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Coexpression cluster:C2625

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Full id: C2625_oral_keratoacanthoma_bronchial_Small_ductal_squamous_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr20:6103574..6103587,-p7@FERMT1
Hg19::chr20:6103596..6103610,-p8@FERMT1
Hg19::chr20:6103612..6103621,-p14@FERMT1
Hg19::chr20:6103666..6103737,-p1@FERMT1


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 cell3.26e-20254
endo-epithelial cell1.60e-1643
endodermal cell1.41e-1559
epithelial cell of alimentary canal4.91e-1121
respiratory epithelial cell9.67e-0913
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.32e-28169
endoderm4.32e-28169
presumptive endoderm4.32e-28169
digestive system1.81e-24155
digestive tract1.81e-24155
primitive gut1.81e-24155
multi-tissue structure1.84e-22347
subdivision of digestive tract1.04e-19129
endodermal part of digestive tract1.04e-19129
mixed endoderm/mesoderm-derived structure1.64e-17130
mesenchyme8.83e-17238
entire embryonic mesenchyme8.83e-17238
respiratory system9.55e-1672
organism subdivision4.40e-15365
foregut7.89e-1398
respiratory tract1.23e-1153
embryo3.62e-11612
segment of respiratory tract7.56e-1146
organ part1.48e-10219
embryonic structure2.80e-10605
developing anatomical structure2.80e-10605
germ layer4.38e-10604
embryonic tissue4.38e-10604
presumptive structure4.38e-10604
epiblast (generic)4.38e-10604
multi-cellular organism8.83e-10659
orifice1.83e-0935
epithelium3.43e-09309
anatomical space4.13e-09104
respiratory primordium4.22e-0938
endoderm of foregut4.22e-0938
cell layer4.23e-09312
organ segment4.37e-0997
endo-epithelium5.65e-0982
anatomical system6.32e-09625
anatomical group6.93e-09626
intestine1.02e-0827
trunk1.15e-08216
immaterial anatomical entity3.14e-08126
gastrointestinal system5.63e-0835
anatomical cluster8.62e-08286
organ1.20e-07511
surface structure2.59e-0795
primordium2.72e-07168
trunk region element4.21e-07107
oral opening4.46e-0721
mouth5.65e-0728
stomodeum5.65e-0728
anatomical conduit8.57e-07241
epithelial bud9.08e-0737
thoracic cavity element9.49e-0734
thoracic cavity9.49e-0734
Disease
Ontology termp-valuen
carcinoma1.28e-16106
cell type cancer6.86e-15143
squamous cell carcinoma7.49e-1014
disease of cellular proliferation2.05e-08239
cancer4.40e-08235


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
CTCF#1066445.360256373075030.001211145381643620.00817969558416182
HDAC2#3066413.41562023662633.0859005065161e-050.00062689819684893
HEY1#2346244.040111043105710.00375304636917980.0186286017656371
HNF4A#3172423.13229036295373.48990320893214e-060.00011570857182148
MAX#414946.452555509007120.0005767613195645490.00485738048979936
MXI1#460149.96157162875930.0001015224754950450.00142512174976169
MYC#460945.22228187160940.001344309395272740.00888372114229874
TAF1#687243.343046285745290.008005664898701650.0322608186269824
TAF7#6879411.43306940492395.85061525419808e-050.000970354782488793
TBP#690843.706770687096390.005296377814784350.0244539523695076
TFAP2C#7022410.80922860986027.32289634782688e-050.00114662064718245



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.