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Coexpression cluster:C3197

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Full id: C3197_breast_salivary_esophagus_tonsil_tongue_nasal_Urothelial



Phase1 CAGE Peaks

Hg19::chr11:67442013..67442036,-p3@ALDH3B2
Hg19::chr11:67442051..67442072,-p2@ALDH3B2
Hg19::chr11:67442079..67442102,-p1@ALDH3B2


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
respiratory system4.81e-2472
endoderm-derived structure5.68e-17169
endoderm5.68e-17169
presumptive endoderm5.68e-17169
oral opening3.74e-1621
orifice5.15e-1635
respiratory tract2.66e-1453
thoracic segment of trunk4.78e-1352
thoracic cavity element1.36e-1234
thoracic cavity1.36e-1234
mouth1.58e-1228
stomodeum1.58e-1228
thoracic segment organ4.53e-1235
anatomical space9.84e-12104
digestive system4.53e-11155
digestive tract4.53e-11155
primitive gut4.53e-11155
saliva-secreting gland1.81e-106
gland of oral region1.81e-106
gland of foregut1.81e-106
oral gland1.81e-106
oral cavity1.81e-106
mixed endoderm/mesoderm-derived structure2.08e-10130
gland of gut1.02e-0910
tracheobronchial tree1.08e-0914
lower respiratory tract1.08e-0914
epithelial bud3.69e-0937
segment of respiratory tract3.69e-0946
subdivision of digestive tract4.28e-09129
endodermal part of digestive tract4.28e-09129
surface structure5.04e-0995
foregut6.64e-0998
immaterial anatomical entity1.69e-08126
neck2.04e-0810
mixed ectoderm/mesoderm/endoderm-derived structure1.09e-0718
mouth mucosa2.10e-075
subdivision of head2.68e-0748
epithelial fold3.22e-0751
subdivision of trunk3.37e-07113
respiratory system epithelium4.18e-0728
respiratory primordium4.41e-0738
endoderm of foregut4.41e-0738
endo-epithelium5.44e-0782
lung7.02e-0722
respiratory tube7.02e-0722
respiration organ7.02e-0722
pair of lungs7.02e-0722
lung primordium7.02e-0722
lung bud7.02e-0722
Disease
Ontology termp-valuen
squamous cell carcinoma4.57e-1014
thoracic cancer6.03e-084
breast cancer6.03e-084


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
EP300#203336.77394172622320.003216880500103790.0166948808661469
ESR1#2099330.76860329615453.43136389821584e-050.000674131328378036
FOXA1#3169311.08141974938550.000734755275698670.00579760548796414
GATA3#2625327.2365163572064.94721007899563e-050.00084910710507843
MYC#460935.22228187160940.007020843755740150.02933234262764
NR3C1#2908314.9730233311730.0002978331194675480.00308004685256672
SP1#666735.69838137814090.005403962701712170.0245576738579809



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.