Personal tools

Coexpression cluster:C2423

From FANTOM5_SSTAR

Revision as of 18:17, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2423_small_signet_papillotubular_malignant_hepatocellular_maxillary_colon



Phase1 CAGE Peaks

Hg19::chr17:56494853..56494874,-p3@RNF43
Hg19::chr17:56494882..56494902,-p1@RNF43
Hg19::chr17:56494908..56494949,-p2@RNF43
Hg19::chr17:56494950..56494961,-p6@RNF43


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 cell4.37e-22254
endodermal cell8.34e-1959
endo-epithelial cell3.92e-1543
epithelial cell of alimentary canal1.67e-0921
respiratory epithelial cell2.61e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.26e-26169
endoderm4.26e-26169
presumptive endoderm4.26e-26169
digestive system1.02e-21155
digestive tract1.02e-21155
primitive gut1.02e-21155
subdivision of digestive tract5.01e-21129
endodermal part of digestive tract5.01e-21129
adult organism7.39e-21115
mixed endoderm/mesoderm-derived structure7.40e-19130
foregut1.05e-1598
respiratory system3.64e-1572
endo-epithelium8.89e-1582
organ part1.97e-13219
multi-tissue structure3.36e-13347
respiratory tract1.11e-1253
organ5.12e-12511
primordium3.65e-10168
trunk region element3.70e-10107
immaterial anatomical entity6.51e-10126
organ segment7.28e-1097
respiratory primordium1.04e-0938
endoderm of foregut1.04e-0938
neural tube1.46e-0957
neural rod1.46e-0957
future spinal cord1.46e-0957
neural keel1.46e-0957
segment of respiratory tract1.91e-0946
anterior region of body1.96e-09129
craniocervical region1.96e-09129
gland3.39e-0959
head1.36e-08123
exocrine gland3.24e-0831
exocrine system3.24e-0831
anatomical conduit3.69e-08241
epithelial bud5.29e-0837
ectoderm-derived structure5.74e-08169
gut epithelium6.80e-0854
subdivision of trunk8.38e-08113
ectoderm1.78e-07173
presumptive ectoderm1.78e-07173
thoracic cavity element1.88e-0734
thoracic cavity1.88e-0734
epithelial fold2.38e-0751
regional part of brain2.54e-0759
organism subdivision2.92e-07365
anatomical cluster3.65e-07286
neural plate3.91e-0786
presumptive neural plate3.91e-0786
anatomical space4.24e-07104
lung5.68e-0722
respiratory tube5.68e-0722
respiration organ5.68e-0722
pair of lungs5.68e-0722
lung primordium5.68e-0722
lung bud5.68e-0722
thoracic segment organ5.82e-0735
Disease
Ontology termp-valuen
carcinoma3.02e-24106
cell type cancer5.79e-16143
squamous cell carcinoma9.61e-0914
cancer1.58e-08235
disease of cellular proliferation1.17e-07239
adenocarcinoma1.69e-0725


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


No analysis results for this cluster

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.