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Coexpression cluster:C4094: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115424129131323!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010920966913592!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197381121627649
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115424129131323!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.010920966913592!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197381121627649
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}}
}}

Revision as of 16:32, 26 November 2012


Full id: C4094_Urothelial_Prostate_serous_Mallassezderived_Keratinocyte_Esophageal_Corneal



Phase1 CAGE Peaks

Hg19::chr22:31644309..31644350,+p3@LIMK2
Hg19::chr22:31644352..31644379,+p2@LIMK2
Hg19::chr22:31644394..31644405,+p4@LIMK2


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>

Cell Type
Ontology termp-valuen
ecto-epithelial cell1.39e-0934
endo-epithelial cell2.66e-0942
extraembryonic cell6.14e-0819
general ecto-epithelial cell2.14e-0714
embryonic cell2.39e-07250
contractile cell3.53e-0759
vascular associated smooth muscle cell9.86e-0732
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.54e-20171
ectoderm2.54e-20171
presumptive ectoderm2.54e-20171
ecto-epithelium2.78e-20104
multi-tissue structure2.92e-18342
multi-cellular organism4.30e-16656
cell layer5.37e-16309
epithelium6.66e-16306
organ part8.54e-15218
developing anatomical structure3.30e-13581
neural plate6.28e-1382
presumptive neural plate6.28e-1382
embryo6.44e-13592
anatomical system1.59e-12624
embryonic structure1.72e-12564
structure with developmental contribution from neural crest2.41e-12132
anatomical group3.07e-12625
anatomical cluster5.26e-12373
neurectoderm1.07e-1186
germ layer3.34e-11560
germ layer / neural crest3.34e-11560
embryonic tissue3.34e-11560
presumptive structure3.34e-11560
germ layer / neural crest derived structure3.34e-11560
epiblast (generic)3.34e-11560
organism subdivision3.80e-11264
neural tube4.28e-1156
neural rod4.28e-1156
future spinal cord4.28e-1156
neural keel4.28e-1156
organ2.38e-10503
regional part of nervous system3.90e-1053
regional part of brain3.90e-1053
pre-chordal neural plate7.83e-1061
central nervous system1.61e-0981
brain2.97e-0968
future brain2.97e-0968
nervous system3.42e-0889
anatomical conduit6.51e-08240
head1.16e-0756
ectodermal placode1.47e-0731
anterior region of body2.09e-0762
craniocervical region2.09e-0762
regional part of forebrain3.11e-0741
forebrain3.11e-0741
anterior neural tube3.11e-0741
future forebrain3.11e-0741
extraembryonic membrane3.30e-0714
membranous layer3.30e-0714
organ segment3.60e-0798
organ system subdivision4.65e-07223
adult organism7.20e-07114
multilaminar epithelium8.74e-0783


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
CEBPB#105137.971147625824820.001974187055288560.0115424129131323
SPI1#668838.204323508522730.001810593189410520.010920966913592
TRIM28#10155318.59052504526250.0001555969297255280.00197381121627649



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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