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Coexpression cluster:C4696: Difference between revisions

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|tf_chipseq_enrich=NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174612982425386
|tf_chipseq_enrich=NANOG#79923;2:19.4965189873418:0.00342725564850102:0.0174612982425386
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}}
}}

Revision as of 16:54, 26 November 2012


Full id: C4696_serous_colon_small_MCF7_thyroid_endometrial_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr7:73183842..73183858,-p@chr7:73183842..73183858
-
Hg19::chr7:73184529..73184547,-p2@CLDN3
Hg19::chr7:73184588..73184611,-p1@CLDN3


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.28e-13253
kidney tubule cell1.56e-1110
nephron tubule epithelial cell1.56e-1110
kidney cell3.02e-0817
kidney epithelial cell3.02e-0817
epithelial cell of nephron3.08e-0815
germ line cell3.89e-077
germ cell3.89e-077
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract2.53e-18118
digestive system1.42e-16145
digestive tract1.42e-16145
primitive gut1.42e-16145
endoderm-derived structure1.90e-14160
endoderm1.90e-14160
presumptive endoderm1.90e-14160
trunk region element2.44e-14101
immaterial anatomical entity7.66e-13117
subdivision of trunk7.92e-13112
foregut8.98e-1287
nephron tubule epithelium1.56e-1110
adult organism1.92e-11114
kidney7.34e-1126
kidney mesenchyme7.34e-1126
upper urinary tract7.34e-1126
kidney rudiment7.34e-1126
kidney field7.34e-1126
endo-epithelium1.32e-1082
abdomen element2.39e-1054
abdominal segment element2.39e-1054
anatomical space4.18e-1095
organ system subdivision2.45e-09223
cavitated compound organ3.83e-0931
excretory tube4.18e-0916
kidney epithelium4.18e-0916
abdominal segment of trunk1.88e-0860
abdomen1.88e-0860
renal system2.11e-0848
gastrointestinal system2.72e-0825
male reproductive organ2.78e-0811
nephron epithelium3.08e-0815
renal tubule3.08e-0815
nephron tubule3.08e-0815
nephron3.08e-0815
uriniferous tubule3.08e-0815
nephrogenic mesenchyme3.08e-0815
intestine4.34e-0817
reproductive structure5.69e-0859
reproductive system5.69e-0859
urinary system structure6.31e-0847
reproductive organ7.89e-0848
lung1.32e-0722
respiratory tube1.32e-0722
respiration organ1.32e-0722
pair of lungs1.32e-0722
lung primordium1.32e-0722
lung bud1.32e-0722
anatomical cluster1.84e-07373
multi-tissue structure2.88e-07342
organ3.14e-07503
primordium8.13e-07160
epithelial bud8.28e-0737
Disease
Ontology termp-valuen
carcinoma3.99e-29106
cell type cancer3.46e-21143
adenocarcinoma2.49e-1525
cancer5.60e-09235
disease of cellular proliferation2.21e-08239
gastrointestinal system cancer7.51e-0814
respiratory system cancer2.29e-0716


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#79923219.49651898734180.003427255648501020.0174612982425386



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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