Personal tools

Coexpression cluster:C1613

From FANTOM5_SSTAR

Revision as of 14:13, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1613_tongue_Sebocyte_esophagus_amniotic_throat_Prostate_Urothelial



Phase1 CAGE Peaks

Hg19::chr11:119982702..119982714,-p@chr11:119982702..119982714
-
Hg19::chr11:119982790..119982805,-p@chr11:119982790..119982805
-
Hg19::chr11:119982836..119982847,-p@chr11:119982836..119982847
-
Hg19::chr11:119986113..119986126,-p1@BX648072
Hg19::chr11:120008074..120008088,-p13@TRIM29


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 cell1.26e-19254
endo-epithelial cell1.87e-1943
endodermal cell2.35e-1259
epithelial cell of alimentary canal6.95e-1221
general ecto-epithelial cell5.94e-1113
respiratory epithelial cell1.22e-0713
acinar cell1.62e-075
Uber Anatomy
Ontology termp-valuen
respiratory system1.61e-2172
endoderm-derived structure5.97e-20169
endoderm5.97e-20169
presumptive endoderm5.97e-20169
respiratory tract1.45e-1553
upper respiratory tract1.99e-1319
digestive system2.31e-13155
digestive tract2.31e-13155
primitive gut2.31e-13155
orifice6.89e-1335
mixed endoderm/mesoderm-derived structure7.04e-13130
larynx1.26e-129
segment of respiratory tract5.01e-1246
extraembryonic membrane8.35e-1214
membranous layer8.35e-1214
subdivision of digestive tract6.03e-11129
endodermal part of digestive tract6.03e-11129
oral opening9.64e-1121
respiratory primordium1.33e-1038
endoderm of foregut1.33e-1038
foregut9.77e-1098
chorion3.57e-097
mouth3.48e-0828
stomodeum3.48e-0828
extraembryonic structure1.59e-0724
organ component layer3.93e-0757
organ4.05e-07511
urothelium6.16e-075
neck6.49e-0710
internal genitalia8.62e-0725
mucosa9.49e-0712
Disease
Ontology termp-valuen
carcinoma2.50e-10106
squamous cell carcinoma1.13e-0914


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.