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Coexpression cluster:C1340: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!4.02e-30!39;DOID:8692!9.39e-27!31;DOID:2531!8.97e-23!51;DOID:0060083!8.97e-23!51;DOID:1036!9.39e-07!8
|ontology_enrichment_disease=DOID:1240!4.02e-30!39;DOID:8692!9.39e-27!31;DOID:2531!8.97e-23!51;DOID:0060083!8.97e-23!51;DOID:1036!9.39e-07!8
|ontology_enrichment_uberon=UBERON:0002390!6.68e-14!102;UBERON:0003061!6.68e-14!102;UBERON:0002193!2.30e-12!112;UBERON:0007023!1.93e-10!115;UBERON:0002371!1.79e-08!80;UBERON:0001474!3.71e-08!86;UBERON:0002405!3.00e-07!115;UBERON:0002384!4.34e-07!375
|ontology_enrichment_uberon=UBERON:0002390!6.68e-14!102;UBERON:0003061!6.68e-14!102;UBERON:0002193!2.30e-12!112;UBERON:0007023!1.93e-10!115;UBERON:0002371!1.79e-08!80;UBERON:0001474!3.71e-08!86;UBERON:0002405!3.00e-07!115;UBERON:0002384!4.34e-07!375
|tf_chipseq_enrich=USF1#7391;4:4.24099951813864:0.00700536775082942:0.0295992233404351
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}}
}}

Revision as of 13:06, 5 September 2012


Full id: C1340_acute_chronic_granulocyte_leukemia_CD34_Mast_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:36119758..36119765,+p9@LDLRAD3
Hg19::chr16:89043350..89043370,-p5@CBFA2T3
Hg19::chr16:89043377..89043406,-p2@CBFA2T3
Hg19::chr19:55671313..55671321,-p@chr19:55671313..55671321
-
Hg19::chr19:55671322..55671342,-p@chr19:55671322..55671342
-
Hg19::chr5:33229366..33229381,+p2@ENST00000503577


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell2.48e-42172
angioblastic mesenchymal cell2.48e-42172
hematopoietic oligopotent progenitor cell1.01e-38165
hematopoietic multipotent progenitor cell1.01e-38165
hematopoietic cell3.45e-38182
myeloid cell5.16e-30112
common myeloid progenitor5.16e-30112
leukocyte4.76e-20140
hematopoietic lineage restricted progenitor cell4.49e-18124
nongranular leukocyte5.27e-16119
lymphocyte of B lineage1.51e-1224
pro-B cell1.51e-1224
myeloid lineage restricted progenitor cell4.70e-1170
granulocyte monocyte progenitor cell2.12e-1071
myeloid leukocyte3.60e-1076
B cell1.30e-0914
lymphocyte3.22e-0853
common lymphoid progenitor3.22e-0853
lymphoid lineage restricted progenitor cell1.04e-0752
mesenchymal cell1.12e-07358
monopoietic cell2.21e-0763
monocyte2.21e-0763
monoblast2.21e-0763
promonocyte2.21e-0763
macrophage dendritic cell progenitor2.60e-0765
connective tissue cell6.61e-07365
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.68e-14102
blood island6.68e-14102
hemolymphoid system2.30e-12112
adult organism1.93e-10115
bone marrow1.79e-0880
bone element3.71e-0886
immune system3.00e-07115
connective tissue4.34e-07375
Disease
Ontology termp-valuen
leukemia4.02e-3039
myeloid leukemia9.39e-2731
hematologic cancer8.97e-2351
immune system cancer8.97e-2351
chronic leukemia9.39e-078


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
USF1#739144.240999518138640.007005367750829420.0295992233404351



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.