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Coexpression cluster:C668: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.26e-47!115;UBERON:0002390!1.33e-10!102;UBERON:0003061!1.33e-10!102;UBERON:0002193!6.89e-10!112;UBERON:0000178!7.41e-09!15;UBERON:0000179!7.41e-09!15;UBERON:0000463!7.41e-09!15
|ontology_enrichment_uberon=UBERON:0007023!5.26e-47!115;UBERON:0002390!1.33e-10!102;UBERON:0003061!1.33e-10!102;UBERON:0002193!6.89e-10!112;UBERON:0000178!7.41e-09!15;UBERON:0000179!7.41e-09!15;UBERON:0000463!7.41e-09!15
|tf_chipseq_enrich=POLR2A#5430;13:2.14745317655807:4.83928878402115e-05:0.000840949220157046!POU2F2#5452;12:8.40565297637771:3.58336042559485e-11:4.10804148725248e-09!TAF1#6872;13:3.34304628574529:1.53362599454097e-07:8.60668271057841e-06
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}}
}}

Revision as of 12:47, 5 September 2012


Full id: C668_lymphangiectasia_lymph_submaxillary_appendix_vein_CD19_lymphoma



Phase1 CAGE Peaks

Hg19::chr2:89156701..89156711,-p@chr2:89156701..89156711
-
Hg19::chr2:89156772..89156782,-p@chr2:89156772..89156782
-
Hg19::chr2:89156903..89156965,+p1@CU688247
p1@CU689025
p1@CU689831
p1@CU689833
p1@CU689835
p1@CU691143
Hg19::chr2:89156917..89156926,-p7@AJ294735
Hg19::chr2:89156940..89156955,-p6@AJ294735
Hg19::chr2:89156976..89157016,+p4@CU688247
p4@CU689025
p4@CU689831
p4@CU689833
p4@CU689835
p4@CU691143
Hg19::chr2:89156995..89157014,-p4@AJ294735
Hg19::chr2:89157015..89157033,-p5@AJ294735
Hg19::chr2:89157041..89157057,-p3@AJ294735
Hg19::chr2:89157058..89157093,-p1@AJ294735
Hg19::chr2:89157095..89157160,-p2@AJ294735
Hg19::chr2:89157161..89157206,-p1@IGKC
Hg19::chr3:186714356..186714377,+p6@ST6GAL1


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:0006955immune response0.00220245711669294
GO:0002376immune system process0.00220245711669294
GO:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.00765268573207231
GO:0009311oligosaccharide metabolic process0.0315506045610944
GO:0032393MHC class I receptor activity0.0363138866499496
GO:0008373sialyltransferase activity0.0363138866499496
GO:0030173integral to Golgi membrane0.0477293874861276
GO:0031228intrinsic to Golgi membrane0.0477293874861276
GO:0006959humoral immune response0.0477293874861276



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
adult organism5.26e-47115
hematopoietic system1.33e-10102
blood island1.33e-10102
hemolymphoid system6.89e-10112
blood7.41e-0915
haemolymphatic fluid7.41e-0915
organism substance7.41e-0915


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
POLR2A#5430132.147453176558074.83928878402115e-050.000840949220157046
POU2F2#5452128.405652976377713.58336042559485e-114.10804148725248e-09
TAF1#6872133.343046285745291.53362599454097e-078.60668271057841e-06



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.