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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.283170292813857,0.27957974710499,0.240426435485783,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.134908379262287,0.136969166919767,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.157182883491893,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.521024293842005,0.72948374362925,0.554033591364562,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.385025702298159,0,0.323420977254527,0.361016943643633,0,0,0,0,0,0,0,0,0,0,0,0,0,0.458589005859429,0.655870419754355,0.453788509586933,0.297791960698471,0.272283065509648,0.140942333732381,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.62408641548959,0.303820231799265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197077988480498,0.361750587179236,0,0,0,0,0,0,0,0,0,0.498131822028796,0.567104148880459,0.943710890136937,0.206001468090966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.370533365729012,0.222795072775063,0,0,0.269748880723171,0.428898149930474,0.443062714183179,0.624913746510849,0,0,0,0,0,0,0,0,0,0,0.0951833797824107,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.04680465889238,0,0,0,0,0,0,0,0,0,0,0,0,0.056685265411804,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11192662148705,0.0697118989465167,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.076245357210966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.214404368077712,0,0,0,0,0,0,0,0,0,0,0,0,0.0968963988523578,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0904423417827262,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.152177775803824,0.210071535945973,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778384462202319,0.0484300422256687,0.135723143846782,0.0474795670351238,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.140912384324609,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150582174035777,0.0684524727462707,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0713494635703484,0.313589818986914,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.122416778853372,0,0,0,0,0,0,0,0,0
|full_id=C362_Small_Mallassezderived_Urothelial_Gingival_Prostate_Keratinocyte_Tracheal
|full_id=C362_Small_Mallassezderived_Urothelial_Gingival_Prostate_Keratinocyte_Tracheal
|gostat_on_coexpression_clusters=GO:0007595!lactation!0.038081176237861!5744$GO:0046058!cAMP metabolic process!0.038081176237861!5744$GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.038081176237861!5744$GO:0009187!cyclic nucleotide metabolic process!0.038081176237861!5744$GO:0048609!reproductive process in a multicellular organism!0.038081176237861!5744$GO:0032504!multicellular organism reproduction!0.038081176237861!5744$GO:0007565!female pregnancy!0.038081176237861!5744$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.038081176237861!5744$GO:0019933!cAMP-mediated signaling!0.038081176237861!5744$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0436693462621119!5744$GO:0019935!cyclic-nucleotide-mediated signaling!0.0436693462621119!5744$GO:0008544!epidermis development!0.0442043833252614!5744$GO:0007398!ectoderm development!0.0442043833252614!5744
|gostat_on_coexpression_clusters=GO:0007595!lactation!0.038081176237861!5744$GO:0046058!cAMP metabolic process!0.038081176237861!5744$GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.038081176237861!5744$GO:0009187!cyclic nucleotide metabolic process!0.038081176237861!5744$GO:0048609!reproductive process in a multicellular organism!0.038081176237861!5744$GO:0032504!multicellular organism reproduction!0.038081176237861!5744$GO:0007565!female pregnancy!0.038081176237861!5744$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.038081176237861!5744$GO:0019933!cAMP-mediated signaling!0.038081176237861!5744$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0436693462621119!5744$GO:0019935!cyclic-nucleotide-mediated signaling!0.0436693462621119!5744$GO:0008544!epidermis development!0.0442043833252614!5744$GO:0007398!ectoderm development!0.0442043833252614!5744

Revision as of 16:35, 12 September 2012


Full id: C362_Small_Mallassezderived_Urothelial_Gingival_Prostate_Keratinocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr12:28124953..28124957,-p6@PTHLH
Hg19::chr12:28126393..28126427,-p@chr12:28126393..28126427
-
Hg19::chr14:51955483..51955495,+p23@FRMD6
Hg19::chr14:51955502..51955515,+p17@FRMD6
Hg19::chr14:51955524..51955550,+p9@FRMD6
Hg19::chr14:51955690..51955699,+p28@FRMD6
Hg19::chr14:51955719..51955733,+p15@FRMD6
Hg19::chr14:51955760..51955769,+p29@FRMD6
Hg19::chr14:51955771..51955826,+p6@FRMD6
Hg19::chr14:51955831..51955864,+p5@FRMD6
Hg19::chr14:51955873..51955899,+p12@FRMD6
Hg19::chr14:51955905..51955921,+p14@FRMD6
Hg19::chr14:51955948..51955957,+p34@FRMD6
Hg19::chr18:9617195..9617198,-p@chr18:9617195..9617198
-
Hg19::chr18:9649081..9649088,+p@chr18:9649081..9649088
+
Hg19::chr1:183213092..183213099,+p@chr1:183213092..183213099
+
Hg19::chr1:183213177..183213210,+p@chr1:183213177..183213210
+
Hg19::chr1:183213228..183213235,+p@chr1:183213228..183213235
+
Hg19::chr1:183213249..183213267,+p@chr1:183213249..183213267
+
Hg19::chr1:183213300..183213316,+p@chr1:183213300..183213316
+
Hg19::chr1:183213326..183213338,+p@chr1:183213326..183213338
+
Hg19::chr1:183213340..183213356,+p@chr1:183213340..183213356
+
Hg19::chr1:183213362..183213385,+p@chr1:183213362..183213385
+
Hg19::chr1:183213387..183213401,+p@chr1:183213387..183213401
+
Hg19::chr1:183213404..183213419,+p@chr1:183213404..183213419
+
Hg19::chr1:183213421..183213517,+p@chr1:183213421..183213517
+
Hg19::chr21:44957893..44957903,-p@chr21:44957893..44957903
-
Hg19::chr2:186298808..186298827,+p@chr2:186298808..186298827
+
Hg19::chr2:186298833..186298844,+p@chr2:186298833..186298844
+
Hg19::chr3:190252374..190252383,-p@chr3:190252374..190252383
-
Hg19::chr9:113802831..113802865,-p@chr9:113802831..113802865
-


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:0007595lactation0.038081176237861
GO:0046058cAMP metabolic process0.038081176237861
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.038081176237861
GO:0009187cyclic nucleotide metabolic process0.038081176237861
GO:0048609reproductive process in a multicellular organism0.038081176237861
GO:0032504multicellular organism reproduction0.038081176237861
GO:0007565female pregnancy0.038081176237861
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.038081176237861
GO:0019933cAMP-mediated signaling0.038081176237861
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0436693462621119
GO:0019935cyclic-nucleotide-mediated signaling0.0436693462621119
GO:0008544epidermis development0.0442043833252614
GO:0007398ectoderm development0.0442043833252614



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 cell6.40e-20254
endo-epithelial cell8.87e-1743
endodermal cell3.95e-1159
embryonic cell1.89e-10248
squamous epithelial cell2.66e-0962
respiratory epithelial cell1.51e-0813
epithelial cell of alimentary canal6.05e-0821
ecto-epithelial cell8.21e-0733
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure7.16e-12169
endoderm7.16e-12169
presumptive endoderm7.16e-12169
respiratory system1.21e-0972
orifice3.12e-0935
digestive system2.19e-08155
digestive tract2.19e-08155
primitive gut2.19e-08155
endo-epithelium2.76e-0782
reproductive structure3.90e-0759
reproductive system3.90e-0759
oral opening4.41e-0721
surface structure5.62e-0795
Disease
Ontology termp-valuen
squamous cell carcinoma1.79e-0914


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
STAT3#6774134.411388547193712.03318712616835e-067.42981211581164e-05



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.