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Coexpression cluster:C2750: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.79095613344956e-05!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268401053676233!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195154253622569!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723500986983916!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000744400002154293!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486051605374017!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249736738674354!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322907209035454
|tf_chipseq_enrich=BATF#10538;4:24.3578017923036:2.83869198020713e-06:9.79095613344956e-05!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268401053676233!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195154253622569!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723500986983916!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000744400002154293!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486051605374017!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249736738674354!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322907209035454
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}}
}}

Revision as of 15:41, 26 November 2012


Full id: C2750_Endothelial_immature_Macrophage_Mast_CD34_Lymphatic_CD14



Phase1 CAGE Peaks

Hg19::chr3:69402726..69402747,-p6@FRMD4B
Hg19::chr3:69402751..69402762,-p17@FRMD4B
Hg19::chr3:69402773..69402820,-p5@FRMD4B
Hg19::chr3:69402828..69402852,-p8@FRMD4B


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><br>

Cell Type
Ontology termp-valuen
myeloid leukocyte2.07e-3972
granulocyte monocyte progenitor cell6.02e-3967
myeloid cell9.26e-36108
common myeloid progenitor9.26e-36108
defensive cell3.40e-3548
phagocyte3.40e-3548
myeloid lineage restricted progenitor cell7.05e-3566
macrophage dendritic cell progenitor3.75e-3461
monopoietic cell2.56e-3259
monocyte2.56e-3259
monoblast2.56e-3259
promonocyte2.56e-3259
classical monocyte6.99e-3142
CD14-positive, CD16-negative classical monocyte6.99e-3142
endothelial cell1.27e-2536
hematopoietic stem cell2.51e-23168
angioblastic mesenchymal cell2.51e-23168
endothelial cell of vascular tree9.31e-2324
leukocyte1.77e-22136
hematopoietic cell6.23e-21177
hematopoietic oligopotent progenitor cell1.32e-20161
hematopoietic multipotent progenitor cell1.32e-20161
meso-epithelial cell1.81e-1745
hematopoietic lineage restricted progenitor cell2.12e-17120
blood vessel endothelial cell2.24e-1718
embryonic blood vessel endothelial progenitor cell2.24e-1718
nongranular leukocyte7.38e-15115
stuff accumulating cell6.81e-1287
lining cell1.56e-1058
barrier cell1.56e-1058
endothelial cell of artery4.77e-109
aortic endothelial cell2.84e-076
vein endothelial cell3.40e-076
lymphangioblast6.24e-076
endothelial cell of lymphatic vessel6.24e-076
vascular lymphangioblast6.24e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.97e-40108
immune system1.44e-3893
lateral plate mesoderm9.05e-37203
hematopoietic system4.53e-3598
blood island4.53e-3598
bone marrow9.23e-3476
bone element2.31e-2982
adult organism1.92e-26114
skeletal element1.75e-2490
skeletal system5.16e-21100
blood vessel endothelium2.24e-1718
endothelium2.24e-1718
cardiovascular system endothelium2.24e-1718
mesoderm8.42e-17315
mesoderm-derived structure8.42e-17315
presumptive mesoderm8.42e-17315
simple squamous epithelium9.93e-1322
squamous epithelium2.78e-1025
endothelial tube4.77e-109
arterial system endothelium4.77e-109
endothelium of artery4.77e-109
germ layer2.55e-09560
germ layer / neural crest2.55e-09560
embryonic tissue2.55e-09560
presumptive structure2.55e-09560
germ layer / neural crest derived structure2.55e-09560
epiblast (generic)2.55e-09560
embryonic structure2.74e-09564
circulatory system3.42e-09112
vessel1.54e-0868
cardiovascular system1.56e-08109
musculoskeletal system1.72e-08167
developing anatomical structure3.96e-08581
embryo1.22e-07592
anatomical system1.24e-07624
anatomical group1.56e-07625
tissue2.56e-07773
splanchnic layer of lateral plate mesoderm5.50e-0783
multi-cellular organism6.02e-07656
anatomical conduit7.60e-07240


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
BATF#10538424.35780179230362.83869198020713e-069.79095613344956e-05
CEBPB#105147.971147625824820.0002476385788090830.00268401053676233
FOS#235348.99795530889440.0001525147711168630.00195154253622569
GATA2#2624412.7449317335543.78864877853583e-050.000723500986983916
JUN#3725412.51282919233634.07770316866756e-050.000744400002154293
MAX#414946.452555509007120.0005767613195645490.00486051605374017
SPI1#668848.204323508522730.000220661881527680.00249736738674354
TAF1#687243.343046285745290.008005664898701650.0322907209035454



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.

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