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Coexpression cluster:C4785: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281591019040587!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.01102060816131
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281591019040587!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.01102060816131
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}}
}}

Revision as of 16:57, 26 November 2012


Full id: C4785_Retinal_hepatoma_small_Lens_prostate_neuroepithelioma_pancreas



Phase1 CAGE Peaks

Hg19::chr8:99076762..99076782,+p3@C8orf47
Hg19::chr8:99076787..99076809,+p1@C8orf47
Hg19::chr8:99076820..99076848,+p2@C8orf47


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
kidney tubule cell6.23e-0910
nephron tubule epithelial cell6.23e-0910
kidney cell1.76e-0717
kidney epithelial cell1.76e-0717
Uber Anatomy
Ontology termp-valuen
adult organism6.05e-16114
pre-chordal neural plate1.75e-1361
multi-tissue structure7.23e-13342
neural plate8.89e-1382
presumptive neural plate8.89e-1382
neurectoderm2.67e-1286
organ2.98e-11503
anatomical cluster3.22e-11373
regional part of forebrain3.22e-1141
forebrain3.22e-1141
anterior neural tube3.22e-1141
future forebrain3.22e-1141
regional part of nervous system7.93e-1153
regional part of brain7.93e-1153
organ part1.27e-10218
organ system subdivision1.67e-10223
neural tube2.65e-1056
neural rod2.65e-1056
future spinal cord2.65e-1056
neural keel2.65e-1056
brain grey matter2.99e-1034
gray matter2.99e-1034
ecto-epithelium3.29e-10104
cerebral hemisphere3.35e-1032
telencephalon7.77e-1034
central nervous system1.41e-0981
brain1.74e-0968
future brain1.74e-0968
regional part of telencephalon2.25e-0932
abdomen element5.23e-0954
abdominal segment element5.23e-0954
nephron tubule epithelium6.23e-0910
nervous system1.32e-0889
kidney1.76e-0826
kidney mesenchyme1.76e-0826
upper urinary tract1.76e-0826
kidney rudiment1.76e-0826
kidney field1.76e-0826
cavitated compound organ1.79e-0831
neocortex1.79e-0820
structure with developmental contribution from neural crest1.87e-08132
abdominal segment of trunk2.16e-0860
abdomen2.16e-0860
trunk region element2.65e-08101
regional part of cerebral cortex4.68e-0822
urinary system structure1.10e-0747
pigment epithelium of eye1.14e-0711
anatomical conduit1.78e-07240
renal system2.39e-0748
ectoderm-derived structure2.51e-07171
ectoderm2.51e-07171
presumptive ectoderm2.51e-07171
tube4.07e-07192
cell layer6.45e-07309


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#1066435.360256373075030.0064925092527670.0281591019040587
ZNF263#1012738.221841637010680.001799043925565870.01102060816131



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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