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Coexpression cluster:C1598: Difference between revisions

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|tf_chipseq_enrich=KAT2A#2648;1:123.218:0.00808948154454081:0.0319912667283993
|tf_chipseq_enrich=KAT2A#2648;1:123.218:0.00808948154454081:0.0319912667283993
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}}
}}

Revision as of 14:59, 26 November 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 cell9.47e-24120
hematopoietic stem cell1.47e-21168
angioblastic mesenchymal cell1.47e-21168
leukocyte1.68e-21136
nongranular leukocyte4.48e-21115
hematopoietic oligopotent progenitor cell6.64e-21161
hematopoietic multipotent progenitor cell6.64e-21161
hematopoietic cell5.89e-19177
classical monocyte5.35e-1842
CD14-positive, CD16-negative classical monocyte5.35e-1842
defensive cell6.45e-1648
phagocyte6.45e-1648
myeloid lineage restricted progenitor cell8.62e-1466
macrophage dendritic cell progenitor4.51e-1361
granulocyte monocyte progenitor cell8.63e-1367
monopoietic cell3.15e-1259
monocyte3.15e-1259
monoblast3.15e-1259
promonocyte3.15e-1259
myeloid cell1.43e-11108
common myeloid progenitor1.43e-11108
stuff accumulating cell1.73e-1187
nucleate cell1.48e-1055
myeloid leukocyte2.08e-1072
stem cell3.80e-10441
native cell5.28e-10722
lymphocyte1.30e-0953
common lymphoid progenitor1.30e-0953
lymphoid lineage restricted progenitor cell2.01e-0952
multi fate stem cell3.23e-09427
somatic stem cell3.56e-09433
mesenchymal cell3.59e-09354
connective tissue cell6.75e-09361
animal cell2.52e-08679
eukaryotic cell2.52e-08679
motile cell3.19e-08386
Uber Anatomy
Ontology termp-valuen
skeletal element4.55e-1290
bone marrow7.03e-1276
bone element1.26e-1182
skeletal system1.60e-10100
immune system2.22e-0993
connective tissue1.38e-08371
hematopoietic system6.17e-0898
blood island6.17e-0898
musculoskeletal system1.30e-07167
hemolymphoid system9.69e-07108


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.