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Coexpression cluster:C3462: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324432517781083!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321319785744711!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319806752025918!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401878296267918!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293887735874046!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329769439126187!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189917745865297
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324432517781083!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321319785744711!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319806752025918!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401878296267918!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293887735874046!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329769439126187!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189917745865297
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3462_Monocytederived_CD14_Macrophage_extraskeletal_schwannoma_Dendritic_Osteoblast



Phase1 CAGE Peaks

Hg19::chr14:93651576..93651587,+p5@C14orf109
Hg19::chr15:65281775..65281821,-p3@SPG21
Hg19::chr3:196065341..196065356,-p4@TM4SF19


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:0042609CD4 receptor binding0.00971359607417973
GO:0050851antigen receptor-mediated signaling pathway0.0228754456591497
GO:0030140trans-Golgi network transport vesicle0.0228754456591497
GO:0002429immune response-activating cell surface receptor signaling pathway0.0228754456591497
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0228754456591497
GO:0002757immune response-activating signal transduction0.0228754456591497
GO:0002764immune response-regulating signal transduction0.0228754456591497
GO:0030133transport vesicle0.0297609038989029
GO:0005798Golgi-associated vesicle0.0297609038989029
GO:0002253activation of immune response0.0297609038989029
GO:0050778positive regulation of immune response0.0297609038989029
GO:0010008endosome membrane0.0297609038989029
GO:0002684positive regulation of immune system process0.0297609038989029
GO:0044440endosomal part0.0297609038989029
GO:0050776regulation of immune response0.029907006894176
GO:0002682regulation of immune system process0.029907006894176
GO:0051240positive regulation of multicellular organismal process0.029907006894176
GO:0030136clathrin-coated vesicle0.0309264398045245
GO:0030135coated vesicle0.0374161160315025
GO:0005768endosome0.0466050765668934



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
monopoietic cell1.20e-4259
monocyte1.20e-4259
monoblast1.20e-4259
promonocyte1.20e-4259
defensive cell6.39e-4148
phagocyte6.39e-4148
macrophage dendritic cell progenitor1.28e-4061
myeloid leukocyte4.84e-4072
myeloid lineage restricted progenitor cell4.20e-3666
granulocyte monocyte progenitor cell2.78e-3567
classical monocyte1.55e-3342
CD14-positive, CD16-negative classical monocyte1.55e-3342
myeloid cell1.23e-26108
common myeloid progenitor1.23e-26108
stuff accumulating cell2.78e-2487
nongranular leukocyte3.60e-16115
leukocyte1.86e-15136
hematopoietic lineage restricted progenitor cell4.30e-14120
hematopoietic oligopotent progenitor cell4.25e-13161
hematopoietic multipotent progenitor cell4.25e-13161
hematopoietic stem cell5.89e-13168
angioblastic mesenchymal cell5.89e-13168
hematopoietic cell2.49e-11177
macrophage5.66e-096
Uber Anatomy
Ontology termp-valuen
immune system2.29e-3093
bone marrow2.57e-3076
bone element9.85e-2782
hemolymphoid system3.19e-24108
hematopoietic system4.11e-2398
blood island4.11e-2398
skeletal element9.80e-2390
skeletal system1.27e-19100
musculoskeletal system1.29e-09167
mesoderm3.29e-09315
mesoderm-derived structure3.29e-09315
presumptive mesoderm3.29e-09315
lateral plate mesoderm1.55e-07203


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
E2F1#186934.907389214879320.008460985347239390.0324432517781083
E2F6#187635.017155731697390.00791769806886330.0321319785744711
EGR1#195834.988179094810140.008056488137383440.0319806752025918
ELK4#2005210.8237877723120.01091284719516480.0401878296267918
MYC#460935.22228187160940.007020843755740150.0293887735874046
SMARCB1#6598212.16847718743830.008675002221921740.0329769439126187
USF1#739136.361499277207960.00388404057290560.0189917745865297



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.