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Coexpression cluster:C3834: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,1.14835,0.824321,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,2.35853,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.265282
}}
}}

Revision as of 16:23, 26 November 2012


Full id: C3834_Endothelial_Hepatic_Renal_Lymphatic_mature_lung_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr19:7861475..7861491,+p@chr19:7861475..7861491
+
Hg19::chr1:172926077..172926120,-p@chr1:172926077..172926120
-
Hg19::chr20:23065602..23065628,-p@chr20:23065602..23065628
-


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
endothelial cell1.37e-8236
endothelial cell of vascular tree8.75e-7024
meso-epithelial cell2.09e-6545
blood vessel endothelial cell2.22e-5018
embryonic blood vessel endothelial progenitor cell2.22e-5018
lining cell5.46e-5058
barrier cell5.46e-5058
vein endothelial cell1.19e-476
fenestrated cell3.71e-255
glomerular endothelial cell3.71e-255
endothelial cell of umbilical vein8.73e-253
mesodermal cell1.36e-24121
endothelial cell of artery7.96e-219
lymphangioblast8.67e-216
endothelial cell of lymphatic vessel8.67e-216
vascular lymphangioblast8.67e-216
glomerular cell4.78e-187
kidney corpuscule cell4.78e-187
squamous epithelial cell4.42e-1363
aortic endothelial cell4.98e-126
kidney cortical cell1.32e-1012
renal cortical epithelial cell1.32e-1012
embryonic cell7.41e-10250
epithelial cell1.09e-08253
epithelial cell of nephron1.64e-0815
kidney cell1.60e-0717
kidney epithelial cell1.60e-0717
Uber Anatomy
Ontology termp-valuen
blood vessel endothelium2.22e-5018
endothelium2.22e-5018
cardiovascular system endothelium2.22e-5018
simple squamous epithelium6.70e-4122
squamous epithelium8.88e-3625
vein1.19e-319
venous blood vessel1.19e-319
venous system1.19e-319
vessel2.71e-2668
vasculature1.51e-2278
vascular system1.51e-2278
endothelial tube7.96e-219
arterial system endothelium7.96e-219
endothelium of artery7.96e-219
primitive nephron4.78e-187
renal glomerulus4.78e-187
renal corpuscle4.78e-187
glomerular capsule4.78e-187
metanephric mesenchyme4.78e-187
glomerular tuft4.78e-187
S-shaped body4.78e-187
renal vesicle4.78e-187
comma-shaped body4.78e-187
epithelial tube open at both ends6.39e-1759
blood vessel6.39e-1759
blood vasculature6.39e-1759
vascular cord6.39e-1759
mesonephric epithelium8.07e-168
mesonephric tubule8.07e-168
nephric duct8.07e-168
renal duct8.07e-168
mesonephric duct8.07e-168
pronephric duct8.07e-168
lymphatic vessel1.18e-158
lymph vasculature1.18e-158
lymphatic part of lymphoid system1.18e-158
cardiovascular system2.71e-15109
umbilical vein4.12e-155
circulatory system8.35e-15112
epithelial tube4.34e-14117
mesonephros4.38e-149
pronephros4.38e-149
nephrogenic cord4.38e-149
pronephric mesoderm4.38e-149
rostral part of nephrogenic cord4.38e-149
presumptive pronephric mesoderm4.38e-149
splanchnic layer of lateral plate mesoderm1.61e-1383
parenchyma6.24e-1315
lymphoid system1.45e-1210
urogenital ridge1.48e-1111
cortex of kidney1.32e-1012
renal parenchyma1.32e-1012
intraembryonic coelom1.32e-1012
duct3.59e-1019
anatomical conduit2.64e-09240
lateral plate mesoderm4.77e-09203
hindlimb bud4.91e-091
soleus muscle4.91e-091
appendage4.91e-091
lower limb segment4.91e-091
multi-limb segment region4.91e-091
hindlimb muscle4.91e-091
hindlimb zeugopod muscle4.91e-091
paired limb/fin4.91e-091
limb4.91e-091
pelvic appendage4.91e-091
limb segment4.91e-091
paired limb/fin segment4.91e-091
limb muscle4.91e-091
pelvic complex muscle4.91e-091
zeugopod4.91e-091
muscle of leg4.91e-091
paired limb/fin bud4.91e-091


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

No analysis results for this cluster

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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