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Coexpression cluster:C275: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal
|full_id=C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal
|gostat_on_coexpression_clusters=GO:0051966!regulation of synaptic transmission, glutamatergic!0.0414160162571539!2897$GO:0035249!synaptic transmission, glutamatergic!0.0414160162571539!2897$GO:0016021!integral to membrane!0.0414160162571539!2897;116534;57084;135152;341359;3773$GO:0031224!intrinsic to membrane!0.0414160162571539!2897;116534;57084;135152;341359;3773$GO:0051179!localization!0.0414160162571539!2897;56751;57084;341359;3773$GO:0015018!galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity!0.0414160162571539!135152$GO:0015277!kainate selective glutamate receptor activity!0.0414160162571539!2897$GO:0044425!membrane part!0.04833425076599!2897;116534;57084;135152;341359;3773
|id=C275
|id=C275
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C275_pons_medulla_cerebellum_locus_thalamus_diencephalon_spinal



Phase1 CAGE Peaks

Hg19::chr10:17045960..17045970,-p@chr10:17045960..17045970
-
Hg19::chr10:61043434..61043446,-p13@FAM13C
Hg19::chr10:61043452..61043467,-p16@FAM13C
Hg19::chr11:22359520..22359556,+p3@SLC17A6
Hg19::chr11:22359562..22359575,+p6@SLC17A6
Hg19::chr11:22359879..22359909,+p2@SLC17A6
Hg19::chr11:3224761..3224787,-p@chr11:3224761..3224787
-
Hg19::chr11:3224982..3224985,-p@chr11:3224982..3224985
-
Hg19::chr11:3224990..3225000,-p@chr11:3224990..3225000
-
Hg19::chr11:3253592..3253608,-p2@MRGPRE
Hg19::chr11:3253635..3253658,-p1@MRGPRE
Hg19::chr11:3253663..3253670,-p4@MRGPRE
Hg19::chr11:3253872..3253882,-p3@MRGPRE
Hg19::chr12:33592574..33592584,-p6@SYT10
Hg19::chr13:93587956..93587973,+p@chr13:93587956..93587973
+
Hg19::chr16:47920709..47920716,-p4@uc002eex.1
Hg19::chr16:49669972..49669983,-p@chr16:49669972..49669983
-
Hg19::chr16:49670005..49670020,-p@chr16:49670005..49670020
-
Hg19::chr16:67237164..67237171,+p@chr16:67237164..67237171
+
Hg19::chr17:68101117..68101162,+p2@KCNJ16
Hg19::chr1:205313500..205313511,-p11@KLHDC8A
Hg19::chr1:216692584..216692595,-p@chr1:216692584..216692595
-
Hg19::chr1:216692717..216692725,-p@chr1:216692717..216692725
-
Hg19::chr1:216692728..216692741,-p@chr1:216692728..216692741
-
Hg19::chr1:218222373..218222381,-p@chr1:218222373..218222381
-
Hg19::chr1:218222386..218222394,-p@chr1:218222386..218222394
-
Hg19::chr21:31312092..31312103,-p7@GRIK1
Hg19::chr2:17381145..17381164,-p@chr2:17381145..17381164
-
Hg19::chr2:72381655..72381673,-p@chr2:72381655..72381673
-
Hg19::chr4:117675601..117675614,+p@chr4:117675601..117675614
+
Hg19::chr4:117675642..117675654,+p@chr4:117675642..117675654
+
Hg19::chr4:186661365..186661384,-p46@SORBS2
Hg19::chr4:82965824..82965835,-p6@ENST00000508294
p6@ENST00000510780
p6@ENST00000512343
p6@ENST00000512716
p6@ENST00000514050
Hg19::chr5:126959224..126959239,+p@chr5:126959224..126959239
+
Hg19::chr5:126959900..126959932,+p@chr5:126959900..126959932
+
Hg19::chr5:126959946..126959960,+p@chr5:126959946..126959960
+
Hg19::chr6:140415977..140415987,-p@chr6:140415977..140415987
-
Hg19::chr6:140415989..140415997,-p@chr6:140415989..140415997
-
Hg19::chr6:140416018..140416025,-p@chr6:140416018..140416025
-
Hg19::chr6:71665623..71665630,-p13@B3GAT2
Hg19::chr7:31569075..31569083,+p3@CCDC129
Hg19::chr7:31569365..31569379,+p1@CCDC129
Hg19::chr9:135457530..135457541,+p2@BARHL1
Hg19::chr9:135457972..135457978,+p8@BARHL1
Hg19::chr9:135458021..135458030,+p6@BARHL1
Hg19::chr9:135458288..135458301,+p3@BARHL1
Hg19::chr9:135458306..135458314,+p9@BARHL1


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:0051966regulation of synaptic transmission, glutamatergic0.0414160162571539
GO:0035249synaptic transmission, glutamatergic0.0414160162571539
GO:0016021integral to membrane0.0414160162571539
GO:0031224intrinsic to membrane0.0414160162571539
GO:0051179localization0.0414160162571539
GO:0015018galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity0.0414160162571539
GO:0015277kainate selective glutamate receptor activity0.0414160162571539
GO:0044425membrane part0.04833425076599



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


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