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Coexpression cluster:C2548

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Full id: C2548_salivary_immature_tongue_esophagus_amniotic_cervical_Corneal



Phase1 CAGE Peaks

Hg19::chr1:201252522..201252533,+p2@PKP1
Hg19::chr1:201252623..201252640,+p1@PKP1
Hg19::chr2:64681348..64681364,+p1@LGALSL
Hg19::chr6:7541895..7541916,+p1@DSP


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


p.valueFDRnGenesnPathwayName
2.63387331172458e-050.01667241806321662147Apoptosis (Reactome):REACT_578



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


GO IDGO nameFDR corrected p-value
GO:0005911intercellular junction0.00104122004525117
GO:0005882intermediate filament0.00104122004525117
GO:0045111intermediate filament cytoskeleton0.00104122004525117
GO:0019215intermediate filament binding0.00191331223659601
GO:0030054cell junction0.00206830683319861
GO:0030280structural constituent of epidermis0.00546596270161619
GO:0030057desmosome0.00546596270161619
GO:0044430cytoskeletal part0.00552645155524017
GO:0005913cell-cell adherens junction0.00552645155524017
GO:0001533cornified envelope0.00841609563968864
GO:0018149peptide cross-linking0.00882703254456832
GO:0005856cytoskeleton0.00882703254456832
GO:0030216keratinocyte differentiation0.00882703254456832
GO:0014704intercalated disc0.012838016257695
GO:0005912adherens junction0.0137653044832711
GO:0044459plasma membrane part0.0175034631324322
GO:0007275multicellular organismal development0.0175034631324322
GO:0005200structural constituent of cytoskeleton0.0180480957314749
GO:0030674protein binding, bridging0.0182357472300847
GO:0032403protein complex binding0.0182357472300847
GO:0043296apical junction complex0.0182357472300847
GO:0016327apicolateral plasma membrane0.0182357472300847
GO:0043232intracellular non-membrane-bound organelle0.0200027457430974
GO:0043228non-membrane-bound organelle0.0200027457430974
GO:0008544epidermis development0.0206233211507383
GO:0007398ectoderm development0.0214424247473283
GO:0032502developmental process0.0233615575638312
GO:0005886plasma membrane0.0283630958363565
GO:0032501multicellular organismal process0.0283630958363565
GO:0044446intracellular organelle part0.0309825493835566
GO:0044422organelle part0.0309825493835566
GO:0009888tissue development0.0363098561462876



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 cell3.30e-25254
endodermal cell4.80e-1759
endo-epithelial cell1.34e-1543
epithelial cell of alimentary canal2.81e-0821
respiratory epithelial cell4.45e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.07e-20169
endoderm4.07e-20169
presumptive endoderm4.07e-20169
digestive system6.22e-16155
digestive tract6.22e-16155
primitive gut6.22e-16155
mixed endoderm/mesoderm-derived structure9.61e-15130
multi-cellular organism4.16e-14659
subdivision of digestive tract5.16e-14129
endodermal part of digestive tract5.16e-14129
respiratory system3.10e-1272
foregut1.09e-1198
organ4.78e-11511
immaterial anatomical entity6.09e-11126
multi-tissue structure3.34e-10347
adult organism5.73e-10115
subdivision of trunk1.05e-09113
organ part1.29e-09219
anatomical group1.68e-09626
anatomical system1.88e-09625
organism subdivision2.27e-09365
mesenchyme4.33e-09238
entire embryonic mesenchyme4.33e-09238
anatomical space6.86e-09104
endo-epithelium1.57e-0882
embryo2.79e-08612
respiratory tract3.45e-0853
trunk region element4.14e-08107
primordium1.33e-07168
embryonic structure2.53e-07605
developing anatomical structure2.53e-07605
exocrine gland3.98e-0731
exocrine system3.98e-0731
germ layer4.70e-07604
embryonic tissue4.70e-07604
presumptive structure4.70e-07604
epiblast (generic)4.70e-07604
gland6.87e-0759
respiratory primordium8.19e-0738
endoderm of foregut8.19e-0738
oral opening8.34e-0721
Disease
Ontology termp-valuen
carcinoma2.91e-15106
cell type cancer4.83e-10143


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


No analysis results for this cluster

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.