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Coexpression cluster:C3311: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!8.48e-07!51;DOID:0060083!8.48e-07!51
|ontology_enrichment_disease=DOID:2531!8.48e-07!51;DOID:0060083!8.48e-07!51
|ontology_enrichment_uberon=UBERON:0002390!2.58e-23!102;UBERON:0003061!2.58e-23!102;UBERON:0002193!2.04e-20!112;UBERON:0002371!3.90e-16!80;UBERON:0001474!2.78e-15!86;UBERON:0002405!9.67e-13!115;UBERON:0004765!1.99e-10!101;UBERON:0001434!1.99e-10!101;UBERON:0007023!2.94e-07!115
|ontology_enrichment_uberon=UBERON:0002390!2.58e-23!102;UBERON:0003061!2.58e-23!102;UBERON:0002193!2.04e-20!112;UBERON:0002371!3.90e-16!80;UBERON:0001474!2.78e-15!86;UBERON:0002405!9.67e-13!115;UBERON:0004765!1.99e-10!101;UBERON:0001434!1.99e-10!101;UBERON:0007023!2.94e-07!115
|tf_chipseq_enrich=BCLAF1#9774;2:14.4350984067479:0.00620114743554613:0.0273763214702203!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329745434945147!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.032893545070923
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}}
}}

Revision as of 13:39, 5 September 2012


Full id: C3311_CD4_CD8_Natural_CD14_Eosinophils_Peripheral_Neutrophils



Phase1 CAGE Peaks

Hg19::chr12:58335137..58335151,-p@chr12:58335137..58335151
-
Hg19::chr22:39098205..39098210,+p@chr22:39098205..39098210
+
Hg19::chr9:100684450..100684473,-p@chr9:100684450..100684473
-


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 cell2.13e-47172
angioblastic mesenchymal cell2.13e-47172
hematopoietic cell1.72e-45182
hematopoietic oligopotent progenitor cell1.30e-43165
hematopoietic multipotent progenitor cell1.30e-43165
leukocyte2.58e-43140
hematopoietic lineage restricted progenitor cell1.20e-35124
nongranular leukocyte2.26e-33119
myeloid cell1.82e-26112
common myeloid progenitor1.82e-26112
classical monocyte5.61e-2445
CD14-positive, CD16-negative classical monocyte6.01e-2442
myeloid leukocyte7.70e-2376
myeloid lineage restricted progenitor cell6.09e-1970
granulocyte monocyte progenitor cell3.04e-1871
macrophage dendritic cell progenitor9.15e-1765
monopoietic cell4.63e-1663
monocyte4.63e-1663
monoblast4.63e-1663
promonocyte4.63e-1663
lymphoid lineage restricted progenitor cell2.05e-1552
lymphocyte2.54e-1553
common lymphoid progenitor2.54e-1553
T cell2.06e-1025
pro-T cell2.06e-1025
mature alpha-beta T cell5.80e-0918
alpha-beta T cell5.80e-0918
immature T cell5.80e-0918
mature T cell5.80e-0918
immature alpha-beta T cell5.80e-0918
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.58e-23102
blood island2.58e-23102
hemolymphoid system2.04e-20112
bone marrow3.90e-1680
bone element2.78e-1586
immune system9.67e-13115
skeletal element1.99e-10101
skeletal system1.99e-10101
adult organism2.94e-07115
Disease
Ontology termp-valuen
hematologic cancer8.48e-0751
immune system cancer8.48e-0751


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
BCLAF1#9774214.43509840674790.006201147435546130.0273763214702203
SMARCB1#6598212.16847718743830.008675002221921740.0329745434945147
TRIM28#10155212.39368336350830.008368344129438470.032893545070923



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3311&oldid=2132456"