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{{Coexpression_clusters
 
{{Coexpression_clusters
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|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
 
|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

Revision as of 06:32, 12 September 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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.33e-4994
nervous system3.33e-4994
adult organism4.26e-48115
central nervous system1.33e-4782
neural tube1.66e-4557
neural rod1.66e-4557
future spinal cord1.66e-4557
neural keel1.66e-4557
regional part of brain2.13e-4159
brain2.39e-3969
future brain2.39e-3969
neurectoderm8.93e-3990
neural plate1.98e-3786
presumptive neural plate1.98e-3786
ectoderm2.48e-33173
presumptive ectoderm2.48e-33173
anterior neural tube2.18e-3242
ectoderm-derived structure6.37e-32169
regional part of forebrain6.99e-3241
forebrain6.99e-3241
future forebrain6.99e-3241
gray matter6.75e-2634
brain grey matter6.75e-2634
telencephalon8.22e-2634
regional part of telencephalon7.54e-2533
cerebral hemisphere4.33e-2432
pre-chordal neural plate1.03e-2361
anterior region of body6.63e-23129
craniocervical region6.63e-23129
head5.83e-22123
regional part of cerebral cortex2.76e-1922
cerebral cortex1.53e-1825
pallium1.53e-1825
neocortex1.23e-1720
posterior neural tube6.23e-1415
chordal neural plate6.23e-1415
segmental subdivision of nervous system7.68e-1213
segmental subdivision of hindbrain3.04e-1112
hindbrain3.04e-1112
presumptive hindbrain3.04e-1112
organ part7.98e-11219
nucleus of brain7.75e-099
neural nucleus7.75e-099
brainstem1.11e-088
basal ganglion1.16e-089
nuclear complex of neuraxis1.16e-089
aggregate regional part of brain1.16e-089
collection of basal ganglia1.16e-089
cerebral subcortex1.16e-089
regional part of metencephalon2.36e-089
metencephalon2.36e-089
future metencephalon2.36e-089
multi-cellular organism3.32e-08659
tube5.04e-08194
organ7.93e-08511
embryo1.09e-07612
diencephalon1.74e-077
future diencephalon1.74e-077
epithelium2.96e-07309
anatomical conduit3.02e-07241
telencephalic nucleus6.44e-077
cell layer6.47e-07312
gyrus6.53e-076
anatomical cluster7.96e-07286


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
SUZ12#2351255.331466054368390.002412655065050490.0135989682302773



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