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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C310_caudate_medulla_spinal_thalamus_locus_globus_hippocampus
|full_id=C310_caudate_medulla_spinal_thalamus_locus_globus_hippocampus
|gostat_on_coexpression_clusters=GO:0005856!cytoskeleton!0.0148251947762522!324;1501;667;10391;2670$GO:0022610!biological adhesion!0.0151374665443906!658;324;1501;667$GO:0007155!cell adhesion!0.0151374665443906!658;324;1501;667$GO:0051983!regulation of chromosome segregation!0.0151374665443906!324$GO:0051988!regulation of attachment of spindle microtubules to kinetochore!0.0151374665443906!324$GO:0008608!attachment of spindle microtubules to kinetochore!0.0151374665443906!324$GO:0005200!structural constituent of cytoskeleton!0.0151374665443906!667;2670$GO:0007050!cell cycle arrest!0.0157391534528605!324;667$GO:0005737!cytoplasm!0.0157391534528605!324;1501;10391;2670;114789;10335;667;10840$GO:0001550!ovarian cumulus expansion!0.0157391534528605!658$GO:0048165!fused antrum stage, oogenesis!0.0157391534528605!658$GO:0022605!oogenesis stage!0.0157391534528605!658$GO:0001547!antral ovarian follicle growth!0.0157391534528605!658$GO:0008092!cytoskeletal protein binding!0.0180510776937678!324;667;10391$GO:0009397!folic acid and derivative catabolic process!0.0180510776937678!10840$GO:0009258!10-formyltetrahydrofolate catabolic process!0.0180510776937678!10840$GO:0009256!10-formyltetrahydrofolate metabolic process!0.0180510776937678!10840$GO:0007010!cytoskeleton organization and biogenesis!0.0208843123068426!324;667;10391$GO:0030877!beta-catenin destruction complex!0.0208843123068426!324$GO:0043232!intracellular non-membrane-bound organelle!0.0208843123068426!324;1501;667;10391;2670$GO:0043228!non-membrane-bound organelle!0.0208843123068426!324;1501;667;10391;2670$GO:0060070!Wnt receptor signaling pathway through beta-catenin!0.0222302899749747!324$GO:0016155!formyltetrahydrofolate dehydrogenase activity!0.0222302899749747!10840$GO:0005025!transforming growth factor beta receptor activity, type I!0.0255610711707634!658$GO:0007158!neuron adhesion!0.028065349005499!1501$GO:0045786!negative regulation of progression through cell cycle!0.028065349005499!324;667$GO:0016328!lateral plasma membrane!0.029204055500909!324$GO:0008605!protein kinase CK2 regulator activity!0.029204055500909!324$GO:0045736!negative regulation of cyclin-dependent protein kinase activity!0.0306597459072613!324$GO:0008013!beta-catenin binding!0.0306597459072613!324$GO:0016020!membrane!0.032026848311643!324;1501;57628;10391;658;114789;10335;10079$GO:0001502!cartilage condensation!0.0340563595119381!658$GO:0016742!hydroxymethyl-, formyl- and related transferase activity!0.0340563595119381!10840$GO:0004274!dipeptidyl-peptidase IV activity!0.0360543689207515!57628$GO:0044425!membrane part!0.0387702042148781!658;324;114789;1501;10335;57628;10079$GO:0045104!intermediate filament cytoskeleton organization and biogenesis!0.038778576974243!667$GO:0045103!intermediate filament-based process!0.038778576974243!667$GO:0046332!SMAD binding!0.038778576974243!658$GO:0016337!cell-cell adhesion!0.038778576974243!658;1501$GO:0048477!oogenesis!0.038778576974243!658$GO:0000074!regulation of progression through cell cycle!0.038778576974243!324;667$GO:0051726!regulation of cell cycle!0.038778576974243!324;667$GO:0004675!transmembrane receptor protein serine/threonine kinase activity!0.038778576974243!658$GO:0001541!ovarian follicle development!0.038778576974243!658$GO:0030509!BMP signaling pathway!0.038778576974243!658$GO:0005024!transforming growth factor beta receptor activity!0.038778576974243!658$GO:0004012!phospholipid-translocating ATPase activity!0.038778576974243!10079$GO:0015247!aminophospholipid transporter activity!0.038778576974243!10079$GO:0008239!dipeptidyl-peptidase activity!0.038778576974243!57628$GO:0016806!dipeptidyl-peptidase and tripeptidyl-peptidase activity!0.038778576974243!57628$GO:0015914!phospholipid transport!0.0423412243388375!10079$GO:0031114!regulation of microtubule depolymerization!0.0423412243388375!324$GO:0007026!negative regulation of microtubule depolymerization!0.0423412243388375!324$GO:0031111!negative regulation of microtubule polymerization or depolymerization!0.04264988463264!324$GO:0007019!microtubule depolymerization!0.04264988463264!324$GO:0022601!menstrual cycle phase!0.0432029043855401!658$GO:0016528!sarcoplasm!0.0432029043855401!10335$GO:0022602!menstrual cycle process!0.0432029043855401!658$GO:0016529!sarcoplasmic reticulum!0.0432029043855401!10335$GO:0003779!actin binding!0.0441054878504274!667;10391$GO:0008585!female gonad development!0.0441054878504274!658$GO:0000287!magnesium ion binding!0.0441054878504274!658;10079$GO:0004372!glycine hydroxymethyltransferase activity!0.0441054878504274!10840$GO:0009953!dorsal/ventral pattern formation!0.0441054878504274!658$GO:0031110!regulation of microtubule polymerization or depolymerization!0.0441054878504274!324$GO:0046660!female sex differentiation!0.0441054878504274!658$GO:0046545!development of primary female sexual characteristics!0.0441054878504274!658$GO:0044464!cell part!0.0457671947271353!324;1501;57628;10391;2670;658;114789;10335;10079;667;10840$GO:0000776!kinetochore!0.0457671947271353!324$GO:0031109!microtubule polymerization or depolymerization!0.0459059997980458!324$GO:0005548!phospholipid transporter activity!0.0459059997980458!10079$GO:0042698!menstrual cycle!0.0459247048038725!658$GO:0043010!camera-type eye development!0.0459247048038725!658$GO:0016646!oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor!0.0459247048038725!10840$GO:0007292!female gamete generation!0.0459247048038725!658$GO:0006996!organelle organization and biogenesis!0.0459247048038725!324;667;10391$GO:0051216!cartilage development!0.0459247048038725!658$GO:0060173!limb development!0.0459247048038725!658$GO:0035107!appendage morphogenesis!0.0459247048038725!658$GO:0035108!limb morphogenesis!0.0459247048038725!658$GO:0048589!developmental growth!0.0459247048038725!658$GO:0048736!appendage development!0.0459247048038725!658
|id=C310
|id=C310
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C310_caudate_medulla_spinal_thalamus_locus_globus_hippocampus



Phase1 CAGE Peaks

Hg19::chr11:10715319..10715330,-p14@MRVI1
Hg19::chr11:121975826..121975852,-p1@ENST00000534195
Hg19::chr11:56998629..56998644,+p@chr11:56998629..56998644
+
Hg19::chr12:22063787..22063800,-p@chr12:22063787..22063800
-
Hg19::chr15:68871022..68871041,+p10@CORO2B
Hg19::chr16:9459384..9459398,+p@chr16:9459384..9459398
+
Hg19::chr17:42984560..42984585,-p12@GFAP
Hg19::chr17:42991062..42991079,-p@chr17:42991062..42991079
-
Hg19::chr17:72809329..72809358,-p@chr17:72809329..72809358
-
Hg19::chr18:24445257..24445287,+p1@CHST9-AS1
Hg19::chr1:110565860..110565886,+p@chr1:110565860..110565886
+
Hg19::chr1:234667532..234667549,-p1@LOC100506795
Hg19::chr1:39570480..39570491,+p@chr1:39570480..39570491
+
Hg19::chr1:39570495..39570532,+p@chr1:39570495..39570532
+
Hg19::chr20:50348989..50349013,-p7@ATP9A
Hg19::chr20:50349144..50349177,-p13@ATP9A
Hg19::chr2:115219171..115219200,+p4@DPP10
Hg19::chr2:115588636..115588637,+p@chr2:115588636..115588637
+
Hg19::chr2:115865026..115865030,+p@chr2:115865026..115865030
+
Hg19::chr3:125899546..125899551,-p9@ALDH1L1
Hg19::chr4:95917070..95917084,+p9@BMPR1B
Hg19::chr5:112074029..112074040,+p9@APC
Hg19::chr5:11385338..11385350,-p27@CTNND2
Hg19::chr5:7802309..7802315,+p@chr5:7802309..7802315
+
Hg19::chr5:81147871..81147905,+p1@ENST00000512859
Hg19::chr6:164348133..164348161,+p@chr6:164348133..164348161
+
Hg19::chr6:168240693..168240704,+p@chr6:168240693..168240704
+
Hg19::chr6:3247609..3247615,-p@chr6:3247609..3247615
-
Hg19::chr6:56716896..56716928,-p8@DST
Hg19::chr7:229611..229617,+p@chr7:229611..229617
+
Hg19::chr8:104153713..104153716,-p1@C8orf56
Hg19::chr8:104184250..104184260,-p1@ENST00000521102
Hg19::chr8:104184325..104184341,-p1@LOC100499183
Hg19::chr8:104184361..104184375,-p2@LOC100499183
Hg19::chr8:145033682..145033707,-p@chr8:145033682..145033707
-
Hg19::chr9:130854016..130854029,+p9@SLC25A25
Hg19::chr9:71939697..71939715,+p@chr9:71939697..71939715
+
Hg19::chr9:71939727..71939735,+p@chr9:71939727..71939735
+
Hg19::chr9:71939745..71939754,+p@chr9:71939745..71939754
+


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:0005856cytoskeleton0.0148251947762522
GO:0022610biological adhesion0.0151374665443906
GO:0007155cell adhesion0.0151374665443906
GO:0051983regulation of chromosome segregation0.0151374665443906
GO:0051988regulation of attachment of spindle microtubules to kinetochore0.0151374665443906
GO:0008608attachment of spindle microtubules to kinetochore0.0151374665443906
GO:0005200structural constituent of cytoskeleton0.0151374665443906
GO:0007050cell cycle arrest0.0157391534528605
GO:0005737cytoplasm0.0157391534528605
GO:0001550ovarian cumulus expansion0.0157391534528605
GO:0048165fused antrum stage, oogenesis0.0157391534528605
GO:0022605oogenesis stage0.0157391534528605
GO:0001547antral ovarian follicle growth0.0157391534528605
GO:0008092cytoskeletal protein binding0.0180510776937678
GO:0009397folic acid and derivative catabolic process0.0180510776937678
GO:000925810-formyltetrahydrofolate catabolic process0.0180510776937678
GO:000925610-formyltetrahydrofolate metabolic process0.0180510776937678
GO:0007010cytoskeleton organization and biogenesis0.0208843123068426
GO:0030877beta-catenin destruction complex0.0208843123068426
GO:0043232intracellular non-membrane-bound organelle0.0208843123068426
GO:0043228non-membrane-bound organelle0.0208843123068426
GO:0060070Wnt receptor signaling pathway through beta-catenin0.0222302899749747
GO:0016155formyltetrahydrofolate dehydrogenase activity0.0222302899749747
GO:0005025transforming growth factor beta receptor activity, type I0.0255610711707634
GO:0007158neuron adhesion0.028065349005499
GO:0045786negative regulation of progression through cell cycle0.028065349005499
GO:0016328lateral plasma membrane0.029204055500909
GO:0008605protein kinase CK2 regulator activity0.029204055500909
GO:0045736negative regulation of cyclin-dependent protein kinase activity0.0306597459072613
GO:0008013beta-catenin binding0.0306597459072613
GO:0016020membrane0.032026848311643
GO:0001502cartilage condensation0.0340563595119381
GO:0016742hydroxymethyl-, formyl- and related transferase activity0.0340563595119381
GO:0004274dipeptidyl-peptidase IV activity0.0360543689207515
GO:0044425membrane part0.0387702042148781
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.038778576974243
GO:0045103intermediate filament-based process0.038778576974243
GO:0046332SMAD binding0.038778576974243
GO:0016337cell-cell adhesion0.038778576974243
GO:0048477oogenesis0.038778576974243
GO:0000074regulation of progression through cell cycle0.038778576974243
GO:0051726regulation of cell cycle0.038778576974243
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.038778576974243
GO:0001541ovarian follicle development0.038778576974243
GO:0030509BMP signaling pathway0.038778576974243
GO:0005024transforming growth factor beta receptor activity0.038778576974243
GO:0004012phospholipid-translocating ATPase activity0.038778576974243
GO:0015247aminophospholipid transporter activity0.038778576974243
GO:0008239dipeptidyl-peptidase activity0.038778576974243
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.038778576974243
GO:0015914phospholipid transport0.0423412243388375
GO:0031114regulation of microtubule depolymerization0.0423412243388375
GO:0007026negative regulation of microtubule depolymerization0.0423412243388375
GO:0031111negative regulation of microtubule polymerization or depolymerization0.04264988463264
GO:0007019microtubule depolymerization0.04264988463264
GO:0022601menstrual cycle phase0.0432029043855401
GO:0016528sarcoplasm0.0432029043855401
GO:0022602menstrual cycle process0.0432029043855401
GO:0016529sarcoplasmic reticulum0.0432029043855401
GO:0003779actin binding0.0441054878504274
GO:0008585female gonad development0.0441054878504274
GO:0000287magnesium ion binding0.0441054878504274
GO:0004372glycine hydroxymethyltransferase activity0.0441054878504274
GO:0009953dorsal/ventral pattern formation0.0441054878504274
GO:0031110regulation of microtubule polymerization or depolymerization0.0441054878504274
GO:0046660female sex differentiation0.0441054878504274
GO:0046545development of primary female sexual characteristics0.0441054878504274
GO:0044464cell part0.0457671947271353
GO:0000776kinetochore0.0457671947271353
GO:0031109microtubule polymerization or depolymerization0.0459059997980458
GO:0005548phospholipid transporter activity0.0459059997980458
GO:0042698menstrual cycle0.0459247048038725
GO:0043010camera-type eye development0.0459247048038725
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.0459247048038725
GO:0007292female gamete generation0.0459247048038725
GO:0006996organelle organization and biogenesis0.0459247048038725
GO:0051216cartilage development0.0459247048038725
GO:0060173limb development0.0459247048038725
GO:0035107appendage morphogenesis0.0459247048038725
GO:0035108limb morphogenesis0.0459247048038725
GO:0048589developmental growth0.0459247048038725
GO:0048736appendage development0.0459247048038725



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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