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Coexpression cluster:C2278: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!1.58e-35!76;UBERON:0002405!3.78e-33!93;UBERON:0001474!1.21e-32!82;UBERON:0002390!4.31e-31!98;UBERON:0003061!4.31e-31!98;UBERON:0002193!1.74e-30!108;UBERON:0004765!5.30e-28!90;UBERON:0001434!2.26e-26!100;UBERON:0002204!9.57e-10!167;UBERON:0003081!2.46e-07!203;UBERON:0000062!5.23e-07!503
|ontology_enrichment_uberon=UBERON:0002371!1.58e-35!76;UBERON:0002405!3.78e-33!93;UBERON:0001474!1.21e-32!82;UBERON:0002390!4.31e-31!98;UBERON:0003061!4.31e-31!98;UBERON:0002193!1.74e-30!108;UBERON:0004765!5.30e-28!90;UBERON:0001434!2.26e-26!100;UBERON:0002204!9.57e-10!167;UBERON:0003081!2.46e-07!203;UBERON:0000062!5.23e-07!503
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}}
}}

Revision as of 15:24, 26 November 2012


Full id: C2278_squamous_CD14_embryonic_mesothelioma_malignant_Monocytederived_glassy



Phase1 CAGE Peaks

Hg19::chr14:103602720..103602729,+p27@TNFAIP2
Hg19::chr14:103602735..103602746,+p9@TNFAIP2
Hg19::chr14:103602748..103602769,+p8@TNFAIP2
Hg19::chr14:103602772..103602786,+p15@TNFAIP2


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
defensive cell5.30e-4548
phagocyte5.30e-4548
macrophage dendritic cell progenitor1.10e-4361
monopoietic cell1.13e-4359
monocyte1.13e-4359
monoblast1.13e-4359
promonocyte1.13e-4359
granulocyte monocyte progenitor cell5.22e-4167
classical monocyte5.69e-4142
CD14-positive, CD16-negative classical monocyte5.69e-4142
myeloid leukocyte2.28e-4072
myeloid lineage restricted progenitor cell5.57e-4066
myeloid cell6.31e-27108
common myeloid progenitor6.31e-27108
leukocyte1.02e-20136
stuff accumulating cell1.52e-2087
nongranular leukocyte7.90e-20115
hematopoietic lineage restricted progenitor cell5.73e-18120
hematopoietic stem cell7.83e-15168
angioblastic mesenchymal cell7.83e-15168
hematopoietic oligopotent progenitor cell3.76e-14161
hematopoietic multipotent progenitor cell3.76e-14161
hematopoietic cell4.56e-13177
Uber Anatomy
Ontology termp-valuen
bone marrow1.58e-3576
immune system3.78e-3393
bone element1.21e-3282
hematopoietic system4.31e-3198
blood island4.31e-3198
hemolymphoid system1.74e-30108
skeletal element5.30e-2890
skeletal system2.26e-26100
musculoskeletal system9.57e-10167
lateral plate mesoderm2.46e-07203
organ5.23e-07503
Disease
Ontology termp-valuen
cell type cancer6.79e-10143
carcinoma4.74e-08106


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)

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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.