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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.44e-17!112;UBERON:0002405!4.15e-17!115;UBERON:0002390!8.28e-15!102;UBERON:0003061!8.28e-15!102;UBERON:0002384!1.38e-12!375;UBERON:0002371!2.14e-11!80;UBERON:0001474!4.47e-09!86;UBERON:0003081!3.21e-08!216;UBERON:0002204!3.43e-08!167;UBERON:0004765!4.33e-08!101;UBERON:0001434!4.33e-08!101
|ontology_enrichment_uberon=UBERON:0002193!3.44e-17!112;UBERON:0002405!4.15e-17!115;UBERON:0002390!8.28e-15!102;UBERON:0003061!8.28e-15!102;UBERON:0002384!1.38e-12!375;UBERON:0002371!2.14e-11!80;UBERON:0001474!4.47e-09!86;UBERON:0003081!3.21e-08!216;UBERON:0002204!3.43e-08!167;UBERON:0004765!4.33e-08!101;UBERON:0001434!4.33e-08!101
|pathway_enrichment=7.03959989046011e-05;0.0222803336533063;2;139;Ubiquitin mediated proteolysis (KEGG):04120!5.70320151504265e-06;0.00361012655902199;3;511;Signaling in Immune system (Reactome):REACT_6900
}}
}}

Revision as of 14:57, 13 July 2012


Full id: C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:57335090..57335155,-p1@UBE2L6
Hg19::chr15:74287118..74287142,+p2@PML
Hg19::chr17:41158760..41158822,+p1@IFI35
Hg19::chr17:41158825..41158847,+p2@IFI35


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


p.valueFDRnGenesnPathwayName
7.03959989046011e-050.02228033365330632139Ubiquitin mediated proteolysis (KEGG):04120
5.70320151504265e-060.003610126559021993511Signaling in Immune system (Reactome):REACT_6900



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


GO IDGO nameFDR corrected p-value
GO:0031571G1 DNA damage checkpoint0.0286350242431562
GO:0006977DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest0.0286350242431562
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.0286350242431562
GO:0031575G1/S transition checkpoint0.0286350242431562
GO:0016605PML body0.0286350242431562
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0286350242431562
GO:0016525negative regulation of angiogenesis0.0286350242431562
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0286350242431562
GO:0005626insoluble fraction0.0286350242431562
GO:0000077DNA damage checkpoint0.0300596940472044
GO:0007093mitotic cell cycle checkpoint0.0300596940472044
GO:0031570DNA integrity checkpoint0.0300596940472044
GO:0008629induction of apoptosis by intracellular signals0.0349571040718196
GO:0045765regulation of angiogenesis0.0349571040718196
GO:0042770DNA damage response, signal transduction0.0369141724117895
GO:0001666response to hypoxia0.0379388436354144
GO:0030308negative regulation of cell growth0.0379388436354144
GO:0045792negative regulation of cell size0.0379388436354144
GO:0000075cell cycle checkpoint0.0379388436354144
GO:0045926negative regulation of growth0.0392541470303728
GO:0007088regulation of mitosis0.0410548490495792



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
nongranular leukocyte8.30e-18119
leukocyte3.21e-17140
CD14-positive, CD16-negative classical monocyte1.57e-1642
hematopoietic lineage restricted progenitor cell9.71e-16124
myeloid leukocyte6.30e-1576
monopoietic cell1.71e-1363
monocyte1.71e-1363
monoblast1.71e-1363
promonocyte1.71e-1363
classical monocyte2.61e-1345
connective tissue cell8.48e-13365
myeloid lineage restricted progenitor cell1.93e-1270
macrophage dendritic cell progenitor3.55e-1265
multi fate stem cell3.85e-12430
hematopoietic stem cell5.54e-12172
angioblastic mesenchymal cell5.54e-12172
mesenchymal cell1.11e-11358
hematopoietic cell1.33e-11182
hematopoietic oligopotent progenitor cell2.33e-11165
hematopoietic multipotent progenitor cell2.33e-11165
granulocyte monocyte progenitor cell3.36e-1171
somatic stem cell5.68e-11436
stem cell1.70e-10444
motile cell4.04e-09390
myeloid cell5.84e-07112
common myeloid progenitor5.84e-07112
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.44e-17112
immune system4.15e-17115
hematopoietic system8.28e-15102
blood island8.28e-15102
connective tissue1.38e-12375
bone marrow2.14e-1180
bone element4.47e-0986
lateral plate mesoderm3.21e-08216
musculoskeletal system3.43e-08167
skeletal element4.33e-08101
skeletal system4.33e-08101


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.