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Coexpression cluster:C3230: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0009409!response to cold!0.0124808665960203!8531$GO:0009266!response to temperature stimulus!0.0226215707052867!8531$GO:0003714!transcription corepressor activity!0.0367739819347025!8531$GO:0003690!double-stranded DNA binding!0.0367739819347025!8531$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0367739819347025!8531$GO:0043566!structure-specific DNA binding!0.0367739819347025!8531$GO:0009628!response to abiotic stimulus!0.0367739819347025!8531$GO:0045892!negative regulation of transcription, DNA-dependent!0.0370959090492824!8531$GO:0016564!transcription repressor activity!0.0370959090492824!8531$GO:0003702!RNA polymerase II transcription factor activity!0.038282658116639!8531$GO:0016481!negative regulation of transcription!0.038282658116639!8531$GO:0003712!transcription cofactor activity!0.038282658116639!8531$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.038282658116639!8531$GO:0031324!negative regulation of cellular metabolic process!0.0400121899695943!8531$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0400121899695943!8531$GO:0008134!transcription factor binding!0.0400121899695943!8531$GO:0009892!negative regulation of metabolic process!0.0400121899695943!8531
|gostat_on_coexpression_clusters=GO:0009409!response to cold!0.0124808665960203!8531$GO:0009266!response to temperature stimulus!0.0226215707052867!8531$GO:0003714!transcription corepressor activity!0.0367739819347025!8531$GO:0003690!double-stranded DNA binding!0.0367739819347025!8531$GO:0000122!negative regulation of transcription from RNA polymerase II promoter!0.0367739819347025!8531$GO:0043566!structure-specific DNA binding!0.0367739819347025!8531$GO:0009628!response to abiotic stimulus!0.0367739819347025!8531$GO:0045892!negative regulation of transcription, DNA-dependent!0.0370959090492824!8531$GO:0016564!transcription repressor activity!0.0370959090492824!8531$GO:0003702!RNA polymerase II transcription factor activity!0.038282658116639!8531$GO:0016481!negative regulation of transcription!0.038282658116639!8531$GO:0003712!transcription cofactor activity!0.038282658116639!8531$GO:0045934!negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.038282658116639!8531$GO:0031324!negative regulation of cellular metabolic process!0.0400121899695943!8531$GO:0006357!regulation of transcription from RNA polymerase II promoter!0.0400121899695943!8531$GO:0008134!transcription factor binding!0.0400121899695943!8531$GO:0009892!negative regulation of metabolic process!0.0400121899695943!8531
|id=C3230
|id=C3230
|ontology_enrichment_celltype=CL:0000860!5.80e-14!45;CL:0002057!3.22e-13!42;CL:0000066!1.08e-09!254;CL:0000076!1.63e-07!62;CL:0002139!3.85e-07!24;CL:0000557!4.19e-07!71;CL:0002009!4.22e-07!65;CL:0000839!7.23e-07!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000926!1.34e-21!448;UBERON:0004120!1.34e-21!448;UBERON:0006603!1.34e-21!448;UBERON:0003081!1.24e-15!216;UBERON:0000468!2.92e-15!659;UBERON:0000467!7.10e-13!625;UBERON:0000480!1.04e-12!626;UBERON:0000922!1.09e-11!612;UBERON:0001009!4.56e-11!113;UBERON:0002050!9.13e-11!605;UBERON:0005423!9.13e-11!605;UBERON:0000923!9.40e-11!604;UBERON:0005291!9.40e-11!604;UBERON:0006598!9.40e-11!604;UBERON:0002532!9.40e-11!604;UBERON:0004535!7.73e-10!110;UBERON:0002193!4.19e-08!112;UBERON:0004872!7.64e-08!84;UBERON:0000055!1.10e-07!69;UBERON:0002204!1.90e-07!167;UBERON:0002390!3.77e-07!102;UBERON:0003061!3.77e-07!102;UBERON:0001981!6.69e-07!60;UBERON:0007500!6.69e-07!60;UBERON:0004537!6.69e-07!60;UBERON:0006965!6.69e-07!60
}}
}}

Revision as of 14:33, 21 May 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>


Uber Anatomy
Ontology termp-valuen
mesoderm1.34e-21448
mesoderm-derived structure1.34e-21448
presumptive mesoderm1.34e-21448
lateral plate mesoderm1.24e-15216
multi-cellular organism2.92e-15659
anatomical system7.10e-13625
anatomical group1.04e-12626
embryo1.09e-11612
circulatory system4.56e-11113
embryonic structure9.13e-11605
developing anatomical structure9.13e-11605
germ layer9.40e-11604
embryonic tissue9.40e-11604
presumptive structure9.40e-11604
epiblast (generic)9.40e-11604
cardiovascular system7.73e-10110
hemolymphoid system4.19e-08112
splanchnic layer of lateral plate mesoderm7.64e-0884
vessel1.10e-0769
musculoskeletal system1.90e-07167
hematopoietic system3.77e-07102
blood island3.77e-07102
blood vessel6.69e-0760
epithelial tube open at both ends6.69e-0760
blood vasculature6.69e-0760
vascular cord6.69e-0760


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.