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Coexpression cluster:C4169: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!4.10e-17!375;UBERON:0002204!8.00e-13!167;UBERON:0004765!1.53e-10!101;UBERON:0001434!1.53e-10!101;UBERON:0000926!8.75e-10!448;UBERON:0004120!8.75e-10!448;UBERON:0006603!8.75e-10!448;UBERON:0002371!8.88e-09!80;UBERON:0001474!5.93e-08!86;UBERON:0001637!8.52e-08!42;UBERON:0003509!8.52e-08!42;UBERON:0004572!8.52e-08!42;UBERON:0001737!2.45e-07!9;UBERON:0003081!6.56e-07!216;UBERON:0002390!8.14e-07!102;UBERON:0003061!8.14e-07!102;UBERON:0002193!9.71e-07!112
|ontology_enrichment_uberon=UBERON:0002384!4.10e-17!375;UBERON:0002204!8.00e-13!167;UBERON:0004765!1.53e-10!101;UBERON:0001434!1.53e-10!101;UBERON:0000926!8.75e-10!448;UBERON:0004120!8.75e-10!448;UBERON:0006603!8.75e-10!448;UBERON:0002371!8.88e-09!80;UBERON:0001474!5.93e-08!86;UBERON:0001637!8.52e-08!42;UBERON:0003509!8.52e-08!42;UBERON:0004572!8.52e-08!42;UBERON:0001737!2.45e-07!9;UBERON:0003081!6.56e-07!216;UBERON:0002390!8.14e-07!102;UBERON:0003061!8.14e-07!102;UBERON:0002193!9.71e-07!112
|tf_chipseq_enrich=BCL3#602;2:23.0314018691589:0.00246467476084291:0.0138562828953907!BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296331884613301!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0402048415484625!GTF2B#2959;2:21.2958866228828:0.00287818058991141:0.0155853322253205!SIX5#147912;2:11.391143570306:0.00987382008142903:0.037083281627027!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156401998574525
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}}
}}

Revision as of 12:53, 5 September 2012


Full id: C4169_Mast_CD14_large_migratory_Synoviocyte_immature_Mammary



Phase1 CAGE Peaks

Hg19::chr2:201676600..201676667,+p1@BZW1
Hg19::chr2:201676675..201676692,+p3@BZW1
Hg19::chr3:172144898..172144914,-p1@BZW1P1


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


GO IDGO nameFDR corrected p-value
GO:0006446regulation of translational initiation0.0351318733074296
GO:0006413translational initiation0.0351318733074296
GO:0003743translation initiation factor activity0.0351318733074296
GO:0022618protein-RNA complex assembly0.0351318733074296
GO:0006417regulation of translation0.0351318733074296
GO:0031326regulation of cellular biosynthetic process0.0351318733074296
GO:0008135translation factor activity, nucleic acid binding0.0351318733074296
GO:0009889regulation of biosynthetic process0.0351318733074296
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0354017033635543



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><br>


Cell Type
Ontology termp-valuen
animal cell2.74e-35679
eukaryotic cell2.74e-35679
native cell2.08e-27722
somatic stem cell8.58e-27436
multi fate stem cell1.37e-26430
somatic cell1.67e-26591
stem cell4.74e-26444
connective tissue cell1.47e-18365
mesenchymal cell5.06e-18358
classical monocyte1.74e-1345
motile cell2.02e-12390
CD14-positive, CD16-negative classical monocyte2.48e-1242
myeloid leukocyte4.20e-1276
granulocyte monocyte progenitor cell8.02e-1071
leukocyte8.84e-10140
macrophage dendritic cell progenitor1.78e-0965
myeloid lineage restricted progenitor cell2.40e-0970
monopoietic cell8.74e-0963
monocyte8.74e-0963
monoblast8.74e-0963
promonocyte8.74e-0963
fibroblast1.37e-0775
non-terminally differentiated cell1.55e-07180
hematopoietic lineage restricted progenitor cell5.29e-07124
myeloid cell7.16e-07112
common myeloid progenitor7.16e-07112
Uber Anatomy
Ontology termp-valuen
connective tissue4.10e-17375
musculoskeletal system8.00e-13167
skeletal element1.53e-10101
skeletal system1.53e-10101
mesoderm8.75e-10448
mesoderm-derived structure8.75e-10448
presumptive mesoderm8.75e-10448
bone marrow8.88e-0980
bone element5.93e-0886
artery8.52e-0842
arterial blood vessel8.52e-0842
arterial system8.52e-0842
larynx2.45e-079
lateral plate mesoderm6.56e-07216
hematopoietic system8.14e-07102
blood island8.14e-07102
hemolymphoid system9.71e-07112


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
BCL3#602223.03140186915890.002464674760842910.0138562828953907
BRCA1#672213.45615376214920.007119807716084560.0296331884613301
ELK4#2005210.8237877723120.01091284719516480.0402048415484625
GTF2B#2959221.29588662288280.002878180589911410.0155853322253205
SIX5#147912211.3911435703060.009873820081429030.037083281627027
ZBTB33#10009221.10981668665410.002928597060603240.0156401998574525



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.