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Coexpression cluster:C4849: Difference between revisions

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|full_id=C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9
|full_id=C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9
|id=C4849
|id=C4849
|ontology_enrichment_celltype=CL:0000037!3.61e-55!172;CL:0000566!3.61e-55!172;CL:0002032!5.29e-52!165;CL:0000837!5.29e-52!165;CL:0000988!8.63e-51!182;CL:0000738!7.37e-40!140;CL:0002087!1.66e-34!119;CL:0002031!2.77e-34!124;CL:0000763!1.52e-32!112;CL:0000049!1.52e-32!112;CL:0000766!3.16e-21!76;CL:0000860!1.53e-19!45;CL:0002057!2.40e-19!42;CL:0000557!4.73e-18!71;CL:0000839!2.62e-17!70;CL:0000542!6.82e-17!53;CL:0000051!6.82e-17!53;CL:0000838!7.51e-17!52;CL:0002194!5.03e-16!63;CL:0000576!5.03e-16!63;CL:0000040!5.03e-16!63;CL:0000559!5.03e-16!63;CL:0002009!7.93e-16!65;CL:0000063!4.16e-09!578;CL:0000084!1.98e-08!25;CL:0000827!1.98e-08!25;CL:0000945!2.53e-08!24;CL:0000826!2.53e-08!24;CL:0000134!5.63e-07!358
|ontology_enrichment_disease=DOID:2531!3.36e-18!51;DOID:0060083!3.36e-18!51;DOID:1240!9.81e-16!39;DOID:8692!1.22e-13!31;DOID:162!3.58e-13!235;DOID:14566!7.37e-13!239;DOID:0050686!4.49e-11!137;DOID:305!1.40e-07!106
|ontology_enrichment_uberon=UBERON:0002390!1.15e-21!102;UBERON:0003061!1.15e-21!102;UBERON:0002193!1.90e-16!112;UBERON:0002371!1.99e-15!80;UBERON:0001474!6.04e-15!86;UBERON:0004765!7.48e-12!101;UBERON:0001434!7.48e-12!101;UBERON:0002405!3.11e-08!115
}}
}}

Revision as of 14:53, 21 May 2012


Full id: C4849_CD14_Mesothelial_Mast_acute_lymphoma_rhabdomyosarcoma_H9



Phase1 CAGE Peaks

Hg19::chrX:131157290..131157309,+p2@MST4
Hg19::chrX:131157322..131157339,+p1@MST4
Hg19::chrX:131157354..131157369,+p3@MST4


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 cell3.61e-55172
angioblastic mesenchymal cell3.61e-55172
hematopoietic oligopotent progenitor cell5.29e-52165
hematopoietic multipotent progenitor cell5.29e-52165
hematopoietic cell8.63e-51182
leukocyte7.37e-40140
nongranular leukocyte1.66e-34119
hematopoietic lineage restricted progenitor cell2.77e-34124
myeloid cell1.52e-32112
common myeloid progenitor1.52e-32112
myeloid leukocyte3.16e-2176
classical monocyte1.53e-1945
CD14-positive, CD16-negative classical monocyte2.40e-1942
granulocyte monocyte progenitor cell4.73e-1871
myeloid lineage restricted progenitor cell2.62e-1770
lymphocyte6.82e-1753
common lymphoid progenitor6.82e-1753
lymphoid lineage restricted progenitor cell7.51e-1752
monopoietic cell5.03e-1663
monocyte5.03e-1663
monoblast5.03e-1663
promonocyte5.03e-1663
macrophage dendritic cell progenitor7.93e-1665
T cell1.98e-0825
pro-T cell1.98e-0825
lymphocyte of B lineage2.53e-0824
pro-B cell2.53e-0824
mesenchymal cell5.63e-07358
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.15e-21102
blood island1.15e-21102
hemolymphoid system1.90e-16112
bone marrow1.99e-1580
bone element6.04e-1586
skeletal element7.48e-12101
skeletal system7.48e-12101
immune system3.11e-08115
Disease
Ontology termp-valuen
hematologic cancer3.36e-1851
immune system cancer3.36e-1851
leukemia9.81e-1639
myeloid leukemia1.22e-1331
cancer3.58e-13235
disease of cellular proliferation7.37e-13239
organ system cancer4.49e-11137
carcinoma1.40e-07106


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


No analysis results for this cluster

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.