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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus
|full_id=C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus
|gostat_on_coexpression_clusters=GO:0016403!dimethylargininase activity!0.0259898459425752!23576$GO:0043121!neurotrophin binding!0.0259898459425752!4915$GO:0007263!nitric oxide mediated signal transduction!0.0259898459425752!23576$GO:0006527!arginine catabolic process!0.0259898459425752!23576$GO:0015250!water channel activity!0.0259898459425752!361$GO:0005372!water transporter activity!0.0297760869891295!361$GO:0009065!glutamine family amino acid catabolic process!0.0396763042251676!23576$GO:0016813!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines!0.0396763042251676!23576$GO:0007399!nervous system development!0.0396763042251676!4915;361$GO:0006525!arginine metabolic process!0.040578659960201!23576$GO:0000051!urea cycle intermediate metabolic process!0.0472042095940519!23576
|gostat_on_coexpression_clusters=GO:0016403!dimethylargininase activity!0.0259898459425752!23576$GO:0043121!neurotrophin binding!0.0259898459425752!4915$GO:0007263!nitric oxide mediated signal transduction!0.0259898459425752!23576$GO:0006527!arginine catabolic process!0.0259898459425752!23576$GO:0015250!water channel activity!0.0259898459425752!361$GO:0005372!water transporter activity!0.0297760869891295!361$GO:0009065!glutamine family amino acid catabolic process!0.0396763042251676!23576$GO:0016813!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines!0.0396763042251676!23576$GO:0007399!nervous system development!0.0396763042251676!4915;361$GO:0006525!arginine metabolic process!0.040578659960201!23576$GO:0000051!urea cycle intermediate metabolic process!0.0472042095940519!23576

Revision as of 18:03, 12 September 2012


Full id: C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:41365353..41365362,+p@chr12:41365353..41365362
+
Hg19::chr15:59664884..59664903,+p4@FAM81A
Hg19::chr17:42991223..42991232,-p@chr17:42991223..42991232
-
Hg19::chr18:24434129..24434169,-p8@AQP4
Hg19::chr18:24434187..24434198,-p13@AQP4
Hg19::chr18:24435190..24435201,-p@chr18:24435190..24435201
-
Hg19::chr18:74691180..74691220,-p@chr18:74691180..74691220
-
Hg19::chr18:74691599..74691602,+p@chr18:74691599..74691602
+
Hg19::chr1:204991565..204991578,+p@chr1:204991565..204991578
+
Hg19::chr1:68849935..68849943,-p@chr1:68849935..68849943
-
Hg19::chr1:85786236..85786252,-p30@DDAH1
Hg19::chr6:164348089..164348100,+p@chr6:164348089..164348100
+
Hg19::chr8:26491964..26491967,+p@chr8:26491964..26491967
+
Hg19::chr8:28965684..28965712,-p4@KIF13B
Hg19::chr9:87426149..87426182,+p25@NTRK2
Hg19::chr9:87426979..87426990,+p54@NTRK2
Hg19::chr9:87427842..87427853,+p46@NTRK2
Hg19::chr9:87429337..87429348,+p57@NTRK2
Hg19::chrX:13792037..13792048,-p@chrX:13792037..13792048
-


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:0016403dimethylargininase activity0.0259898459425752
GO:0043121neurotrophin binding0.0259898459425752
GO:0007263nitric oxide mediated signal transduction0.0259898459425752
GO:0006527arginine catabolic process0.0259898459425752
GO:0015250water channel activity0.0259898459425752
GO:0005372water transporter activity0.0297760869891295
GO:0009065glutamine family amino acid catabolic process0.0396763042251676
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.0396763042251676
GO:0007399nervous system development0.0396763042251676
GO:0006525arginine metabolic process0.040578659960201
GO:0000051urea cycle intermediate metabolic process0.0472042095940519



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
central nervous system6.28e-3682
neural tube6.29e-3557
neural rod6.29e-3557
future spinal cord6.29e-3557
neural keel6.29e-3557
regional part of nervous system4.38e-3294
nervous system4.38e-3294
brain5.70e-3069
future brain5.70e-3069
adult organism1.53e-29115
ectoderm2.77e-29173
presumptive ectoderm2.77e-29173
regional part of brain8.32e-2959
ectoderm-derived structure1.48e-28169
neurectoderm1.70e-2890
neural plate5.50e-2886
presumptive neural plate5.50e-2886
regional part of forebrain3.13e-2741
forebrain3.13e-2741
future forebrain3.13e-2741
anterior neural tube3.24e-2742
head1.54e-23123
gray matter2.72e-2334
brain grey matter2.72e-2334
telencephalon4.01e-2334
anterior region of body1.13e-22129
craniocervical region1.13e-22129
regional part of telencephalon1.57e-2233
cerebral hemisphere9.13e-2232
pre-chordal neural plate4.23e-1961
cerebral cortex3.34e-1725
pallium3.34e-1725
regional part of cerebral cortex1.20e-1522
neocortex2.92e-1420
organism subdivision1.50e-12365
organ4.02e-11511
multi-cellular organism6.17e-10659
anatomical conduit1.76e-09241
organ part7.45e-09219
posterior neural tube8.53e-0915
chordal neural plate8.53e-0915
anatomical group9.27e-09626
anatomical system1.31e-08625
anatomical cluster1.77e-08286
nucleus of brain1.52e-079
neural nucleus1.52e-079
basal ganglion1.88e-079
nuclear complex of neuraxis1.88e-079
aggregate regional part of brain1.88e-079
collection of basal ganglia1.88e-079
cerebral subcortex1.88e-079
segmental subdivision of nervous system1.92e-0713
embryo2.29e-07612
multi-tissue structure2.31e-07347
tube3.55e-07194
embryonic structure7.21e-07605
developing anatomical structure7.21e-07605
segmental subdivision of hindbrain8.38e-0712
hindbrain8.38e-0712
presumptive hindbrain8.38e-0712


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.