32115
brain2.77e-2869
future brain2.77e-2869
neural tube1.68e-2657
neural rod1.68e-2657
future spinal cord1.68e-2657
neural keel1.68e-2657
neural plate8.60e-2586
presumptive neural plate8.60e-2586
neurectoderm1.92e-2490
regional part of brain3.13e-2459
anterior neural tube2.86e-2242
regional part of forebrain3.84e-2241
forebrain3.84e-2241
future forebrain3.84e-2241
ectoderm5.29e-21173
presumptive ectoderm5.29e-21173
ectoderm-derived structure6.01e-21169
pre-chordal neural plate6.66e-2161
telencephalon1.77e-2034
gray matter2.04e-2034
brain grey matter2.04e-2034
cerebral hemisphere3.03e-2032
regional part of telencephalon8.37e-2033
head2.63e-19123
anterior region of body7.50e-19129
craniocervical region7.50e-19129
anatomical conduit2.05e-18241
tube2.76e-18194
multi-cellular organism1.36e-17659
anatomical cluster1.19e-16286
cerebral cortex1.60e-1625
pallium1.60e-1625
epithelium9.61e-16309
cell layer1.02e-15312
regional part of cerebral cortex1.24e-1522
neocortex8.95e-1520
organism subdivision2.68e-14365
anatomical system1.14e-13625
anatomical group1.94e-13626
embryo4.25e-10612
organ part3.40e-09219
embryonic structure7.99e-09605
developing anatomical structure7.99e-09605
germ layer1.62e-08604
embryonic tissue1.62e-08604
presumptive structure1.62e-08604
epiblast (generic)1.62e-08604
multi-tissue structure3.59e-08347
organ4.25e-07511
endothelium8.59e-0718
blood vessel endothelium8.59e-0718
cardiovascular system endothelium8.59e-0718


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#1066435.360256373075030.0064925092527670.0280380075194233
CTCFL#140690319.74647435897440.0001298372005551160.0017212576020279
E2F1#186934.907389214879320.008460985347239390.0326506373293059
EP300#203336.77394172622320.003216880500103790.0167908332525533
RAD21#5885310.35503389545630.0009004912073565420.00666239736505454
ZNF143#7702313.50087655222790.0004062804962997170.00389959826790241



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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