Personal tools

Coexpression cluster:C3802

From FANTOM5_SSTAR

Revision as of 11:33, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3802_Sebocyte_Urothelial_Corneal_Mammary_large_salivary_Bronchial



Phase1 CAGE Peaks

Hg19::chr19:45908278..45908282,-p5@PPP1R13L
Hg19::chr19:45908286..45908291,-p3@PPP1R13L
Hg19::chr19:45908292..45908374,-p1@PPP1R13L


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 cell9.26e-45254
squamous epithelial cell1.53e-1462
endo-epithelial cell2.69e-1443
endodermal cell1.64e-1259
embryonic cell9.46e-11248
respiratory epithelial cell3.80e-0813
endothelial cell of vascular tree9.26e-0724
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.53e-16169
endoderm3.53e-16169
presumptive endoderm3.53e-16169
immaterial anatomical entity1.85e-14126
anatomical space4.71e-14104
anatomical conduit5.75e-12241
organism subdivision9.91e-12365
digestive system1.28e-11155
digestive tract1.28e-11155
primitive gut1.28e-11155
primordium1.29e-11168
respiratory system2.45e-1172
multi-cellular organism3.01e-11659
anatomical cluster3.07e-11286
mesenchyme3.62e-11238
entire embryonic mesenchyme3.62e-11238
multi-tissue structure4.54e-11347
subdivision of trunk9.76e-11113
mixed endoderm/mesoderm-derived structure1.21e-10130
organ part3.04e-10219
anatomical cavity5.21e-1070
trunk6.50e-09216
foregut7.62e-0998
anatomical system8.27e-09625
anatomical group9.36e-09626
subdivision of digestive tract1.70e-08129
endodermal part of digestive tract1.70e-08129
epithelial tube1.90e-08118
cell layer3.49e-08312
body cavity precursor6.15e-0863
epithelium7.20e-08309
trunk region element7.96e-08107
respiratory tract9.72e-0853
thoracic segment of trunk1.62e-0752
female organism3.03e-0741
oral opening4.73e-0721
reproductive organ8.57e-0748
respiratory primordium9.33e-0738
endoderm of foregut9.33e-0738
Disease
Ontology termp-valuen
carcinoma6.30e-15106
cell type cancer3.75e-12143
squamous cell carcinoma4.72e-0714
reproductive organ cancer6.99e-0729


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
ESR1#2099330.76860329615453.43136389821584e-050.000676294044472096
ETS1#211339.728760922202340.001085840092584840.00762124014982982
JUND#372736.994663941871030.002921845042734990.0156762855449604
MYC#460935.22228187160940.007020843755740150.0294466045944238
SIX5#147912317.0867153554590.0002004060546325010.00239695464266649
TCF7L2#6934310.77017656313730.0008003181298398380.00613643823231355
TFAP2A#7020211.01242291536330.01054990655215560.0390135858083911
ZBTB7A#5134137.35190930787590.002516255860282270.0140164939885871
ZNF143#7702313.50087655222790.0004062804962997170.00388958921560602



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.