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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:10, 17 September 2013


Full id: C271_pineal_spinal_locus_globus_medulla_thalamus_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:103599591..103599635,-p3@KCNIP2
Hg19::chr10:64133934..64133954,+p6@ZNF365
Hg19::chr10:94000157..94000191,-p6@CPEB3
Hg19::chr11:131240498..131240532,+p1@NTM
Hg19::chr11:131240536..131240547,+p4@NTM
Hg19::chr11:131240548..131240559,+p10@NTM
Hg19::chr11:131240565..131240572,+p13@NTM
Hg19::chr12:131201033..131201041,-p3@RIMBP2
Hg19::chr12:22487588..22487616,-p3@ST8SIA1
Hg19::chr12:22487618..22487648,-p1@ST8SIA1
Hg19::chr12:26274116..26274141,-p2@AK094422
Hg19::chr12:71314617..71314622,-p16@PTPRR
Hg19::chr14:32547434..32547446,+p11@ARHGAP5
Hg19::chr15:79575073..79575138,+p1@ANKRD34C
Hg19::chr17:55757077..55757089,+p@chr17:55757077..55757089
+
Hg19::chr17:7554234..7554251,+p1@ATP1B2
Hg19::chr17:7556683..7556703,+p@chr17:7556683..7556703
+
Hg19::chr17:7556754..7556788,+p@chr17:7556754..7556788
+
Hg19::chr17:7557938..7557979,+p@chr17:7557938..7557979
+
Hg19::chr17:7559125..7559140,+p@chr17:7559125..7559140
+
Hg19::chr17:7559212..7559223,+p@chr17:7559212..7559223
+
Hg19::chr17:7559305..7559325,+p@chr17:7559305..7559325
+
Hg19::chr17:7559346..7559354,+p@chr17:7559346..7559354
+
Hg19::chr17:7559648..7559652,+p16@ATP1B2
Hg19::chr17:7560487..7560497,+p11@ATP1B2
Hg19::chr17:7560507..7560534,+p2@ATP1B2
Hg19::chr17:7560542..7560578,+p4@ATP1B2
Hg19::chr17:7560589..7560611,+p8@ATP1B2
Hg19::chr17:7560617..7560658,+p5@ATP1B2
Hg19::chr17:7560779..7560820,+p3@ATP1B2
Hg19::chr19:30715705..30715726,+p@chr19:30715705..30715726
+
Hg19::chr19:52452374..52452419,+p1@ENST00000500242
p1@uc002pyb.2
p1@uc002pyc.2
Hg19::chr1:10436637..10436646,+p@chr1:10436637..10436646
+
Hg19::chr1:197237352..197237414,+p2@CRB1
Hg19::chr1:216680100..216680145,-p@chr1:216680100..216680145
-
Hg19::chr2:220154660..220154662,-p@chr2:220154660..220154662
-
Hg19::chr4:170581337..170581344,+p10@CLCN3
Hg19::chr4:187112411..187112444,+p7@CYP4V2
Hg19::chr6:87646995..87647024,+p2@HTR1E
Hg19::chr7:128864848..128864913,+p1@AHCYL2
Hg19::chr7:130152491..130152507,+p@chr7:130152491..130152507
+
Hg19::chr9:35829208..35829308,+p1@TMEM8B
Hg19::chr9:99449322..99449347,+p1@ENST00000423924
Hg19::chrX:144899314..144899392,+p1@SLITRK2
Hg19::chrX:144899416..144899486,+p3@SLITRK2
Hg19::chrX:144899488..144899501,+p4@SLITRK2
Hg19::chrX:144903040..144903070,+p2@SLITRK2


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:0044425membrane part0.0157114682679854
GO:0016020membrane0.0157114682679854
GO:0016021integral to membrane0.0157114682679854
GO:0016324apical plasma membrane0.0157114682679854
GO:0031224intrinsic to membrane0.0157114682679854
GO:0032501multicellular organismal process0.0157114682679854
GO:0048388endosomal lumen acidification0.0157114682679854
GO:0045163clustering of voltage-gated potassium channels0.0157114682679854
GO:0045177apical part of cell0.0191512452993784
GO:0009653anatomical structure morphogenesis0.01982022288438
GO:0005250A-type (transient outward) potassium channel activity0.01982022288438
GO:0032989cellular structure morphogenesis0.01982022288438
GO:0000902cell morphogenesis0.01982022288438
GO:0048856anatomical structure development0.01982022288438
GO:0019904protein domain specific binding0.0229795800062908
GO:0032502developmental process0.0229795800062908
GO:0050877neurological system process0.0229795800062908
GO:0030955potassium ion binding0.0229795800062908
GO:0044459plasma membrane part0.0229795800062908
GO:0015271outward rectifier potassium channel activity0.0229795800062908
GO:0003828alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity0.0229795800062908
GO:0009986cell surface0.0229795800062908
GO:0048666neuron development0.0237715222228541
GO:0045161neuronal ion channel clustering0.0253099614812186
GO:0007267cell-cell signaling0.0253099614812186
GO:0045851pH reduction0.0296281311295286
GO:0051453regulation of cellular pH0.0296281311295286
GO:0051452cellular pH reduction0.0296281311295286
GO:0046923ER retention sequence binding0.0296281311295286
GO:0003008system process0.0296281311295286
GO:0007032endosome organization and biogenesis0.0304581850844502
GO:0005513detection of calcium ion0.0304581850844502
GO:0030182neuron differentiation0.0304581850844502
GO:0031420alkali metal ion binding0.0313964221689795
GO:0007601visual perception0.0313964221689795
GO:0050953sensory perception of light stimulus0.0313964221689795
GO:0006688glycosphingolipid biosynthetic process0.0330198688334164
GO:0042551neuron maturation0.0330198688334164
GO:0048699generation of neurons0.0339901125499411
GO:0006813potassium ion transport0.0367104905655899
GO:0030641cellular hydrogen ion homeostasis0.0367104905655899
GO:0022008neurogenesis0.0368328655832253
GO:0004993serotonin receptor activity0.0379126926495747
GO:0030004cellular monovalent inorganic cation homeostasis0.0400758765880435
GO:0009247glycolipid biosynthetic process0.0400758765880435
GO:0055067monovalent inorganic cation homeostasis0.0400758765880435
GO:0007268synaptic transmission0.0400758765880435
GO:0031901early endosome membrane0.0409695555806811
GO:0005391sodium:potassium-exchanging ATPase activity0.0409695555806811
GO:0042169SH2 domain binding0.0409695555806811
GO:0009593detection of chemical stimulus0.0409695555806811
GO:0022832voltage-gated channel activity0.0409695555806811
GO:0005244voltage-gated ion channel activity0.0409695555806811
GO:0019198transmembrane receptor protein phosphatase activity0.0409695555806811
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0409695555806811
GO:0006687glycosphingolipid metabolic process0.0409695555806811
GO:0012505endomembrane system0.0409695555806811
GO:0016043cellular component organization and biogenesis0.0409695555806811
GO:0019226transmission of nerve impulse0.0409695555806811
GO:0030165PDZ domain binding0.041745255595325
GO:0005048signal sequence binding0.0424104566331044
GO:0030148sphingolipid biosynthetic process0.0424104566331044
GO:0000139Golgi membrane0.0465679210758911
GO:0005100Rho GTPase activator activity0.046927511566585



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 tube2.12e-10756
neural rod2.12e-10756
future spinal cord2.12e-10756
neural keel2.12e-10756
central nervous system3.42e-10281
regional part of nervous system1.24e-9953
regional part of brain1.24e-9953
brain1.70e-9168
future brain1.70e-9168
nervous system1.16e-9089
neural plate1.35e-8482
presumptive neural plate1.35e-8482
regional part of forebrain2.55e-8341
forebrain2.55e-8341
anterior neural tube2.55e-8341
future forebrain2.55e-8341
neurectoderm5.07e-8086
adult organism6.55e-67114
brain grey matter7.67e-6734
gray matter7.67e-6734
telencephalon3.39e-6634
ecto-epithelium9.49e-64104
pre-chordal neural plate9.63e-6261
regional part of telencephalon9.76e-6232
cerebral hemisphere1.15e-6132
structure with developmental contribution from neural crest2.25e-53132
regional part of cerebral cortex1.65e-5122
ectoderm-derived structure2.66e-47171
ectoderm2.66e-47171
presumptive ectoderm2.66e-47171
neocortex1.75e-4620
cerebral cortex8.51e-4525
pallium8.51e-4525
organ system subdivision1.17e-32223
tube1.52e-30192
posterior neural tube6.79e-2415
chordal neural plate6.79e-2415
basal ganglion1.61e-239
nuclear complex of neuraxis1.61e-239
aggregate regional part of brain1.61e-239
collection of basal ganglia1.61e-239
cerebral subcortex1.61e-239
neural nucleus1.69e-239
nucleus of brain1.69e-239
anatomical conduit1.63e-21240
anatomical cluster1.44e-20373
telencephalic nucleus1.72e-187
diencephalon3.74e-187
future diencephalon3.74e-187
segmental subdivision of hindbrain5.26e-1712
hindbrain5.26e-1712
presumptive hindbrain5.26e-1712
epithelium3.81e-16306
gyrus4.65e-166
brainstem4.90e-166
cell layer7.61e-16309
segmental subdivision of nervous system1.52e-1513
limbic system6.90e-145
temporal lobe8.64e-146
occipital lobe1.44e-135
organ part2.11e-13218
parietal lobe2.89e-135
multi-tissue structure1.13e-12342
regional part of diencephalon6.47e-124
corpus striatum2.65e-114
striatum2.65e-114
ventral part of telencephalon2.65e-114
future corpus striatum2.65e-114
gland of diencephalon4.47e-114
neuroendocrine gland4.47e-114
regional part of metencephalon1.57e-109
metencephalon1.57e-109
future metencephalon1.57e-109
organ3.74e-10503
embryo1.85e-09592
caudate-putamen4.34e-093
dorsal striatum4.34e-093
spinal cord5.37e-093
dorsal region element5.37e-093
dorsum5.37e-093
pons6.63e-093
medulla oblongata7.97e-093
myelencephalon7.97e-093
future myelencephalon7.97e-093
developing anatomical structure9.71e-09581
frontal cortex1.15e-083
germ layer1.43e-08560
germ layer / neural crest1.43e-08560
embryonic tissue1.43e-08560
presumptive structure1.43e-08560
germ layer / neural crest derived structure1.43e-08560
epiblast (generic)1.43e-08560
embryonic structure2.18e-08564
anatomical system1.70e-07624
anatomical group1.86e-07625
pineal body4.89e-072
regional part of epithalamus4.89e-072
secretory circumventricular organ4.89e-072
circumventricular organ4.89e-072
epithalamus4.89e-072


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)
MA0003.10.159322
MA0004.10.143101
MA0006.10.641878
MA0007.10.301699
MA0009.10.275766
MA0014.10.492152
MA0017.10.155235
MA0019.10.0887288
MA0024.10.590327
MA0025.10.376628
MA0027.11.7662
MA0028.10.00904529
MA0029.10.216921
MA0030.10.209437
MA0031.10.169247
MA0038.10.245663
MA0040.10.22078
MA0041.10.159732
MA0042.10.131646
MA0043.10.275993
MA0046.10.267991
MA0048.10.44608
MA0050.11.74588
MA0051.10.240959
MA0052.10.635267
MA0055.10.000148357
MA0056.10
MA0057.10.922737
MA0058.10.0155786
MA0059.10.36391
MA0060.10.0260418
MA0061.10.624595
MA0063.10
MA0066.10.526753
MA0067.10.529198
MA0068.11.25405
MA0069.10.265257
MA0070.10.257372
MA0071.10.204012
MA0072.10.254227
MA0073.113.6389
MA0074.10.240126
MA0076.10.0822353
MA0077.10.248866
MA0078.10.360912
MA0081.11.26097
MA0083.10.281174
MA0084.10.695499
MA0087.10.252522
MA0088.10.418374
MA0089.10
MA0090.10.0920042
MA0091.10.337537
MA0092.10.275148
MA0093.10.0401794
MA0095.10
MA0098.10
MA0100.10.261383
MA0101.10.667006
MA0103.10.217682
MA0105.10.463525
MA0106.10.293574
MA0107.10.598268
MA0108.20.501004
MA0109.10
MA0111.10.470228
MA0113.10.313585
MA0114.10.0152793
MA0115.10.464275
MA0116.10.862315
MA0117.10.303182
MA0119.10.164909
MA0122.10.322548
MA0124.10.429905
MA0125.10.362554
MA0130.10
MA0131.10.121301
MA0132.10
MA0133.10
MA0135.10.297838
MA0136.10.0726858
MA0139.10.150236
MA0140.10.44418
MA0141.10.0703447
MA0142.10.150759
MA0143.10.647667
MA0144.10.733994
MA0145.10.0762875
MA0146.10.908332
MA0147.10.882517
MA0148.10.0430398
MA0149.16.24226
MA0062.20.000448472
MA0035.20.0544556
MA0039.20.993789
MA0138.20.362512
MA0002.20.0565951
MA0137.21.03962
MA0104.20.386804
MA0047.20.0817751
MA0112.20.751125
MA0065.20.29265
MA0150.10.221137
MA0151.10
MA0152.10.0569756
MA0153.10.349438
MA0154.10.956989
MA0155.10.301857
MA0156.10.0100543
MA0157.10.135578
MA0158.10
MA0159.10.422206
MA0160.10.180181
MA0161.10
MA0162.10.185583
MA0163.10.212826
MA0164.11.64551
MA0080.20.240349
MA0018.20.295242
MA0099.20.0571009
MA0079.210.9989
MA0102.20.729507
MA0258.11.88301
MA0259.10.0205559
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

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