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Coexpression cluster:C3831: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!9.32e-21!51;DOID:0060083!9.32e-21!51;DOID:1240!4.63e-19!39;DOID:8692!1.77e-16!31
|ontology_enrichment_disease=DOID:2531!9.32e-21!51;DOID:0060083!9.32e-21!51;DOID:1240!4.63e-19!39;DOID:8692!1.77e-16!31
|ontology_enrichment_uberon=UBERON:0002390!2.84e-42!102;UBERON:0003061!2.84e-42!102;UBERON:0002193!2.78e-37!112;UBERON:0002371!1.84e-28!80;UBERON:0001474!2.27e-24!86;UBERON:0007023!1.11e-22!115;UBERON:0002405!1.65e-21!115;UBERON:0004765!1.06e-17!101;UBERON:0001434!1.06e-17!101;UBERON:0002384!9.34e-12!375;UBERON:0000178!2.24e-11!15;UBERON:0000179!2.24e-11!15;UBERON:0000463!2.24e-11!15;UBERON:0003081!1.05e-07!216
|ontology_enrichment_uberon=UBERON:0002390!2.84e-42!102;UBERON:0003061!2.84e-42!102;UBERON:0002193!2.78e-37!112;UBERON:0002371!1.84e-28!80;UBERON:0001474!2.27e-24!86;UBERON:0007023!1.11e-22!115;UBERON:0002405!1.65e-21!115;UBERON:0004765!1.06e-17!101;UBERON:0001434!1.06e-17!101;UBERON:0002384!9.34e-12!375;UBERON:0000178!2.24e-11!15;UBERON:0000179!2.24e-11!15;UBERON:0000463!2.24e-11!15;UBERON:0003081!1.05e-07!216
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462341630962943!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294525185172616
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}}
}}

Revision as of 11:54, 5 September 2012


Full id: C3831_granulocyte_CD14_CD14CD16_Neutrophils_acute_Eosinophils_immature



Phase1 CAGE Peaks

Hg19::chr19:7414040..7414081,+p@chr19:7414040..7414081
+
Hg19::chr19:7414085..7414096,+p@chr19:7414085..7414096
+
Hg19::chr7:50344289..50344323,+p1@IKZF1


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 cell6.82e-92172
angioblastic mesenchymal cell6.82e-92172
hematopoietic cell7.52e-87182
hematopoietic oligopotent progenitor cell3.66e-86165
hematopoietic multipotent progenitor cell3.66e-86165
leukocyte2.16e-71140
hematopoietic lineage restricted progenitor cell1.36e-58124
nongranular leukocyte2.28e-57119
myeloid cell8.10e-57112
common myeloid progenitor8.10e-57112
myeloid leukocyte6.79e-3876
granulocyte monocyte progenitor cell3.29e-3371
myeloid lineage restricted progenitor cell4.30e-3270
macrophage dendritic cell progenitor3.58e-3065
monopoietic cell2.71e-2963
monocyte2.71e-2963
monoblast2.71e-2963
promonocyte2.71e-2963
CD14-positive, CD16-negative classical monocyte3.72e-2842
classical monocyte7.81e-2545
lymphocyte5.33e-2453
common lymphoid progenitor5.33e-2453
lymphoid lineage restricted progenitor cell1.82e-2352
mesenchymal cell3.46e-14358
connective tissue cell6.80e-13365
lymphocyte of B lineage1.75e-1224
pro-B cell1.75e-1224
T cell1.29e-1025
pro-T cell1.29e-1025
B cell4.47e-1014
motile cell7.80e-09390
intermediate monocyte8.76e-099
CD14-positive, CD16-positive monocyte8.76e-099
mature alpha-beta T cell1.28e-0818
alpha-beta T cell1.28e-0818
immature T cell1.28e-0818
mature T cell1.28e-0818
immature alpha-beta T cell1.28e-0818
granulocyte7.01e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.84e-42102
blood island2.84e-42102
hemolymphoid system2.78e-37112
bone marrow1.84e-2880
bone element2.27e-2486
adult organism1.11e-22115
immune system1.65e-21115
skeletal element1.06e-17101
skeletal system1.06e-17101
connective tissue9.34e-12375
blood2.24e-1115
haemolymphatic fluid2.24e-1115
organism substance2.24e-1115
lateral plate mesoderm1.05e-07216
Disease
Ontology termp-valuen
hematologic cancer9.32e-2151
immune system cancer9.32e-2151
leukemia4.63e-1939
myeloid leukemia1.77e-1631


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
ELF1#199734.258097958807540.01295179875054610.0462341630962943
MYC#460935.22228187160940.007020843755740150.0294525185172616



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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