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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal
|full_id=C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal
|gostat_on_coexpression_clusters=GO:0051093!negative regulation of developmental process!0.011056054917044!5594;57142$GO:0004423!iduronate-2-sulfatase activity!0.0148286915920051!3423$GO:0019858!cytosine metabolic process!0.0148286915920051!5594$GO:0019987!negative regulation of anti-apoptosis!0.0148286915920051!57142$GO:0043330!response to exogenous dsRNA!0.0148286915920051!5594$GO:0030517!negative regulation of axon extension!0.0148286915920051!57142$GO:0050793!regulation of developmental process!0.0148286915920051!5594;57142$GO:0032496!response to lipopolysaccharide!0.014872125970684!5594$GO:0031663!lipopolysaccharide-mediated signaling pathway!0.014872125970684!5594$GO:0001784!phosphotyrosine binding!0.014872125970684!5594$GO:0045309!protein phosphorylated amino acid binding!0.014872125970684!5594$GO:0043331!response to dsRNA!0.014872125970684!5594$GO:0050771!negative regulation of axonogenesis!0.014872125970684!57142$GO:0002237!response to molecule of bacterial origin!0.0214743725119483!5594$GO:0051219!phosphoprotein binding!0.0214743725119483!5594$GO:0050768!negative regulation of neurogenesis!0.0214743725119483!57142$GO:0045767!regulation of anti-apoptosis!0.0214743725119483!57142$GO:0030516!regulation of axon extension!0.0214743725119483!57142$GO:0006206!pyrimidine base metabolic process!0.0220381900309618!5594$GO:0048675!axon extension!0.027371766138232!57142$GO:0042981!regulation of apoptosis!0.0276148747912329!5594;57142$GO:0043067!regulation of programmed cell death!0.0276148747912329!5594;57142$GO:0043229!intracellular organelle!0.0291760839094347!5594;3423;57142;7562;6844$GO:0043226!organelle!0.0291760839094347!5594;3423;57142;7562;6844$GO:0009112!nucleobase metabolic process!0.0296154479966804!5594$GO:0050770!regulation of axonogenesis!0.0321850191184355!57142$GO:0008484!sulfuric ester hydrolase activity!0.0381317353245734!3423$GO:0004707!MAP kinase activity!0.0390634055895234!5594$GO:0019717!synaptosome!0.0399303007690236!6844$GO:0050767!regulation of neurogenesis!0.0407388984608223!57142$GO:0006915!apoptosis!0.0418259096100216!5594;57142$GO:0012501!programmed cell death!0.0418259096100216!5594;57142$GO:0008219!cell death!0.0435619786122206!5594;57142$GO:0016265!death!0.0435619786122206!5594;57142$GO:0030203!glycosaminoglycan metabolic process!0.0446382964742239!3423$GO:0006022!aminoglycan metabolic process!0.0446382964742239!3423$GO:0030176!integral to endoplasmic reticulum membrane!0.0460296366314013!57142$GO:0044424!intracellular part!0.0465090500924841!5594;3423;57142;7562;6844$GO:0030334!regulation of cell migration!0.0477864562370677!57142$GO:0009653!anatomical structure morphogenesis!0.0477864562370677!5594;57142$GO:0031227!intrinsic to endoplasmic reticulum membrane!0.0477864562370677!57142$GO:0045596!negative regulation of cell differentiation!0.0493315820358417!5594$GO:0005737!cytoplasm!0.0493315820358417!5594;3423;57142;6844$GO:0051270!regulation of cell motility!0.0498513608352335!57142$GO:0048523!negative regulation of cellular process!0.0498513608352335!5594;57142$GO:0040012!regulation of locomotion!0.0498513608352335!57142$GO:0040011!locomotion!0.0498513608352335!57142
|id=C317
|id=C317
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C317_Neutrophils_medial_amygdala_occipital_hippocampus_brain_parietal



Phase1 CAGE Peaks

Hg19::chr10:12872736..12872766,+p@chr10:12872736..12872766
+
Hg19::chr10:28872321..28872338,+p@chr10:28872321..28872338
+
Hg19::chr17:8063613..8063632,-p19@VAMP2
Hg19::chr17:8063633..8063652,-p13@VAMP2
Hg19::chr17:8063773..8063784,-p17@VAMP2
Hg19::chr17:8063896..8063935,-p5@VAMP2
Hg19::chr17:8063940..8064027,-p3@VAMP2
Hg19::chr17:8064030..8064075,-p4@VAMP2
Hg19::chr17:8064076..8064105,-p7@VAMP2
Hg19::chr17:8064108..8064167,-p2@VAMP2
Hg19::chr17:8064820..8064846,-p@chr17:8064820..8064846
-
Hg19::chr17:8064981..8064994,-p@chr17:8064981..8064994
-
Hg19::chr17:8065006..8065022,-p@chr17:8065006..8065022
-
Hg19::chr17:8065032..8065092,-p@chr17:8065032..8065092
-
Hg19::chr17:8065618..8065647,-p6@VAMP2
Hg19::chr19:21476394..21476407,-p5@ZNF708
Hg19::chr1:182352898..182352944,-p@chr1:182352898..182352944
-
Hg19::chr22:22162032..22162049,-p@chr22:22162032..22162049
-
Hg19::chr22:22221658..22221669,-p2@MAPK1
Hg19::chr2:55252842..55252854,-p37@RTN4
Hg19::chr2:55253582..55253618,-p21@RTN4
Hg19::chr4:146296807..146296819,+p2@RTN3P1
Hg19::chr5:108714170..108714199,-p@chr5:108714170..108714199
-
Hg19::chr5:108714529..108714568,-p@chr5:108714529..108714568
-
Hg19::chr5:108717346..108717361,-p@chr5:108717346..108717361
-
Hg19::chr7:135614485..135614494,-p@chr7:135614485..135614494
-
Hg19::chrX:148561290..148561301,-p@chrX:148561290..148561301
-
Hg19::chrX:148561796..148561820,-p7@IDS
Hg19::chrX:148562594..148562662,-p9@IDS
Hg19::chrX:148562710..148562819,-p5@IDS
Hg19::chrX:148563677..148563702,-p15@IDS
Hg19::chrX:148564109..148564137,-p@chrX:148564109..148564137
-
Hg19::chrX:148564140..148564173,-p@chrX:148564140..148564173
-
Hg19::chrX:148564210..148564228,-p@chrX:148564210..148564228
-
Hg19::chrX:148568487..148568517,-p@chrX:148568487..148568517
-
Hg19::chrX:148579666..148579690,-p12@IDS
Hg19::chrX:17095433..17095443,+p@chrX:17095433..17095443
+


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:0051093negative regulation of developmental process0.011056054917044
GO:0004423iduronate-2-sulfatase activity0.0148286915920051
GO:0019858cytosine metabolic process0.0148286915920051
GO:0019987negative regulation of anti-apoptosis0.0148286915920051
GO:0043330response to exogenous dsRNA0.0148286915920051
GO:0030517negative regulation of axon extension0.0148286915920051
GO:0050793regulation of developmental process0.0148286915920051
GO:0032496response to lipopolysaccharide0.014872125970684
GO:0031663lipopolysaccharide-mediated signaling pathway0.014872125970684
GO:0001784phosphotyrosine binding0.014872125970684
GO:0045309protein phosphorylated amino acid binding0.014872125970684
GO:0043331response to dsRNA0.014872125970684
GO:0050771negative regulation of axonogenesis0.014872125970684
GO:0002237response to molecule of bacterial origin0.0214743725119483
GO:0051219phosphoprotein binding0.0214743725119483
GO:0050768negative regulation of neurogenesis0.0214743725119483
GO:0045767regulation of anti-apoptosis0.0214743725119483
GO:0030516regulation of axon extension0.0214743725119483
GO:0006206pyrimidine base metabolic process0.0220381900309618
GO:0048675axon extension0.027371766138232
GO:0042981regulation of apoptosis0.0276148747912329
GO:0043067regulation of programmed cell death0.0276148747912329
GO:0043229intracellular organelle0.0291760839094347
GO:0043226organelle0.0291760839094347
GO:0009112nucleobase metabolic process0.0296154479966804
GO:0050770regulation of axonogenesis0.0321850191184355
GO:0008484sulfuric ester hydrolase activity0.0381317353245734
GO:0004707MAP kinase activity0.0390634055895234
GO:0019717synaptosome0.0399303007690236
GO:0050767regulation of neurogenesis0.0407388984608223
GO:0006915apoptosis0.0418259096100216
GO:0012501programmed cell death0.0418259096100216
GO:0008219cell death0.0435619786122206
GO:0016265death0.0435619786122206
GO:0030203glycosaminoglycan metabolic process0.0446382964742239
GO:0006022aminoglycan metabolic process0.0446382964742239
GO:0030176integral to endoplasmic reticulum membrane0.0460296366314013
GO:0044424intracellular part0.0465090500924841
GO:0030334regulation of cell migration0.0477864562370677
GO:0009653anatomical structure morphogenesis0.0477864562370677
GO:0031227intrinsic to endoplasmic reticulum membrane0.0477864562370677
GO:0045596negative regulation of cell differentiation0.0493315820358417
GO:0005737cytoplasm0.0493315820358417
GO:0051270regulation of cell motility0.0498513608352335
GO:0048523negative regulation of cellular process0.0498513608352335
GO:0040012regulation of locomotion0.0498513608352335
GO:0040011locomotion0.0498513608352335



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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