Personal tools

Coexpression cluster:C4437: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS |id=C4437 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS
|full_id=C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS
|id=C4437
|id=C4437
|ontology_enrichment_celltype=CL:0002139!1.17e-33!24;CL:0000213!2.17e-29!57;CL:0000215!2.17e-29!57;CL:0000115!2.49e-29!35;CL:0000071!5.39e-25!18;CL:0002546!5.39e-25!18;CL:0002078!5.85e-25!44;CL:0002321!1.49e-19!248;CL:0000220!3.04e-18!246;CL:0000222!9.81e-16!119;CL:1000413!2.08e-15!9;CL:0000076!2.33e-12!62;CL:0000066!1.05e-11!254;CL:0002544!7.16e-11!6;CL:0002543!8.42e-11!6;CL:0005020!3.35e-10!6;CL:0002138!3.35e-10!6;CL:0005022!3.35e-10!6;CL:0002322!8.83e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001986!5.39e-25!18;UBERON:0004638!5.39e-25!18;UBERON:0004852!5.39e-25!18;UBERON:0000487!3.19e-24!22;UBERON:0006914!1.65e-20!25;UBERON:0002049!5.25e-19!79;UBERON:0007798!5.25e-19!79;UBERON:0000055!1.16e-18!69;UBERON:0003915!2.08e-15!9;UBERON:0004700!2.08e-15!9;UBERON:0001917!2.08e-15!9;UBERON:0001981!3.60e-14!60;UBERON:0007500!3.60e-14!60;UBERON:0004537!3.60e-14!60;UBERON:0006965!3.60e-14!60;UBERON:0004535!6.19e-12!110;UBERON:0001009!2.61e-11!113;UBERON:0004872!4.24e-10!84;UBERON:0003914!1.33e-09!118;UBERON:0001638!1.22e-08!9;UBERON:0003920!1.22e-08!9;UBERON:0004582!1.22e-08!9;UBERON:0001637!1.42e-08!42;UBERON:0003509!1.42e-08!42;UBERON:0004572!1.42e-08!42;UBERON:0001473!2.35e-07!8;UBERON:0004536!2.35e-07!8;UBERON:0006558!2.35e-07!8;UBERON:0000947!4.94e-07!21;UBERON:0010191!4.94e-07!21
}}
}}

Revision as of 14:48, 21 May 2012


Full id: C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS



Phase1 CAGE Peaks

Hg19::chr4:85791617..85791626,-p@chr4:85791617..85791626
-
Hg19::chr4:85791647..85791659,-p@chr4:85791647..85791659
-
Hg19::chr4:85791667..85791699,-p@chr4:85791667..85791699
-


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>


Uber Anatomy
Ontology termp-valuen
endothelium5.39e-2518
blood vessel endothelium5.39e-2518
cardiovascular system endothelium5.39e-2518
simple squamous epithelium3.19e-2422
squamous epithelium1.65e-2025
vasculature5.25e-1979
vascular system5.25e-1979
vessel1.16e-1869
endothelial tube2.08e-159
arterial system endothelium2.08e-159
endothelium of artery2.08e-159
blood vessel3.60e-1460
epithelial tube open at both ends3.60e-1460
blood vasculature3.60e-1460
vascular cord3.60e-1460
cardiovascular system6.19e-12110
circulatory system2.61e-11113
splanchnic layer of lateral plate mesoderm4.24e-1084
epithelial tube1.33e-09118
vein1.22e-089
venous blood vessel1.22e-089
venous system1.22e-089
artery1.42e-0842
arterial blood vessel1.42e-0842
arterial system1.42e-0842
lymphatic vessel2.35e-078
lymph vasculature2.35e-078
lymphatic part of lymphoid system2.35e-078
aorta4.94e-0721
aortic system4.94e-0721


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.