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Coexpression cluster:C3179: Difference between revisions

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|full_id=C3179_smooth_aorta_heart_vagina_umbilical_bladder_left
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|ontology_enrichment_celltype=CL:0000055!3.42e-09!180;CL:0000222!1.75e-08!119;CL:0000057!2.33e-07!75
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|ontology_enrichment_uberon=UBERON:0007023!3.25e-18!115;UBERON:0000477!6.76e-18!286;UBERON:0004111!1.23e-17!241;UBERON:0000468!8.50e-17!659;UBERON:0000025!1.88e-14!194;UBERON:0000467!3.11e-14!625;UBERON:0000475!5.32e-14!365;UBERON:0000480!5.65e-14!626;UBERON:0000481!5.71e-14!347;UBERON:0000483!2.65e-12!309;UBERON:0000119!4.33e-12!312;UBERON:0004872!6.23e-12!84;UBERON:0003914!2.47e-11!118;UBERON:0000055!2.86e-09!69;UBERON:0000062!3.75e-09!511;UBERON:0005256!6.56e-09!143;UBERON:0001981!1.01e-08!60;UBERON:0007500!1.01e-08!60;UBERON:0004537!1.01e-08!60;UBERON:0006965!1.01e-08!60;UBERON:0002100!1.35e-08!216;UBERON:0002049!1.89e-08!79;UBERON:0007798!1.89e-08!79;UBERON:0000064!2.42e-08!219;UBERON:0003103!9.28e-08!69;UBERON:0003104!9.47e-08!238;UBERON:0009142!9.47e-08!238;UBERON:0001009!1.76e-07!113;UBERON:0000922!3.86e-07!612;UBERON:0002417!7.21e-07!61;UBERON:0000916!7.21e-07!61
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Revision as of 14:33, 21 May 2012


Full id: C3179_smooth_aorta_heart_vagina_umbilical_bladder_left



Phase1 CAGE Peaks

Hg19::chr11:6340354..6340378,+p@chr11:6340354..6340378
+
Hg19::chr11:6340392..6340420,+p@chr11:6340392..6340420
+
Hg19::chr2:128433033..128433085,-p2@LIMS2


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><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell3.42e-09180
mesodermal cell1.75e-08119
fibroblast2.33e-0775
Uber Anatomy
Ontology termp-valuen
adult organism3.25e-18115
anatomical cluster6.76e-18286
anatomical conduit1.23e-17241
multi-cellular organism8.50e-17659
tube1.88e-14194
anatomical system3.11e-14625
organism subdivision5.32e-14365
anatomical group5.65e-14626
multi-tissue structure5.71e-14347
epithelium2.65e-12309
cell layer4.33e-12312
splanchnic layer of lateral plate mesoderm6.23e-1284
epithelial tube2.47e-11118
vessel2.86e-0969
organ3.75e-09511
trunk mesenchyme6.56e-09143
blood vessel1.01e-0860
epithelial tube open at both ends1.01e-0860
blood vasculature1.01e-0860
vascular cord1.01e-0860
trunk1.35e-08216
vasculature1.89e-0879
vascular system1.89e-0879
organ part2.42e-08219
compound organ9.28e-0869
mesenchyme9.47e-08238
entire embryonic mesenchyme9.47e-08238
circulatory system1.76e-07113
embryo3.86e-07612
abdominal segment of trunk7.21e-0761
abdomen7.21e-0761


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.