Personal tools

Coexpression cluster:C885

From FANTOM5_SSTAR

Revision as of 03:02, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C885_breast_Intestinal_MCF7_Prostate_small_colon_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr11:72493722..72493753,-p9@STARD10
Hg19::chr14:38060540..38060566,-p@chr14:38060540..38060566
-
Hg19::chr14:38061906..38061927,-p@chr14:38061906..38061927
-
Hg19::chr14:38064495..38064506,-p4@FOXA1
Hg19::chr14:38064536..38064550,-p7@FOXA1
Hg19::chr14:38064554..38064559,-p12@FOXA1
Hg19::chr14:38064572..38064584,-p5@FOXA1
Hg19::chr14:38064590..38064606,-p2@FOXA1
Hg19::chr14:38064797..38064843,+p1@TTC6


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


GO IDGO nameFDR corrected p-value
GO:0042593glucose homeostasis0.0231308033864625
GO:0033500carbohydrate homeostasis0.0231308033864625
GO:0048754branching morphogenesis of a tube0.0231308033864625
GO:0001763morphogenesis of a branching structure0.0231308033864625
GO:0030855epithelial cell differentiation0.0231308033864625
GO:0030324lung development0.0231308033864625
GO:0030323respiratory tube development0.0231308033864625
GO:0002009morphogenesis of an epithelium0.029644417655839
GO:0035239tube morphogenesis0.033114259988823
GO:0042445hormone metabolic process0.033114259988823
GO:0035295tube development0.0400073614017467
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0435551382564899



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 cell1.78e-26254
endodermal cell7.40e-1559
endo-epithelial cell7.65e-1143
epithelial cell of lung3.06e-0719
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract6.19e-28129
endodermal part of digestive tract6.19e-28129
endoderm-derived structure5.04e-27169
endoderm5.04e-27169
presumptive endoderm5.04e-27169
digestive system6.31e-26155
digestive tract6.31e-26155
primitive gut6.31e-26155
mixed endoderm/mesoderm-derived structure1.92e-20130
endo-epithelium1.17e-1682
foregut1.78e-1698
respiratory primordium1.97e-1538
endoderm of foregut1.97e-1538
respiratory tract7.77e-1553
trunk region element1.27e-14107
respiratory system4.93e-1372
subdivision of trunk5.66e-13113
segment of respiratory tract3.33e-1146
epithelial bud2.86e-1037
immaterial anatomical entity4.87e-10126
multi-tissue structure9.21e-10347
thoracic cavity element1.07e-0934
thoracic cavity1.07e-0934
lung2.28e-0922
respiratory tube2.28e-0922
respiration organ2.28e-0922
pair of lungs2.28e-0922
lung primordium2.28e-0922
lung bud2.28e-0922
thoracic segment organ3.58e-0935
organ part1.33e-08219
mesenchyme2.27e-08238
entire embryonic mesenchyme2.27e-08238
gut epithelium2.34e-0854
epithelial fold4.30e-0851
abdomen element8.45e-0855
abdominal segment element8.45e-0855
mucosa1.06e-0712
epithelium of foregut-midgut junction1.13e-0725
anatomical boundary1.13e-0725
hepatobiliary system1.13e-0725
foregut-midgut junction1.13e-0725
septum transversum1.13e-0725
organ segment1.15e-0797
thoracic segment of trunk1.76e-0752
respiratory tract epithelium3.06e-0719
lung epithelium3.06e-0719
sac3.79e-0726
renal system4.72e-0745
intermediate mesoderm5.72e-0737
gastrointestinal system8.24e-0735
hindgut8.39e-0719
Disease
Ontology termp-valuen
carcinoma3.72e-37106
cell type cancer1.01e-31143
cancer4.18e-19235
disease of cellular proliferation6.66e-18239
adenocarcinoma9.74e-1225
disease of anatomical entity4.35e-0839
respiratory system cancer2.32e-0716
lung cancer9.91e-0715


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
E2F1#186963.271592809919550.003389959241809890.0173008186696336
EP300#203364.515961150815470.0005799248109934980.00486597311282638
FOXA1#316967.387613166256973.56196695095157e-050.000689926310071275
FOXA2#3170616.42030916844353.37701953018255e-071.67789030786268e-05
GATA3#2625618.15767757147071.86572751230391e-071.01804971607894e-05
HEY1#2346273.142308589082220.001258763462843770.00845699564464074
HNF4A#3172512.85127242386321.64120812799935e-050.000378965588503481
MYC#460974.061774789029540.0002355556796573370.00256743890917686
POLR2A#543092.147453176558070.001029412892608020.00728442666109421
RXRA#6256613.38307809275551.12450168564813e-064.62551522439564e-05
SIN3A#2594263.605923151210090.002003057991334320.0116466637098856
ZBTB7A#5134164.901272871917260.0003669910981056530.00365622276972778



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.