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Coexpression cluster:C842: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C842_Neutrophils_CD14CD16_CD14_Eosinophils_migratory_Mesenchymal_Fibroblast
|full_id=C842_Neutrophils_CD14CD16_CD14_Eosinophils_migratory_Mesenchymal_Fibroblast
|gostat_on_coexpression_clusters=GO:0031280!negative regulation of cyclase activity!0.0155978685153231!2771$GO:0007194!negative regulation of adenylate cyclase activity!0.0155978685153231!2771$GO:0051350!negative regulation of lyase activity!0.0155978685153231!2771$GO:0045761!regulation of adenylate cyclase activity!0.0187100024153625!2771$GO:0007584!response to nutrient!0.0187100024153625!2771$GO:0031279!regulation of cyclase activity!0.0187100024153625!2771$GO:0051339!regulation of lyase activity!0.0187100024153625!2771$GO:0031667!response to nutrient levels!0.0225929366485817!2771$GO:0009991!response to extracellular stimulus!0.0225929366485817!2771$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0225929366485817!2771$GO:0019933!cAMP-mediated signaling!0.0225929366485817!2771$GO:0043086!negative regulation of catalytic activity!0.0225929366485817!2771$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0271420350435088!2771$GO:0019935!cyclic-nucleotide-mediated signaling!0.0271420350435088!2771
|gostat_on_coexpression_clusters=GO:0031280!negative regulation of cyclase activity!0.0155978685153231!2771$GO:0007194!negative regulation of adenylate cyclase activity!0.0155978685153231!2771$GO:0051350!negative regulation of lyase activity!0.0155978685153231!2771$GO:0045761!regulation of adenylate cyclase activity!0.0187100024153625!2771$GO:0007584!response to nutrient!0.0187100024153625!2771$GO:0031279!regulation of cyclase activity!0.0187100024153625!2771$GO:0051339!regulation of lyase activity!0.0187100024153625!2771$GO:0031667!response to nutrient levels!0.0225929366485817!2771$GO:0009991!response to extracellular stimulus!0.0225929366485817!2771$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0225929366485817!2771$GO:0019933!cAMP-mediated signaling!0.0225929366485817!2771$GO:0043086!negative regulation of catalytic activity!0.0225929366485817!2771$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0271420350435088!2771$GO:0019935!cyclic-nucleotide-mediated signaling!0.0271420350435088!2771

Revision as of 18:35, 12 September 2012


Full id: C842_Neutrophils_CD14CD16_CD14_Eosinophils_migratory_Mesenchymal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr16:84600281..84600315,-p@chr16:84600281..84600315
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Hg19::chr16:84600344..84600356,-p@chr16:84600344..84600356
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Hg19::chr16:84600375..84600405,-p@chr16:84600375..84600405
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Hg19::chr16:84600432..84600461,-p@chr16:84600432..84600461
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Hg19::chr16:84600468..84600488,-p@chr16:84600468..84600488
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Hg19::chr16:84623794..84623816,-p3@COTL1
Hg19::chr16:84623843..84623875,-p4@COTL1
Hg19::chr16:84651647..84651667,-p2@COTL1
Hg19::chr16:84651673..84651691,-p1@COTL1
Hg19::chr3:50294928..50294962,+p1@AY555145


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:0031280negative regulation of cyclase activity0.0155978685153231
GO:0007194negative regulation of adenylate cyclase activity0.0155978685153231
GO:0051350negative regulation of lyase activity0.0155978685153231
GO:0045761regulation of adenylate cyclase activity0.0187100024153625
GO:0007584response to nutrient0.0187100024153625
GO:0031279regulation of cyclase activity0.0187100024153625
GO:0051339regulation of lyase activity0.0187100024153625
GO:0031667response to nutrient levels0.0225929366485817
GO:0009991response to extracellular stimulus0.0225929366485817
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0225929366485817
GO:0019933cAMP-mediated signaling0.0225929366485817
GO:0043086negative regulation of catalytic activity0.0225929366485817
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0271420350435088
GO:0019935cyclic-nucleotide-mediated signaling0.0271420350435088



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
somatic cell1.50e-32591
native cell9.24e-29722
animal cell4.88e-27679
eukaryotic cell4.88e-27679
CD14-positive, CD16-negative classical monocyte1.12e-2642
myeloid leukocyte1.07e-2576
classical monocyte1.39e-2445
multi fate stem cell1.74e-23430
monopoietic cell1.81e-2363
monocyte1.81e-2363
monoblast1.81e-2363
promonocyte1.81e-2363
somatic stem cell5.10e-23436
macrophage dendritic cell progenitor9.32e-2265
stem cell1.07e-21444
myeloid lineage restricted progenitor cell1.35e-1970
granulocyte monocyte progenitor cell2.38e-1971
mesodermal cell5.39e-17119
leukocyte2.36e-14140
connective tissue cell3.11e-13365
myeloid cell3.79e-13112
common myeloid progenitor3.79e-13112
nongranular leukocyte4.31e-13119
mesenchymal cell2.12e-12358
contractile cell1.92e-1159
muscle precursor cell1.75e-1057
myoblast1.75e-1057
multi-potent skeletal muscle stem cell1.75e-1057
muscle cell3.03e-1054
hematopoietic lineage restricted progenitor cell4.44e-10124
smooth muscle cell1.41e-0942
smooth muscle myoblast1.41e-0942
electrically responsive cell1.53e-0960
electrically active cell1.53e-0960
motile cell3.08e-09390
hematopoietic oligopotent progenitor cell1.97e-08165
hematopoietic multipotent progenitor cell1.97e-08165
vascular associated smooth muscle cell4.03e-0832
hematopoietic stem cell6.95e-08172
angioblastic mesenchymal cell6.95e-08172
hematopoietic cell1.81e-07182
lining cell2.86e-0757
barrier cell2.86e-0757
non-terminally differentiated cell3.30e-07180
embryonic cell6.08e-07248
Uber Anatomy
Ontology termp-valuen
musculoskeletal system5.51e-22167
lateral plate mesoderm2.80e-21216
hemolymphoid system2.42e-18112
bone marrow2.38e-1780
hematopoietic system4.49e-17102
blood island4.49e-17102
bone element2.17e-1486
skeletal element5.81e-14101
skeletal system5.81e-14101
connective tissue2.11e-11375
immune system3.00e-11115
dermomyotome6.13e-1070
mesoderm6.55e-10448
mesoderm-derived structure6.55e-10448
presumptive mesoderm6.55e-10448
somite8.32e-1083
paraxial mesoderm8.32e-1083
presomitic mesoderm8.32e-1083
presumptive segmental plate8.32e-1083
trunk paraxial mesoderm8.32e-1083
presumptive paraxial mesoderm8.32e-1083
multilaminar epithelium1.33e-0982
cardiovascular system2.93e-09110
vasculature1.90e-0879
vascular system1.90e-0879
skeletal muscle tissue4.57e-0861
striated muscle tissue4.57e-0861
myotome4.57e-0861
circulatory system5.14e-08113
muscle tissue2.53e-0763
musculature2.53e-0763
musculature of body2.53e-0763
artery2.53e-0742
arterial blood vessel2.53e-0742
arterial system2.53e-0742
vessel5.74e-0769


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
SP1#666773.988866964698630.0003734365591501510.00371193878377107



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.