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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 system3.27e-2274
endoderm-derived structure2.49e-16160
endoderm2.49e-16160
presumptive endoderm2.49e-16160
oral opening6.36e-1522
respiratory tract9.77e-1454
orifice2.37e-1336
saliva-secreting gland1.29e-126
gland of oral region1.29e-126
gland of foregut1.29e-126
oral gland1.29e-126
oral cavity1.29e-126
mouth4.31e-1229
stomodeum4.31e-1229
foregut4.65e-1287
gland of gut5.94e-1210
digestive system9.08e-12145
digestive tract9.08e-12145
primitive gut9.08e-12145
thoracic segment of trunk1.90e-1152
subdivision of digestive tract3.34e-11118
anatomical space5.84e-1195
thoracic cavity element7.55e-1134
thoracic cavity7.55e-1134
anterior region of body1.06e-1062
craniocervical region1.06e-1062
organism subdivision1.35e-10264
thoracic segment organ2.03e-1035
surface structure7.29e-1099
tracheobronchial tree2.88e-0915
lower respiratory tract2.88e-0915
segment of respiratory tract7.86e-0947
immaterial anatomical entity4.16e-08117
neck4.67e-0810
head4.89e-0856
pharynx9.09e-0811
subdivision of head1.02e-0749
lower respiratory tract epithelium5.29e-073
epithelium of bronchus5.29e-073
trachea6.44e-077
respiratory airway6.44e-077
Disease
Ontology termp-valuen
thoracic cancer1.50e-094
breast cancer1.50e-094


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.