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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal
|full_id=C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal
|id=C1813
|id=C1813

Revision as of 14:26, 12 September 2012


Full id: C1813_somatostatinoma_melanoma_mesenchymal_placenta_smallcell_Keratocytes_renal



Phase1 CAGE Peaks

Hg19::chr19:18496957..18496977,+p1@GDF15
Hg19::chr19:18499119..18499128,+p9@GDF15
Hg19::chr19:18499150..18499175,+p3@GDF15
Hg19::chr19:18499210..18499232,+p4@GDF15
Hg19::chr19:18499287..18499309,+p2@GDF15


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.69e-28254
embryonic cell1.51e-23248
mesodermal cell2.28e-19119
animal cell1.21e-13679
eukaryotic cell1.21e-13679
non-terminally differentiated cell1.21e-12180
endothelial cell of vascular tree1.60e-1124
meso-epithelial cell5.53e-1144
lining cell5.54e-1157
barrier cell5.54e-1157
endothelial cell1.61e-1035
contractile cell1.46e-0959
smooth muscle cell3.08e-0942
smooth muscle myoblast3.08e-0942
blood vessel endothelial cell1.12e-0818
embryonic blood vessel endothelial progenitor cell1.12e-0818
muscle cell4.08e-0854
muscle precursor cell5.15e-0857
myoblast5.15e-0857
multi-potent skeletal muscle stem cell5.15e-0857
kidney cell2.01e-0718
kidney epithelial cell2.01e-0718
squamous epithelial cell5.17e-0762
electrically responsive cell7.17e-0760
electrically active cell7.17e-0760
Uber Anatomy
Ontology termp-valuen
trunk2.76e-19216
epithelial tube4.23e-18118
vasculature1.89e-1679
vascular system1.89e-1679
vessel5.48e-1569
unilaminar epithelium1.32e-14138
mesenchyme1.70e-14238
entire embryonic mesenchyme1.70e-14238
immaterial anatomical entity1.74e-14126
subdivision of trunk1.59e-13113
splanchnic layer of lateral plate mesoderm1.42e-1284
blood vessel2.24e-1260
epithelial tube open at both ends2.24e-1260
blood vasculature2.24e-1260
vascular cord2.24e-1260
anatomical space2.40e-12104
body cavity precursor6.08e-1263
trunk mesenchyme1.80e-11143
anatomical cavity1.24e-1070
multi-cellular organism1.94e-10659
trunk region element2.42e-10107
artery2.91e-1042
arterial blood vessel2.91e-1042
arterial system2.91e-1042
mesoderm7.59e-10448
mesoderm-derived structure7.59e-10448
presumptive mesoderm7.59e-10448
urinary system structure1.45e-0944
renal system2.69e-0945
abdominal segment of trunk9.95e-0961
abdomen9.95e-0961
endothelium1.12e-0818
blood vessel endothelium1.12e-0818
cardiovascular system endothelium1.12e-0818
simple squamous epithelium1.21e-0822
systemic artery1.61e-0833
systemic arterial system1.61e-0833
cardiovascular system2.51e-08110
squamous epithelium5.30e-0825
circulatory system5.53e-08113
cell layer7.98e-08312
primordium8.46e-08168
intermediate mesoderm1.06e-0737
abdomen element1.19e-0755
abdominal segment element1.19e-0755
endoderm-derived structure1.22e-07169
endoderm1.22e-07169
presumptive endoderm1.22e-07169
body cavity1.29e-0746
multi-tissue structure1.48e-07347
epithelium1.55e-07309
reproductive structure1.98e-0759
reproductive system1.98e-0759
body cavity or lining2.16e-0749
subdivision of digestive tract2.77e-07129
endodermal part of digestive tract2.77e-07129
aorta3.50e-0721
aortic system3.50e-0721
skeletal muscle tissue4.00e-0761
striated muscle tissue4.00e-0761
myotome4.00e-0761
anatomical conduit6.46e-07241
anatomical system7.57e-07625
muscle tissue7.80e-0763
musculature7.80e-0763
musculature of body7.80e-0763
Disease
Ontology termp-valuen
carcinoma3.63e-07106


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
CCNT2#90556.336201576962639.78880505817628e-050.00139074005097384
CTCF#1066455.360256373075030.0002259278299937090.00249821880748681
CTCFL#140690311.84788461538460.001201770348538230.00815116855636993
ETS1#211347.783008737761870.0005121035947688870.00444068310644867
HDAC2#3066410.7324961893010.0001450965797478750.00188596660762766
HEY1#2346254.040111043105710.0009288852205177990.00674395853636833
RAD21#588536.21302033727380.007751055068811640.0318944265526031
RXRA#6256312.044770283480.001145262162836830.00783608720024345
SMARCC1#6599326.19801559177890.0001159625626060410.00157654439937676
SMC3#912639.02695970695970.002650964449467550.0146388238850495
STAT1#6772416.56526999775942.61308619905866e-050.000563743254582704
SUZ12#23512440.09262472885037.78750287036555e-073.41157303807931e-05
TAF1#687253.343046285745290.002394600090870310.0135388500915117
TAF7#687936.859841642954350.005843286407019040.0262480425403295
TCF12#693836.380678941311850.007185168653258840.0298327037042896



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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