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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1119_nonsmall_smallcell_argyrophil_small_duodenum_esophagus_cerebellum
|full_id=C1119_nonsmall_smallcell_argyrophil_small_duodenum_esophagus_cerebellum
|gostat_on_coexpression_clusters=GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.0100553396915107!114131$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0100553396915107!114131$GO:0019933!cAMP-mediated signaling!0.0100553396915107!114131$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0100553396915107!114131$GO:0019935!cyclic-nucleotide-mediated signaling!0.0100553396915107!114131$GO:0005179!hormone activity!0.0149044311001217!114131$GO:0019932!second-messenger-mediated signaling!0.0157776992817614!114131
|gostat_on_coexpression_clusters=GO:0007189!G-protein signaling, adenylate cyclase activating pathway!0.0100553396915107!114131$GO:0007188!G-protein signaling, coupled to cAMP nucleotide second messenger!0.0100553396915107!114131$GO:0019933!cAMP-mediated signaling!0.0100553396915107!114131$GO:0007187!G-protein signaling, coupled to cyclic nucleotide second messenger!0.0100553396915107!114131$GO:0019935!cyclic-nucleotide-mediated signaling!0.0100553396915107!114131$GO:0005179!hormone activity!0.0149044311001217!114131$GO:0019932!second-messenger-mediated signaling!0.0157776992817614!114131

Revision as of 13:35, 12 September 2012


Full id: C1119_nonsmall_smallcell_argyrophil_small_duodenum_esophagus_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:5406920..5406934,+p2@UCN3
Hg19::chr10:5406935..5406962,+p1@UCN3
Hg19::chr10:5407062..5407072,+p3@UCN3
Hg19::chr10:5407085..5407093,+p5@UCN3
Hg19::chr2:241836244..241836276,-p2@C2orf54
Hg19::chr6:18208375..18208387,+p@chr6:18208375..18208387
+
Hg19::chr8:141018677..141018706,-p5@TRAPPC9


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:0007189G-protein signaling, adenylate cyclase activating pathway0.0100553396915107
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0100553396915107
GO:0019933cAMP-mediated signaling0.0100553396915107
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0100553396915107
GO:0019935cyclic-nucleotide-mediated signaling0.0100553396915107
GO:0005179hormone activity0.0149044311001217
GO:0019932second-messenger-mediated signaling0.0157776992817614



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
endodermal cell9.48e-0859
Uber Anatomy
Ontology termp-valuen
adult organism2.84e-25115
subdivision of digestive tract3.01e-16129
endodermal part of digestive tract3.01e-16129
digestive system3.47e-15155
digestive tract3.47e-15155
primitive gut3.47e-15155
endoderm-derived structure5.14e-15169
endoderm5.14e-15169
presumptive endoderm5.14e-15169
neural tube4.32e-1257
neural rod4.32e-1257
future spinal cord4.32e-1257
neural keel4.32e-1257
mixed endoderm/mesoderm-derived structure6.39e-12130
endo-epithelium3.71e-1182
foregut7.87e-1198
multi-tissue structure4.01e-10347
regional part of brain1.71e-0959
thoracic cavity element1.94e-0934
thoracic cavity1.94e-0934
thoracic segment organ5.20e-0935
organ part8.29e-09219
anatomical conduit1.13e-08241
organism subdivision1.42e-08365
lung1.66e-0822
respiratory tube1.66e-0822
respiration organ1.66e-0822
pair of lungs1.66e-0822
lung primordium1.66e-0822
lung bud1.66e-0822
anterior region of body1.83e-08129
craniocervical region1.83e-08129
neural plate3.78e-0886
presumptive neural plate3.78e-0886
organ4.44e-08511
neurectoderm5.67e-0890
tube7.22e-08194
organ segment9.30e-0897
trunk region element9.39e-08107
posterior neural tube1.21e-0715
chordal neural plate1.21e-0715
segmental subdivision of nervous system1.28e-0713
central nervous system1.40e-0782
respiratory system1.96e-0772
brain2.07e-0769
future brain2.07e-0769
head3.90e-07123
regional part of forebrain5.08e-0741
forebrain5.08e-0741
future forebrain5.08e-0741
respiratory tract8.48e-0753
epithelial bud8.72e-0737
anterior neural tube9.77e-0742
Disease
Ontology termp-valuen
carcinoma7.64e-08106


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.

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