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Coexpression cluster:C2988: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163008011364674!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894436862048999!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00435759001216151!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00442936100794762
|tf_chipseq_enrich=ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163008011364674!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00894436862048999!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00435759001216151!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00442936100794762
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,1.39614,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282
}}
}}

Revision as of 15:51, 26 November 2012


Full id: C2988_CD14_Endothelial_Peripheral_Basophils_Hepatic_Skeletal_Mast



Phase1 CAGE Peaks

Hg19::chr10:129777410..129777418,-p@chr10:129777410..129777418
-
Hg19::chr10:31987035..31987065,+p@chr10:31987035..31987065
+
Hg19::chr3:15678163..15678169,+p@chr3:15678163..15678169
+


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
classical monocyte3.49e-3742
CD14-positive, CD16-negative classical monocyte3.49e-3742
myeloid leukocyte9.86e-3572
defensive cell2.28e-3448
phagocyte2.28e-3448
endothelial cell of vascular tree1.16e-3024
endothelial cell6.40e-3036
blood vessel endothelial cell9.15e-2918
embryonic blood vessel endothelial progenitor cell9.15e-2918
myeloid lineage restricted progenitor cell1.29e-2866
monopoietic cell2.44e-2859
monocyte2.44e-2859
monoblast2.44e-2859
promonocyte2.44e-2859
granulocyte monocyte progenitor cell4.47e-2867
macrophage dendritic cell progenitor3.50e-2761
meso-epithelial cell8.80e-2345
leukocyte1.08e-20136
myeloid cell2.80e-20108
common myeloid progenitor2.80e-20108
stuff accumulating cell9.08e-1987
vein endothelial cell2.14e-176
nongranular leukocyte3.18e-17115
lining cell2.04e-1658
barrier cell2.04e-1658
hematopoietic stem cell6.55e-15168
angioblastic mesenchymal cell6.55e-15168
hematopoietic lineage restricted progenitor cell1.30e-14120
hematopoietic cell1.14e-13177
hematopoietic oligopotent progenitor cell1.10e-12161
hematopoietic multipotent progenitor cell1.10e-12161
single nucleate cell6.12e-103
mononuclear cell6.12e-103
basophil1.04e-093
somatic cell3.42e-09588
capillary endothelial cell3.91e-093
endothelial cell of umbilical vein9.82e-093
endothelial cell of artery4.42e-089
aortic endothelial cell4.57e-086
mesodermal cell1.88e-07121
endothelial cell of sinusoid3.71e-072
endothelial cell of hepatic sinusoid3.71e-072
mesenchymal cell5.26e-07354
thoracic aorta endothelial cell8.71e-072
multi fate stem cell9.40e-07427
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm7.79e-33203
blood vessel endothelium9.15e-2918
endothelium9.15e-2918
cardiovascular system endothelium9.15e-2918
hemolymphoid system9.18e-25108
immune system2.06e-2493
bone marrow7.34e-2476
hematopoietic system4.45e-2398
blood island4.45e-2398
simple squamous epithelium7.07e-2322
bone element1.45e-2182
squamous epithelium1.06e-1925
mesoderm4.03e-19315
mesoderm-derived structure4.03e-19315
presumptive mesoderm4.03e-19315
skeletal element5.55e-1990
skeletal system2.43e-16100
vessel1.05e-1468
cardiovascular system2.68e-13109
epithelial tube open at both ends6.81e-1359
blood vessel6.81e-1359
blood vasculature6.81e-1359
vascular cord6.81e-1359
circulatory system9.44e-13112
splanchnic layer of lateral plate mesoderm3.21e-1283
vasculature4.23e-1278
vascular system4.23e-1278
vein2.41e-119
venous blood vessel2.41e-119
venous system2.41e-119
musculoskeletal system3.43e-09167
microcirculatory vessel3.91e-093
endothelium of capillary3.91e-093
capillary3.91e-093
endothelial tube4.42e-089
arterial system endothelium4.42e-089
endothelium of artery4.42e-089
epithelial tube6.51e-08117
umbilical blood vessel1.72e-079
hepatic sinusoid3.71e-072
abdomen blood vessel3.71e-072
sinusoid3.71e-072
abdominal segment blood vessel3.71e-072
segment of aorta8.71e-072
thoracic aorta8.71e-072


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
ESR1#2099220.51240219743630.003099741577095180.0163008011364674
FOS#235338.99795530889440.001372499272417130.00894436862048999
GATA2#2624312.7449317335540.0004829527704283790.00435759001216151
JUN#3725312.51282919233630.0005103313992726250.00442936100794762



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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