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Coexpression cluster:C2310: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!2.00e-14!7;UBERON:0002106!7.51e-10!3;UBERON:0004854!7.51e-10!3;UBERON:0009034!7.51e-10!3;UBERON:0002095!7.51e-10!3;UBERON:0004782!7.51e-10!3;UBERON:0003281!7.51e-10!3;UBERON:0009664!7.51e-10!3;UBERON:0002296!7.51e-10!3;UBERON:0005602!7.51e-10!3;UBERON:0001179!7.51e-10!3;UBERON:0006293!7.51e-10!3;UBERON:0000974!1.81e-09!10
|ontology_enrichment_uberon=UBERON:0004177!2.00e-14!7;UBERON:0002106!7.51e-10!3;UBERON:0004854!7.51e-10!3;UBERON:0009034!7.51e-10!3;UBERON:0002095!7.51e-10!3;UBERON:0004782!7.51e-10!3;UBERON:0003281!7.51e-10!3;UBERON:0009664!7.51e-10!3;UBERON:0002296!7.51e-10!3;UBERON:0005602!7.51e-10!3;UBERON:0001179!7.51e-10!3;UBERON:0006293!7.51e-10!3;UBERON:0000974!1.81e-09!10
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296184611657696!CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297215017452622!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199437159671785!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428290763384231!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428305717670662!SMARCC1#6599;2:21.8316796598157:0.00305120745616205:0.0160925692108932!SMARCC2#6601;2:47.0776872134488:0.000666928296709587:0.00544975544793463!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613061238862465
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}}
}}

Revision as of 12:40, 5 September 2012


Full id: C2310_splenic_hereditary_thyroid_B_lymphangiectasia_plasma_throat



Phase1 CAGE Peaks

Hg19::chr14:72944640..72944682,+p@chr14:72944640..72944682
+
Hg19::chr3:58200719..58200729,-p16@DNASE1L3
Hg19::chr3:58200737..58200748,-p14@DNASE1L3
Hg19::chr8:21344673..21344682,-p@chr8:21344673..21344682
-


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
astrocyte of the cerebral cortex4.00e-103
plasmacytoid dendritic cell4.80e-103
lymphocyte of B lineage4.50e-0924
pro-B cell4.50e-0924
oligodendrocyte4.33e-077
macroglial cell4.33e-077
astrocyte4.33e-077
oligodendrocyte precursor cell4.33e-077
Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.00e-147
spleen7.51e-103
gastrointestinal system mesentery7.51e-103
stomach region7.51e-103
mesentery7.51e-103
gastrointestinal system serosa7.51e-103
mesentery of stomach7.51e-103
gut mesentery7.51e-103
dorsal mesentery7.51e-103
dorsal mesogastrium7.51e-103
peritoneal cavity7.51e-103
spleen primordium7.51e-103
neck1.81e-0910


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
BCL11A#53335214.18472755180350.007108328585298740.0296184611657696
CEBPB#105135.978360719368610.007153832484726970.0297215017452622
EBF1#187948.9064668465690.00015887907472010.00199437159671785
IRF4#3662210.95725634337210.01174530180688030.0428290763384231
PBX3#5090210.95725634337210.01174530180688030.0428305717670662
SMARCC1#6599221.83167965981570.003051207456162050.0160925692108932
SMARCC2#6601247.07768721344880.0006669282967095870.00544975544793463
ZEB1#6935312.66632401315790.000793336075912850.00613061238862465



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.

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