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Coexpression cluster:C1598: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1598_CD34_CD133_CD4_CD8_Smooth_Cardiac_acute
|full_id=C1598_CD34_CD133_CD4_CD8_Smooth_Cardiac_acute
|gostat_on_coexpression_clusters=GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!0.0405039444248204!6189$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.0405039444248204!6189$GO:0006413!translational initiation!0.0405039444248204!6189$GO:0015935!small ribosomal subunit!0.0405039444248204!6189$GO:0022618!protein-RNA complex assembly!0.0405039444248204!6189$GO:0044445!cytosolic part!0.0405039444248204!6189$GO:0006917!induction of apoptosis!0.0405039444248204!6189$GO:0012502!induction of programmed cell death!0.0405039444248204!6189$GO:0033279!ribosomal subunit!0.0405039444248204!6189$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0405039444248204!6189$GO:0043065!positive regulation of apoptosis!0.0405039444248204!6189$GO:0043068!positive regulation of programmed cell death!0.0405039444248204!6189
|gostat_on_coexpression_clusters=GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!0.0405039444248204!6189$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.0405039444248204!6189$GO:0006413!translational initiation!0.0405039444248204!6189$GO:0015935!small ribosomal subunit!0.0405039444248204!6189$GO:0022618!protein-RNA complex assembly!0.0405039444248204!6189$GO:0044445!cytosolic part!0.0405039444248204!6189$GO:0006917!induction of apoptosis!0.0405039444248204!6189$GO:0012502!induction of programmed cell death!0.0405039444248204!6189$GO:0033279!ribosomal subunit!0.0405039444248204!6189$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0405039444248204!6189$GO:0043065!positive regulation of apoptosis!0.0405039444248204!6189$GO:0043068!positive regulation of programmed cell death!0.0405039444248204!6189

Revision as of 14:11, 12 September 2012


Full id: C1598_CD34_CD133_CD4_CD8_Smooth_Cardiac_acute



Phase1 CAGE Peaks

Hg19::chr10:89705236..89705239,+p1@ENST00000395256
Hg19::chr17:37011443..37011449,+p1@ENST00000462007
Hg19::chr4:138369206..138369216,+p1@ENST00000463671
Hg19::chr4:152020736..152020788,+p1@RPS3A
Hg19::chr9:74204452..74204456,+p1@ENST00000437667


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:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0405039444248204
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0405039444248204
GO:0006413translational initiation0.0405039444248204
GO:0015935small ribosomal subunit0.0405039444248204
GO:0022618protein-RNA complex assembly0.0405039444248204
GO:0044445cytosolic part0.0405039444248204
GO:0006917induction of apoptosis0.0405039444248204
GO:0012502induction of programmed cell death0.0405039444248204
GO:0033279ribosomal subunit0.0405039444248204
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0405039444248204
GO:0043065positive regulation of apoptosis0.0405039444248204
GO:0043068positive regulation of programmed cell death0.0405039444248204



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
hematopoietic lineage restricted progenitor cell5.70e-22124
hematopoietic oligopotent progenitor cell5.77e-20165
hematopoietic multipotent progenitor cell5.77e-20165
hematopoietic stem cell1.02e-19172
angioblastic mesenchymal cell1.02e-19172
leukocyte1.22e-18140
nongranular leukocyte3.91e-18119
classical monocyte9.85e-1845
CD14-positive, CD16-negative classical monocyte1.02e-1742
hematopoietic cell1.29e-16182
myeloid lineage restricted progenitor cell1.67e-1370
macrophage dendritic cell progenitor9.78e-1365
granulocyte monocyte progenitor cell1.45e-1271
myeloid cell3.48e-12112
common myeloid progenitor3.48e-12112
monopoietic cell6.99e-1263
monocyte6.99e-1263
monoblast6.99e-1263
promonocyte6.99e-1263
myeloid leukocyte3.53e-1076
stem cell8.96e-09444
native cell2.75e-08722
lymphoid lineage restricted progenitor cell4.70e-0852
multi fate stem cell5.66e-08430
lymphocyte6.31e-0853
common lymphoid progenitor6.31e-0853
mesenchymal cell7.05e-08358
somatic stem cell7.06e-08436
connective tissue cell1.73e-07365
motile cell5.90e-07390
Uber Anatomy
Ontology termp-valuen
bone marrow1.02e-1180
bone element3.85e-1186
skeletal element1.24e-10101
skeletal system1.24e-10101
musculoskeletal system1.76e-07167
connective tissue2.89e-07375
hematopoietic system4.61e-07102
blood island4.61e-07102


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
KAT2A#26481123.2180.008089481544540810.0319912667283993



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.