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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C481_lymph_vein_tonsil_appendix_submaxillary_trachea_temporal
|full_id=C481_lymph_vein_tonsil_appendix_submaxillary_trachea_temporal
|gostat_on_coexpression_clusters=GO:0006954!inflammatory response!0.000145883258857863!6614;6366;6363$GO:0009611!response to wounding!0.000224102063886895!6614;6366;6363$GO:0006952!defense response!0.000298296102949237!6614;6366;6363$GO:0009605!response to external stimulus!0.000298296102949237!6614;6366;6363$GO:0008009!chemokine activity!0.000298296102949237!6366;6363$GO:0042379!chemokine receptor binding!0.000298296102949237!6366;6363$GO:0001664!G-protein-coupled receptor binding!0.000467526340171569!6366;6363$GO:0042330!taxis!0.000697921044060905!6366;6363$GO:0006935!chemotaxis!0.000697921044060905!6366;6363$GO:0006955!immune response!0.000888594413708518!3500;6366;6363$GO:0007626!locomotory behavior!0.000888594413708518!6366;6363$GO:0006950!response to stress!0.000888594413708518!6614;6366;6363$GO:0002376!immune system process!0.00119268236723501!3500;6366;6363$GO:0007610!behavior!0.00186582398897099!6366;6363$GO:0005125!cytokine activity!0.00193525642725649!6366;6363$GO:0005615!extracellular space!0.00522505994912853!6366;6363$GO:0042221!response to chemical stimulus!0.0061060531140756!6366;6363$GO:0044421!extracellular region part!0.013598993597661!6366;6363$GO:0005515!protein binding!0.0153227288807027!3500;6614;6366;6363$GO:0005102!receptor binding!0.015815430263547!6366;6363$GO:0009615!response to virus!0.0309701819201496!6363$GO:0007160!cell-matrix adhesion!0.0309701819201496!6614$GO:0031589!cell-substrate adhesion!0.0309701819201496!6614$GO:0006874!cellular calcium ion homeostasis!0.031476901111509!6363$GO:0055074!calcium ion homeostasis!0.031476901111509!6363$GO:0006875!cellular metal ion homeostasis!0.031476901111509!6363$GO:0055065!metal ion homeostasis!0.031476901111509!6363$GO:0003823!antigen binding!0.0420367370657912!3500$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0420367370657912!6363$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0420367370657912!6363$GO:0030003!cellular cation homeostasis!0.0429745128846612!6363$GO:0055080!cation homeostasis!0.0429745128846612!6363$GO:0051707!response to other organism!0.0429745128846612!6363$GO:0055082!cellular chemical homeostasis!0.0465524847824084!6363$GO:0006873!cellular ion homeostasis!0.0465524847824084!6363
|id=C481
|id=C481
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C481_lymph_vein_tonsil_appendix_submaxillary_trachea_temporal



Phase1 CAGE Peaks

Hg19::chr14:106208703..106208728,-p1@JN222933
p1@S76144
Hg19::chr14:106209113..106209156,+p@chr14:106209113..106209156
+
Hg19::chr14:106209338..106209364,+p@chr14:106209338..106209364
+
Hg19::chr14:106209368..106209399,-p1@IGHG1
Hg19::chr14:106236279..106236286,-p@chr14:106236279..106236286
-
Hg19::chr14:106237042..106237061,-p@chr14:106237042..106237061
-
Hg19::chr14:106321278..106321330,-p1@J00257
Hg19::chr14:106642049..106642054,-p1@IGHV1-18
Hg19::chr20:3687858..3687862,-p1@SIGLEC1
Hg19::chr22:22676808..22676813,+p1@IGLV1-51
Hg19::chr22:23237875..23237897,+p@chr22:23237875..23237897
+
Hg19::chr22:23237884..23237916,-p@chr22:23237884..23237916
-
Hg19::chr2:89156823..89156840,-p@chr2:89156823..89156840
-
Hg19::chr2:89156853..89156874,-p@chr2:89156853..89156874
-
Hg19::chr2:89157057..89157073,+p5@CU688247
p5@CU689025
p5@CU689831
p5@CU689833
p5@CU689835
p5@CU691143
Hg19::chr2:90007649..90007660,+p1@IGKV1D-27
Hg19::chr9:34691263..34691278,-p1@CCL19
Hg19::chr9:34709547..34709591,+p@chr9:34709547..34709591
+
Hg19::chr9:34709874..34709885,-p@chr9:34709874..34709885
-
Hg19::chr9:34710125..34710140,-p1@CCL21


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:0006954inflammatory response0.000145883258857863
GO:0009611response to wounding0.000224102063886895
GO:0006952defense response0.000298296102949237
GO:0009605response to external stimulus0.000298296102949237
GO:0008009chemokine activity0.000298296102949237
GO:0042379chemokine receptor binding0.000298296102949237
GO:0001664G-protein-coupled receptor binding0.000467526340171569
GO:0042330taxis0.000697921044060905
GO:0006935chemotaxis0.000697921044060905
GO:0006955immune response0.000888594413708518
GO:0007626locomotory behavior0.000888594413708518
GO:0006950response to stress0.000888594413708518
GO:0002376immune system process0.00119268236723501
GO:0007610behavior0.00186582398897099
GO:0005125cytokine activity0.00193525642725649
GO:0005615extracellular space0.00522505994912853
GO:0042221response to chemical stimulus0.0061060531140756
GO:0044421extracellular region part0.013598993597661
GO:0005515protein binding0.0153227288807027
GO:0005102receptor binding0.015815430263547
GO:0009615response to virus0.0309701819201496
GO:0007160cell-matrix adhesion0.0309701819201496
GO:0031589cell-substrate adhesion0.0309701819201496
GO:0006874cellular calcium ion homeostasis0.031476901111509
GO:0055074calcium ion homeostasis0.031476901111509
GO:0006875cellular metal ion homeostasis0.031476901111509
GO:0055065metal ion homeostasis0.031476901111509
GO:0003823antigen binding0.0420367370657912
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0420367370657912
GO:0055066di-, tri-valent inorganic cation homeostasis0.0420367370657912
GO:0030003cellular cation homeostasis0.0429745128846612
GO:0055080cation homeostasis0.0429745128846612
GO:0051707response to other organism0.0429745128846612
GO:0055082cellular chemical homeostasis0.0465524847824084
GO:0006873cellular ion homeostasis0.0465524847824084



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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