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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C278_amygdala_hippocampus_insula_medial_putamen_temporal_olfactory
|full_id=C278_amygdala_hippocampus_insula_medial_putamen_temporal_olfactory
|id=C278
|id=C278

Revision as of 15:34, 12 September 2012


Full id: C278_amygdala_hippocampus_insula_medial_putamen_temporal_olfactory



Phase1 CAGE Peaks

Hg19::chr10:126694575..126694592,-p16@CTBP2
Hg19::chr11:134282221..134282236,-p6@B3GAT1
Hg19::chr12:123466296..123466326,+p9@ARL6IP4
Hg19::chr13:101712292..101712306,-p@chr13:101712292..101712306
-
Hg19::chr13:44721892..44721904,-p@chr13:44721892..44721904
-
Hg19::chr14:23983481..23983496,+p@chr14:23983481..23983496
+
Hg19::chr14:71905725..71905743,+p@chr14:71905725..71905743
+
Hg19::chr14:76241843..76241862,+p@chr14:76241843..76241862
+
Hg19::chr14:94640408..94640419,+p7@PPP4R4
Hg19::chr15:26147599..26147637,+p1@ENST00000557171
Hg19::chr15:77988462..77988479,-p15@LINGO1
Hg19::chr16:19183650..19183662,+p8@SYT17
Hg19::chr16:19183671..19183690,+p5@SYT17
Hg19::chr16:19183729..19183750,+p7@SYT17
Hg19::chr16:57980465..57980483,-p@chr16:57980465..57980483
-
Hg19::chr16:84002103..84002117,+p2@NECAB2
Hg19::chr17:1029026..1029035,-p37@ABR
Hg19::chr17:57604227..57604236,-p@chr17:57604227..57604236
-
Hg19::chr18:32402321..32402331,+p@chr18:32402321..32402331
+
Hg19::chr19:10506556..10506567,-p6@CDC37
Hg19::chr1:95975684..95975731,+p1@ENST00000432146
p1@ENST00000440116
p1@ENST00000456933
Hg19::chr22:39178758..39178776,-p2@DNAL4
Hg19::chr2:10508688..10508712,+p8@HPCAL1
Hg19::chr2:10508772..10508805,+p4@HPCAL1
Hg19::chr2:183387791..183387813,-p12@PDE1A
Hg19::chr2:242811874..242811904,+p1@CXXC11
Hg19::chr2:242814260..242814263,+p@chr2:242814260..242814263
+
Hg19::chr3:113023094..113023109,-p3@WDR52
Hg19::chr3:113023157..113023168,-p4@WDR52
Hg19::chr3:131756559..131756572,-p7@CPNE4
Hg19::chr3:131756595..131756614,-p4@CPNE4
Hg19::chr3:131756632..131756637,-p11@CPNE4
Hg19::chr3:131756644..131756651,-p13@CPNE4
Hg19::chr3:71777824..71777833,-p28@EIF4E3
Hg19::chr4:118735142..118735153,-p@chr4:118735142..118735153
-
Hg19::chr4:139230927..139230941,+p2@ENST00000510736
p2@ENST00000515282
Hg19::chr4:46391095..46391114,-p14@GABRA2
Hg19::chr6:76072731..76072770,-p8@FILIP1
Hg19::chr6:90272488..90272510,+p7@ANKRD6
Hg19::chr7:13141010..13141018,+p2@ENST00000443947
Hg19::chr7:29845734..29845742,+p16@WIPF3
Hg19::chr8:54752406..54752429,-p5@ATP6V1H
Hg19::chr8:89554843..89554848,+p2@ENST00000518631
Hg19::chr8:89554909..89554920,+p3@ENST00000518631
Hg19::chr9:13165461..13165485,-p13@MPDZ


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


p.valueFDRnGenesnPathwayName
1.85355118110106e-050.01173297897636974220Signalling by NGF (Reactome):REACT_11061



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


No GOStat results

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
neural tube4.35e-2957
neural rod4.35e-2957
future spinal cord4.35e-2957
neural keel4.35e-2957
central nervous system5.95e-2882
regional part of nervous system4.11e-2794
nervous system4.11e-2794
brain4.61e-2469
future brain4.61e-2469
regional part of brain4.70e-2459
anterior neural tube6.06e-2442
regional part of forebrain1.18e-2341
forebrain1.18e-2341
future forebrain1.18e-2341
neurectoderm8.13e-2390
adult organism2.09e-22115
telencephalon4.72e-2134
gray matter5.44e-2134
brain grey matter5.44e-2134
neural plate8.49e-2186
presumptive neural plate8.49e-2186
regional part of telencephalon2.22e-2033
cerebral hemisphere6.31e-2032
regional part of cerebral cortex3.47e-1622
cerebral cortex1.62e-1525
pallium1.62e-1525
pre-chordal neural plate2.11e-1561
neocortex8.51e-1520
ectoderm1.57e-13173
presumptive ectoderm1.57e-13173
ectoderm-derived structure3.95e-12169
head1.13e-09123
anterior region of body3.92e-09129
craniocervical region3.92e-09129
basal ganglion3.82e-079
nuclear complex of neuraxis3.82e-079
aggregate regional part of brain3.82e-079
collection of basal ganglia3.82e-079
cerebral subcortex3.82e-079
nucleus of brain6.07e-079
neural nucleus6.07e-079


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