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Coexpression cluster:C2879: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma
|full_id=C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma
|id=C2879
|id=C2879

Revision as of 15:40, 12 September 2012


Full id: C2879_salivary_Fibroblast_vagina_liver_Hepatocyte_Skeletal_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:134576184..134576236,+p2@CALD1
Hg19::chr7:134576237..134576280,+p5@CALD1
Hg19::chr7:134576283..134576309,+p9@CALD1
Hg19::chr7:134576317..134576374,+p3@CALD1


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
non-terminally differentiated cell1.81e-07180
Uber Anatomy
Ontology termp-valuen
multi-tissue structure7.84e-26347
organism subdivision4.41e-24365
multi-cellular organism6.61e-17659
endoderm-derived structure1.29e-15169
endoderm1.29e-15169
presumptive endoderm1.29e-15169
mesenchyme1.74e-15238
entire embryonic mesenchyme1.74e-15238
embryo4.77e-14612
anatomical system1.01e-13625
digestive system1.07e-13155
digestive tract1.07e-13155
primitive gut1.07e-13155
anatomical group1.98e-13626
organ2.22e-13511
embryonic structure2.87e-13605
developing anatomical structure2.87e-13605
cell layer3.69e-13312
germ layer5.25e-13604
embryonic tissue5.25e-13604
presumptive structure5.25e-13604
epiblast (generic)5.25e-13604
epithelium1.14e-12309
trunk5.61e-12216
ectoderm2.28e-11173
presumptive ectoderm2.28e-11173
ectoderm-derived structure2.54e-11169
anatomical cluster5.42e-11286
mixed endoderm/mesoderm-derived structure6.06e-11130
surface structure1.26e-1095
subdivision of digestive tract2.00e-10129
endodermal part of digestive tract2.00e-10129
trunk mesenchyme2.90e-10143
primordium1.05e-09168
organ part1.68e-09219
gland2.00e-0859
adult organism2.99e-08115
head5.14e-08123
orifice8.20e-0835
anterior region of body1.68e-07129
craniocervical region1.68e-07129
anatomical conduit3.92e-07241
trunk region element6.99e-07107


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
CEBPB#105147.971147625824820.0002476385788090830.00268651973950782
EP300#203346.77394172622320.0004748459821442640.00435288681902614
FOXA1#3169411.08141974938556.62943068949433e-050.00107344358415519
FOXA2#3170424.63046375266522.71504128667089e-069.4550249062561e-05
GATA2#2624412.7449317335543.78864877853583e-050.000724428212708722
GTF2F1#2962412.73966087675773.79492332235515e-050.000719306709371053
HDAC2#3066413.41562023662633.0859005065161e-050.000628610031207402
HEY1#2346244.040111043105710.00375304636917980.01866052890982
MAX#414946.452555509007120.0005767613195645490.00486522699733478
MXI1#460149.96157162875930.0001015224754950450.00142761624050451
MYC#460945.22228187160940.001344309395272740.00889892431595927
NR3C1#2908414.9730233311731.98868032687801e-050.000444649506869647
RAD21#5885410.35503389545638.6948481184721e-050.00129930067627001
RFX5#5993412.04791082719514.74457429336527e-050.000828626412416012
SMARCB1#6598418.25271578115749.00423392720929e-060.000242182123905179
SP1#666745.69838137814090.0009482606065333980.00685698189335606
TAF1#687243.343046285745290.008005664898701650.0323319271599189
TBP#690843.706770687096390.005296377814784350.0245016124467693
TCF7L2#6934410.77017656313737.42969445082454e-050.00115761578211199
TRIM28#10155418.59052504526258.36730015875654e-060.000231060936351236
USF1#739146.361499277207960.0006105011399140830.00509062902606682
USF2#7392412.99219738506963.50833029870167e-050.000683084466939044
YY1#752844.911170749853860.00171871838055440.0107088192904618
ZNF263#1012748.221841637010680.0002187871180958320.00249944299133785



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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