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Coexpression cluster:C1716: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic
|full_id=C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic
|id=C1716
|id=C1716

Revision as of 14:19, 12 September 2012


Full id: C1716_Corneal_oral_Keratinocyte_mesothelioma_Esophageal_Urothelial_anaplastic



Phase1 CAGE Peaks

Hg19::chr14:23451697..23451713,-p4@AJUBA
Hg19::chr14:23451725..23451742,-p1@AJUBA
Hg19::chr14:23451753..23451767,-p2@AJUBA
Hg19::chr14:23451797..23451814,-p3@AJUBA
Hg19::chr14:23451816..23451828,-p5@AJUBA


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>

Uber Anatomy
Ontology termp-valuen
mesenchyme2.97e-19238
entire embryonic mesenchyme2.97e-19238
endoderm-derived structure7.38e-19169
endoderm7.38e-19169
presumptive endoderm7.38e-19169
trunk2.51e-16216
multi-tissue structure4.08e-16347
organism subdivision4.14e-16365
digestive system7.61e-14155
digestive tract7.61e-14155
primitive gut7.61e-14155
trunk mesenchyme1.12e-13143
unilaminar epithelium3.89e-12138
cell layer1.28e-11312
multi-cellular organism1.30e-11659
epithelium1.51e-11309
surface structure2.44e-1195
endo-epithelium2.46e-1182
mixed endoderm/mesoderm-derived structure2.71e-11130
subdivision of trunk8.08e-11113
urinary system structure2.42e-1044
trunk region element3.69e-10107
renal system5.01e-1045
immaterial anatomical entity7.07e-10126
primordium7.63e-10168
epithelial tube1.18e-09118
subdivision of digestive tract1.59e-09129
endodermal part of digestive tract1.59e-09129
anatomical system3.66e-09625
gut epithelium6.45e-0954
anatomical group6.53e-09626
abdomen element8.24e-0955
abdominal segment element8.24e-0955
abdominal segment of trunk1.66e-0861
abdomen1.66e-0861
ectodermal placode2.20e-0829
subdivision of head3.76e-0848
anatomical cluster5.18e-08286
intermediate mesoderm6.25e-0837
foregut1.04e-0798
duct1.73e-0726
nephron epithelium3.51e-0716
nephron3.51e-0716
uriniferous tubule3.51e-0716
metanephric mesenchyme3.51e-0716
nephrogenic mesenchyme3.51e-0716
gland3.73e-0759
respiratory system4.53e-0772
exocrine gland6.07e-0731
exocrine system6.07e-0731
skin of body8.39e-0740
organ part8.52e-07219
Disease
Ontology termp-valuen
cell type cancer1.27e-12143
carcinoma2.32e-12106
disease of anatomical entity7.21e-0939


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-050.00138979474098814
CHD2#1106510.34402283411698.43981772346334e-060.000230142590919266
CTBP2#1488562.71700033932811.02712351233917e-099.50148383571214e-08
CTCF#1066455.360256373075030.0002259278299937090.00249663280464638
E2F1#186954.907389214879320.0003512818099256460.00352493475661266
E2F6#187655.017155731697390.0003144978599297790.00322650707202418
EGR1#195854.988179094810140.0003237398000590710.00330638186762853
ELF1#199754.258097958807540.0007142416939776840.00572835879875099
HDAC2#3066410.7324961893010.0001450965797478750.00188549728658558
IRF1#365957.63716375356393.84754333311872e-050.000723763649437295
JUND#372756.994663941871035.97069468343598e-050.000983709389562028
MXI1#460159.96157162875931.01894348670516e-050.000266509989501628
MYC#460955.22228187160940.0002573944848850610.00276336581074331
RFX5#5993512.04791082719513.93714721313598e-060.000127461784808651
SMARCB1#6598518.25271578115744.93125075403021e-072.31467369662994e-05
SP1#666755.69838137814090.000166391843712550.00204156458711173
SRF#6722513.79717826216781.9987012616697e-067.31915712017959e-05
TAF1#687253.343046285745290.002394600090870310.0135264015842071
TBP#690853.706770687096390.001428755106721120.00918263105174445
TCF7L2#6934510.77017656313736.89693748574565e-060.000199697603014635
TRIM28#10155518.59052504526254.49912775886781e-072.13583820003816e-05
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815443010860592
ZNF263#1012758.221841637010682.6606316672286e-050.000570816989921299



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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