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Coexpression cluster:C632: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte
|full_id=C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte
|id=C632
|id=C632

Revision as of 18:16, 12 September 2012


Full id: C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte



Phase1 CAGE Peaks

Hg19::chr18:3466261..3466312,+p@chr18:3466261..3466312
+
Hg19::chr20:57571799..57571828,+p@chr20:57571799..57571828
+
Hg19::chr8:11702366..11702398,+p@chr8:11702366..11702398
+
Hg19::chr8:11702610..11702625,+p@chr8:11702610..11702625
+
Hg19::chr8:11704610..11704653,+p@chr8:11704610..11704653
+
Hg19::chr8:11705180..11705213,+p@chr8:11705180..11705213
+
Hg19::chr8:11705214..11705244,+p@chr8:11705214..11705244
+
Hg19::chr8:11705265..11705300,+p@chr8:11705265..11705300
+
Hg19::chr8:11706577..11706604,+p@chr8:11706577..11706604
+
Hg19::chr8:11710161..11710184,+p@chr8:11710161..11710184
+
Hg19::chr8:11710828..11710871,+p@chr8:11710828..11710871
+
Hg19::chr8:11710864..11710931,-p3@CTSB
Hg19::chr8:11710941..11710962,-p8@CTSB
Hg19::chr8:11725589..11725605,-p1@CTSB


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
somatic cell4.36e-17591
non-terminally differentiated cell5.80e-16180
mesodermal cell3.22e-14119
embryonic cell3.17e-11248
monopoietic cell1.55e-1063
monocyte1.55e-1063
monoblast1.55e-1063
promonocyte1.55e-1063
macrophage dendritic cell progenitor4.51e-1065
muscle precursor cell7.39e-1057
myoblast7.39e-1057
multi-potent skeletal muscle stem cell7.39e-1057
contractile cell2.15e-0959
muscle cell4.40e-0954
fibroblast5.60e-0975
smooth muscle cell9.55e-0942
smooth muscle myoblast9.55e-0942
myeloid lineage restricted progenitor cell1.96e-0870
multi fate stem cell4.48e-08430
CD14-positive, CD16-negative classical monocyte6.93e-0842
granulocyte monocyte progenitor cell9.27e-0871
endothelial cell1.11e-0735
somatic stem cell1.41e-07436
animal cell4.99e-07679
eukaryotic cell4.99e-07679
electrically responsive cell6.03e-0760
electrically active cell6.03e-0760
Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.53e-21659
anatomical system2.23e-19625
anatomical group4.28e-19626
lateral plate mesoderm2.91e-18216
mesoderm1.28e-17448
mesoderm-derived structure1.28e-17448
presumptive mesoderm1.28e-17448
musculoskeletal system1.82e-17167
embryonic structure7.32e-13605
developing anatomical structure7.32e-13605
germ layer8.49e-13604
embryonic tissue8.49e-13604
presumptive structure8.49e-13604
epiblast (generic)8.49e-13604
splanchnic layer of lateral plate mesoderm3.72e-1284
embryo4.99e-12612
multilaminar epithelium8.94e-1282
somite4.08e-1183
paraxial mesoderm4.08e-1183
presomitic mesoderm4.08e-1183
presumptive segmental plate4.08e-1183
trunk paraxial mesoderm4.08e-1183
presumptive paraxial mesoderm4.08e-1183
circulatory system6.05e-11113
vasculature7.75e-1179
vascular system7.75e-1179
cardiovascular system9.00e-11110
vessel1.11e-1069
epithelial tube1.17e-10118
unilaminar epithelium1.76e-10138
trunk mesenchyme4.49e-10143
artery5.06e-1042
arterial blood vessel5.06e-1042
arterial system5.06e-1042
dermomyotome6.06e-1070
blood vessel7.50e-1060
epithelial tube open at both ends7.50e-1060
blood vasculature7.50e-1060
vascular cord7.50e-1060
immune system9.43e-09115
skeletal muscle tissue1.73e-0861
striated muscle tissue1.73e-0861
myotome1.73e-0861
muscle tissue2.10e-0863
musculature2.10e-0863
musculature of body2.10e-0863
systemic artery2.16e-0833
systemic arterial system2.16e-0833
skeletal element3.14e-08101
skeletal system3.14e-08101
bone marrow3.22e-0880
bone element5.99e-0786
organ8.34e-07511
Disease
Ontology termp-valuen
ovarian cancer3.31e-0714


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#60237.402950600801070.006944266328473380.0293731412692654
FOSL2#235544.837200172731910.007541622873992410.0310914440191408
POLR2A#5430121.840674151335490.003085141629167310.0162625097970325



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.