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{{Coexpression_clusters
{
|full_id=C310_caudate_medulla_spinal_thalamus_locus_globus_hippocampus
 

Latest revision as of 11:19, 17 September 2013


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube5.21e-13156
neural rod5.21e-13156
future spinal cord5.21e-13156
neural keel5.21e-13156
regional part of nervous system3.67e-11953
regional part of brain3.67e-11953
central nervous system3.33e-10081
brain1.67e-9968
future brain1.67e-9968
regional part of forebrain2.21e-9841
forebrain2.21e-9841
anterior neural tube2.21e-9841
future forebrain2.21e-9841
nervous system1.69e-8989
neural plate3.96e-8782
presumptive neural plate3.96e-8782
brain grey matter8.90e-8634
gray matter8.90e-8634
telencephalon4.48e-8534
neurectoderm1.05e-8286
regional part of telencephalon7.34e-7832
cerebral hemisphere1.23e-7732
adult organism4.41e-67114
ecto-epithelium5.87e-67104
pre-chordal neural plate4.05e-6461
regional part of cerebral cortex2.53e-5922
structure with developmental contribution from neural crest1.37e-53132
cerebral cortex6.21e-5225
pallium6.21e-5225
neocortex8.79e-5220
ectoderm-derived structure6.46e-43171
ectoderm6.46e-43171
presumptive ectoderm6.46e-43171
neural nucleus8.66e-379
nucleus of brain8.66e-379
basal ganglion1.37e-369
nuclear complex of neuraxis1.37e-369
aggregate regional part of brain1.37e-369
collection of basal ganglia1.37e-369
cerebral subcortex1.37e-369
organ system subdivision2.34e-32223
tube3.29e-32192
posterior neural tube1.26e-3115
chordal neural plate1.26e-3115
telencephalic nucleus1.05e-287
brainstem2.46e-256
anatomical conduit6.23e-24240
gyrus9.07e-246
segmental subdivision of hindbrain5.10e-2112
hindbrain5.10e-2112
presumptive hindbrain5.10e-2112
limbic system6.34e-215
segmental subdivision of nervous system2.68e-1913
corpus striatum4.90e-174
striatum4.90e-174
ventral part of telencephalon4.90e-174
future corpus striatum4.90e-174
epithelium9.17e-17306
cell layer1.64e-16309
regional part of diencephalon1.67e-164
anatomical cluster1.23e-15373
organ part6.58e-15218
temporal lobe1.43e-146
diencephalon2.68e-147
future diencephalon2.68e-147
medulla oblongata1.05e-133
myelencephalon1.05e-133
future myelencephalon1.05e-133
spinal cord1.67e-133
dorsal region element1.67e-133
dorsum1.67e-133
caudate-putamen1.90e-133
dorsal striatum1.90e-133
pons2.15e-133
occipital lobe2.60e-135
parietal lobe3.47e-135
frontal cortex8.35e-133
multi-tissue structure5.50e-12342
regional part of metencephalon3.89e-119
metencephalon3.89e-119
future metencephalon3.89e-119
dorsal plus ventral thalamus8.13e-102
locus ceruleus8.13e-102
brainstem nucleus8.13e-102
hindbrain nucleus8.13e-102
thalamic complex8.13e-102
globus pallidus1.19e-092
pallidum1.19e-092
caudate nucleus1.24e-092
future caudate nucleus1.24e-092
amygdala1.30e-092
Ammon's horn1.89e-092
lobe parts of cerebral cortex1.89e-092
hippocampal formation1.89e-092
limbic lobe1.89e-092
middle frontal gyrus2.06e-092
middle temporal gyrus3.53e-092
organ4.65e-09503
pineal body1.98e-082
regional part of epithalamus1.98e-082


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)
MA0003.10.00387792
MA0004.10.0566508
MA0006.10.0696281
MA0007.10.418327
MA0009.10.88381
MA0014.10.00211649
MA0017.10.096641
MA0019.10.122811
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.017688
MA0029.10.268301
MA0030.10.260095
MA0031.10.215562
MA0038.10.673838
MA0040.10.272523
MA0041.10.227378
MA0042.10.428611
MA0043.10.332327
MA0046.10.865123
MA0048.10.757337
MA0050.10.430337
MA0051.10.0979546
MA0052.10.755709
MA0055.10.232674
MA0056.10
MA0057.10.250203
MA0058.10.116428
MA0059.10.277816
MA0060.10.0557315
MA0061.10.182822
MA0063.10
MA0066.10.32926
MA0067.10.597968
MA0068.10.110422
MA0069.10.320777
MA0070.10.312273
MA0071.10.588101
MA0072.10.308875
MA0073.13.75216e-07
MA0074.10.322317
MA0076.10.129848
MA0077.10.818719
MA0078.10.897097
MA0081.10.115503
MA0083.10.896748
MA0084.10.768496
MA0087.10.307032
MA0088.10.0876906
MA0089.10
MA0090.10.142663
MA0091.10.799469
MA0092.10.687103
MA0093.10.0154139
MA0095.10
MA0098.10
MA0100.10.106764
MA0101.10.617442
MA0103.10.169168
MA0105.10.203426
MA0106.10.12076
MA0107.10.380955
MA0108.20.612085
MA0109.10
MA0111.10.0397253
MA0113.10.807431
MA0114.10.366131
MA0115.10.530757
MA0116.10.613342
MA0117.10.36143
MA0119.10.473302
MA0122.10.382044
MA0124.10.494979
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.103403
MA0139.10.42985
MA0140.10.0810116
MA0141.10.113951
MA0142.10.194761
MA0143.10.406261
MA0144.11.05303
MA0145.10.395589
MA0146.10.0193469
MA0147.10.401599
MA0148.11.30961
MA0149.10.0768601
MA0062.20.00144723
MA0035.20.0807052
MA0039.28.78168e-05
MA0138.20.460666
MA0002.20.112762
MA0137.20.997725
MA0104.20.243491
MA0047.20.114453
MA0112.20.0545862
MA0065.20.12116
MA0150.10.0342009
MA0151.10
MA0152.10.5966
MA0153.11.05663
MA0154.10.0634095
MA0155.10.00310384
MA0156.10.0861658
MA0157.10.177496
MA0158.10
MA0159.10.630496
MA0160.10.0721072
MA0161.10
MA0162.10.00057372
MA0163.10.0606262
MA0164.10.136341
MA0080.20.071606
MA0018.20.121488
MA0099.20.285408
MA0079.21.15386e-08
MA0102.20.803155
MA0258.10.163134
MA0259.10.244533
MA0442.10



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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