Personal tools

Coexpression cluster:C2185

From FANTOM5_SSTAR

Revision as of 14:58, 13 July 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2185_mature_Adipocyte_Hepatocyte_skin_liver_skeletal_left



Phase1 CAGE Peaks

Hg19::chr12:109577279..109577289,+p15@ACACB
Hg19::chr12:109577376..109577404,+p21@ACACB
Hg19::chr20:33464407..33464423,+p1@ACSS2
Hg19::chr4:185726631..185726658,-p@chr4:185726631..185726658
-


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
1.91447319275479e-060.000403953843671262240Pyruvate metabolism (KEGG):00620
1.21740859436715e-060.000385309820117203232Propanoate metabolism (KEGG):00640
5.66978599392766e-070.000358897453415621222Fatty Acid Biosynthesis (Wikipathways):WP357



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:0008610lipid biosynthetic process0.00264916256568538
GO:0003989acetyl-CoA carboxylase activity0.00264916256568538
GO:0004075biotin carboxylase activity0.00264916256568538
GO:0016421CoA carboxylase activity0.00298004468581734
GO:0016874ligase activity0.00298004468581734
GO:0016885ligase activity, forming carbon-carbon bonds0.00298004468581734
GO:0044255cellular lipid metabolic process0.00298004468581734
GO:0003987acetate-CoA ligase activity0.00298004468581734
GO:0016405CoA-ligase activity0.00348582846459488
GO:0006629lipid metabolic process0.00348582846459488
GO:0009374biotin binding0.00419351958115085
GO:0016878acid-thiol ligase activity0.00419351958115085
GO:0016208AMP binding0.00427828266515267
GO:0016877ligase activity, forming carbon-sulfur bonds0.00529637549745431
GO:0006633fatty acid biosynthetic process0.0128793076472514
GO:0046394carboxylic acid biosynthetic process0.0129189165628106
GO:0016053organic acid biosynthetic process0.0129189165628106
GO:0009058biosynthetic process0.0130401524453593
GO:0032559adenyl ribonucleotide binding0.0162566837917713
GO:0030554adenyl nucleotide binding0.0167888630484699
GO:0030145manganese ion binding0.0185048333400419
GO:0032553ribonucleotide binding0.0206711729655838
GO:0032555purine ribonucleotide binding0.0206711729655838
GO:0006631fatty acid metabolic process0.0206711729655838
GO:0017076purine nucleotide binding0.0206711729655838
GO:0019842vitamin binding0.0248743443344147
GO:0000166nucleotide binding0.026251361438029
GO:0032787monocarboxylic acid metabolic process0.0270404086116589
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0337074386028396



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
CD14-positive, CD16-negative classical monocyte6.02e-0842
classical monocyte9.40e-0845
fat cell5.89e-0715
macrophage dendritic cell progenitor8.69e-0765
Uber Anatomy
Ontology termp-valuen
embryonic structure5.58e-22605
developing anatomical structure5.58e-22605
germ layer7.24e-22604
embryonic tissue7.24e-22604
presumptive structure7.24e-22604
epiblast (generic)7.24e-22604
embryo4.82e-21612
organ1.25e-20511
anatomical system2.15e-20625
anatomical group2.18e-20626
multi-cellular organism1.69e-19659
mesoderm6.15e-14448
mesoderm-derived structure6.15e-14448
presumptive mesoderm6.15e-14448
multi-tissue structure2.03e-12347
endoderm-derived structure8.59e-11169
endoderm8.59e-11169
presumptive endoderm8.59e-11169
mesenchyme3.81e-10238
entire embryonic mesenchyme3.81e-10238
digestive system1.33e-09155
digestive tract1.33e-09155
primitive gut1.33e-09155
epithelium3.01e-09309
cell layer7.98e-09312
trunk1.21e-08216
adult organism2.03e-08115
trunk region element3.11e-08107
subdivision of digestive tract4.69e-08129
endodermal part of digestive tract4.69e-08129
organism subdivision6.04e-08365
anatomical cluster6.37e-08286
compound organ1.51e-0769
immune system4.87e-07115
subdivision of trunk5.26e-07113
trunk mesenchyme6.39e-07143
mixed endoderm/mesoderm-derived structure8.83e-07130


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.