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Coexpression cluster:C3230: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000926!1.59e-14!315;UBERON:0004120!1.59e-14!315;UBERON:0006603!1.59e-14!315;UBERON:0003081!1.06e-12!203;UBERON:0001009!7.29e-12!112;UBERON:0000468!1.63e-11!656;UBERON:0004535!1.36e-10!109;UBERON:0000467!2.34e-09!624;UBERON:0000480!2.49e-09!625;UBERON:0000055!5.64e-09!68;UBERON:0007500!3.59e-08!59;UBERON:0001981!3.59e-08!59;UBERON:0004537!3.59e-08!59;UBERON:0006965!3.59e-08!59;UBERON:0004872!3.86e-08!83;UBERON:0000922!6.44e-08!592;UBERON:0002050!1.38e-07!564;UBERON:0000923!1.76e-07!560;UBERON:0010316!1.76e-07!560;UBERON:0005291!1.76e-07!560;UBERON:0006598!1.76e-07!560;UBERON:0010317!1.76e-07!560;UBERON:0002532!1.76e-07!560;UBERON:0005423!1.81e-07!581;UBERON:0002049!2.12e-07!78;UBERON:0007798!2.12e-07!78
|ontology_enrichment_uberon=UBERON:0000926!1.59e-14!315;UBERON:0004120!1.59e-14!315;UBERON:0006603!1.59e-14!315;UBERON:0003081!1.06e-12!203;UBERON:0001009!7.29e-12!112;UBERON:0000468!1.63e-11!656;UBERON:0004535!1.36e-10!109;UBERON:0000467!2.34e-09!624;UBERON:0000480!2.49e-09!625;UBERON:0000055!5.64e-09!68;UBERON:0007500!3.59e-08!59;UBERON:0001981!3.59e-08!59;UBERON:0004537!3.59e-08!59;UBERON:0006965!3.59e-08!59;UBERON:0004872!3.86e-08!83;UBERON:0000922!6.44e-08!592;UBERON:0002050!1.38e-07!564;UBERON:0000923!1.76e-07!560;UBERON:0010316!1.76e-07!560;UBERON:0005291!1.76e-07!560;UBERON:0006598!1.76e-07!560;UBERON:0010317!1.76e-07!560;UBERON:0002532!1.76e-07!560;UBERON:0005423!1.81e-07!581;UBERON:0002049!2.12e-07!78;UBERON:0007798!2.12e-07!78
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}}
}}

Revision as of 16:00, 26 November 2012


Full id: C3230_skeletal_Whole_blood_tongue_heart_penis_left



Phase1 CAGE Peaks

Hg19::chr12:10865870..10865888,-p6@CSDA
Hg19::chr12:10865922..10865934,-p15@CSDA
Hg19::chr16:31581029..31581037,-p1@CSDAP1


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


GO IDGO nameFDR corrected p-value
GO:0009409response to cold0.0124808665960203
GO:0009266response to temperature stimulus0.0226215707052867
GO:0003714transcription corepressor activity0.0367739819347025
GO:0003690double-stranded DNA binding0.0367739819347025
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0367739819347025
GO:0043566structure-specific DNA binding0.0367739819347025
GO:0009628response to abiotic stimulus0.0367739819347025
GO:0045892negative regulation of transcription, DNA-dependent0.0370959090492824
GO:0016564transcription repressor activity0.0370959090492824
GO:0003702RNA polymerase II transcription factor activity0.038282658116639
GO:0016481negative regulation of transcription0.038282658116639
GO:0003712transcription cofactor activity0.038282658116639
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.038282658116639
GO:0031324negative regulation of cellular metabolic process0.0400121899695943
GO:0006357regulation of transcription from RNA polymerase II promoter0.0400121899695943
GO:0008134transcription factor binding0.0400121899695943
GO:0009892negative regulation of metabolic process0.0400121899695943



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
classical monocyte5.60e-1142
CD14-positive, CD16-negative classical monocyte5.60e-1142
defensive cell3.86e-0948
phagocyte3.86e-0948
epithelial cell1.32e-08253
squamous epithelial cell1.44e-0763
Uber Anatomy
Ontology termp-valuen
mesoderm1.59e-14315
mesoderm-derived structure1.59e-14315
presumptive mesoderm1.59e-14315
lateral plate mesoderm1.06e-12203
circulatory system7.29e-12112
multi-cellular organism1.63e-11656
cardiovascular system1.36e-10109
anatomical system2.34e-09624
anatomical group2.49e-09625
vessel5.64e-0968
epithelial tube open at both ends3.59e-0859
blood vessel3.59e-0859
blood vasculature3.59e-0859
vascular cord3.59e-0859
splanchnic layer of lateral plate mesoderm3.86e-0883
embryo6.44e-08592
embryonic structure1.38e-07564
germ layer1.76e-07560
germ layer / neural crest1.76e-07560
embryonic tissue1.76e-07560
presumptive structure1.76e-07560
germ layer / neural crest derived structure1.76e-07560
epiblast (generic)1.76e-07560
developing anatomical structure1.81e-07581
vasculature2.12e-0778
vascular system2.12e-0778


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)

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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.