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{{Coexpression_clusters
{
|full_id=C642_Whole_blood_optic_substantia_globus_corpus_thalamus
|

Latest revision as of 11:27, 17 September 2013


Full id: C642_Whole_blood_optic_substantia_globus_corpus_thalamus



Phase1 CAGE Peaks

Hg19::chr10:111985777..111985788,+p4@MXI1
Hg19::chr10:22825620..22825656,-p2@PIP4K2A
Hg19::chr10:22825878..22825894,-p5@PIP4K2A
Hg19::chr10:22830771..22830779,-p@chr10:22830771..22830779
-
Hg19::chr10:23002092..23002110,-p@chr10:23002092..23002110
-
Hg19::chr10:23003155..23003214,+p@chr10:23003155..23003214
+
Hg19::chr10:23003406..23003417,-p4@PIP4K2A
Hg19::chr10:23003436..23003459,-p3@PIP4K2A
Hg19::chr10:23003460..23003562,-p1@PIP4K2A
Hg19::chr12:21680866..21680902,+p6@C12orf39
Hg19::chr14:105147464..105147523,+p1@ENST00000540171
Hg19::chr4:90758153..90758176,-p5@SNCA
Hg19::chr8:27468262..27468277,-p27@CLU


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:0006629lipid metabolic process0.0108070060423257
GO:0006916anti-apoptosis0.0108070060423257
GO:0016235aggresome0.0108070060423257
GO:0048523negative regulation of cellular process0.0108070060423257
GO:0006644phospholipid metabolic process0.0108070060423257
GO:0048519negative regulation of biological process0.0108070060423257
GO:0043066negative regulation of apoptosis0.0108070060423257
GO:0001956positive regulation of neurotransmitter secretion0.0108070060423257
GO:00163091-phosphatidylinositol-5-phosphate 4-kinase activity0.0108070060423257
GO:0043069negative regulation of programmed cell death0.0108070060423257
GO:0048169regulation of long-term neuronal synaptic plasticity0.0116053713801532
GO:0042416dopamine biosynthetic process0.0116053713801532
GO:0006643membrane lipid metabolic process0.0116053713801532
GO:0016234inclusion body0.0141251242095994
GO:0031018endocrine pancreas development0.0141251242095994
GO:0001963synaptic transmission, dopaminergic0.0154484450428978
GO:00163081-phosphatidylinositol-4-phosphate 5-kinase activity0.0155330633749191
GO:0042994cytoplasmic sequestering of transcription factor0.0155330633749191
GO:0048168regulation of neuronal synaptic plasticity0.0155330633749191
GO:0031016pancreas development0.0155330633749191
GO:0051220cytoplasmic sequestering of protein0.0155330633749191
GO:0042423catecholamine biosynthetic process0.0155330633749191
GO:0042308negative regulation of protein import into nucleus0.0155330633749191
GO:0042992negative regulation of transcription factor import into nucleus0.0155330633749191
GO:0042417dopamine metabolic process0.0155330633749191
GO:0046928regulation of neurotransmitter secretion0.0156890392781357
GO:0046823negative regulation of nucleocytoplasmic transport0.0156890392781357
GO:0042127regulation of cell proliferation0.0158233579816069
GO:0051224negative regulation of protein transport0.0158233579816069
GO:0048167regulation of synaptic plasticity0.0182152392557906
GO:0042136neurotransmitter biosynthetic process0.0182152392557906
GO:0050803regulation of synapse structure and activity0.0184797701797707
GO:0048489synaptic vesicle transport0.0184797701797707
GO:0042981regulation of apoptosis0.0184797701797707
GO:0043067regulation of programmed cell death0.0184797701797707
GO:0007270nerve-nerve synaptic transmission0.0184797701797707
GO:0042221response to chemical stimulus0.0184797701797707
GO:0042990regulation of transcription factor import into nucleus0.0184797701797707
GO:0042991transcription factor import into nucleus0.0184797701797707
GO:0042306regulation of protein import into nucleus0.0184797701797707
GO:0033157regulation of intracellular protein transport0.0184797701797707
GO:0016307phosphatidylinositol phosphate kinase activity0.0184797701797707
GO:0032507maintenance of cellular protein localization0.0191052624903955
GO:0051651maintenance of cellular localization0.0191052624903955
GO:0046488phosphatidylinositol metabolic process0.0191052624903955
GO:0032386regulation of intracellular transport0.0191052624903955
GO:0045185maintenance of protein localization0.0191052624903955
GO:0006584catecholamine metabolic process0.0191052624903955
GO:0018958phenol metabolic process0.0192959568263883
GO:0051223regulation of protein transport0.0192959568263883
GO:0006958complement activation, classical pathway0.0192959568263883
GO:0007399nervous system development0.0192959568263883
GO:0046822regulation of nucleocytoplasmic transport0.0192959568263883
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0195905268674936
GO:0051051negative regulation of transport0.0196979209913166
GO:0008283cell proliferation0.0196979209913166
GO:0042133neurotransmitter metabolic process0.0197944119925687
GO:0035270endocrine system development0.0198421677209551
GO:0044255cellular lipid metabolic process0.0198421677209551
GO:0042401biogenic amine biosynthetic process0.0199776320823133
GO:0019717synaptosome0.0208035701289321
GO:0001727lipid kinase activity0.0214492439905879
GO:0006956complement activation0.0214492439905879
GO:0002541activation of plasma proteins during acute inflammatory response0.0214492439905879
GO:0007269neurotransmitter secretion0.0214492439905879
GO:0006915apoptosis0.0214492439905879
GO:0051235maintenance of localization0.0214492439905879
GO:0012501programmed cell death0.0214492439905879
GO:0042398amino acid derivative biosynthetic process0.0214492439905879
GO:0008219cell death0.0228610036321127
GO:0016265death0.0228610036321127
GO:0045597positive regulation of cell differentiation0.0229958414124646
GO:0016064immunoglobulin mediated immune response0.0245579892626077
GO:0019724B cell mediated immunity0.0245579892626077
GO:0016043cellular component organization and biogenesis0.0245579892626077
GO:0045055regulated secretory pathway0.0245579892626077
GO:0051046regulation of secretion0.0269735680637904
GO:0042493response to drug0.0284263292519867
GO:0048471perinuclear region of cytoplasm0.0285103237305022
GO:0004428inositol or phosphatidylinositol kinase activity0.0289770518895741
GO:0051649establishment of cellular localization0.0289770518895741
GO:0051094positive regulation of developmental process0.0290514758545434
GO:0003001generation of a signal involved in cell-cell signaling0.0290514758545434
GO:0051641cellular localization0.0290514758545434
GO:0002253activation of immune response0.0290514758545434
GO:0002449lymphocyte mediated immunity0.0290514758545434
GO:0040012regulation of locomotion0.0290514758545434
GO:0040011locomotion0.0290514758545434
GO:0006576biogenic amine metabolic process0.0290514758545434
GO:0006959humoral immune response0.0290514758545434
GO:0002250adaptive immune response0.0290514758545434
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0290514758545434
GO:0002443leukocyte mediated immunity0.029178169694758
GO:0001505regulation of neurotransmitter levels0.029178169694758
GO:0002526acute inflammatory response0.0292394509575832
GO:0030384phosphoinositide metabolic process0.0292994125000015
GO:0048468cell development0.0304863311065692
GO:0050778positive regulation of immune response0.0304863311065692
GO:0002684positive regulation of immune system process0.0305316306197012
GO:0006575amino acid derivative metabolic process0.0316247408588697
GO:0006606protein import into nucleus0.0333872700655214
GO:0050776regulation of immune response0.033417100397404
GO:0051170nuclear import0.033417100397404
GO:0002682regulation of immune system process0.0337672299085275
GO:0006650glycerophospholipid metabolic process0.0337781048632552
GO:0051240positive regulation of multicellular organismal process0.0347763791412003
GO:0003714transcription corepressor activity0.0351034490641594
GO:0002252immune effector process0.0354192425605005
GO:0051049regulation of transport0.0354192425605005
GO:0045087innate immune response0.0363649480858612
GO:0009309amine biosynthetic process0.0369227283928866
GO:0048667neuron morphogenesis during differentiation0.0369227283928866
GO:0006979response to oxidative stress0.0369227283928866
GO:0048812neurite morphogenesis0.0369227283928866
GO:0017038protein import0.0372073074498277
GO:0000904cellular morphogenesis during differentiation0.0380869794858592
GO:0031175neurite development0.0404372637687916
GO:0048731system development0.0412386355147545
GO:0045595regulation of cell differentiation0.0423856905548066
GO:0044271nitrogen compound biosynthetic process0.0429005750847962
GO:0048666neuron development0.0441884666926329
GO:0006913nucleocytoplasmic transport0.0441884666926329
GO:0051169nuclear transport0.0443931938023867
GO:0048869cellular developmental process0.0489034391672832
GO:0030154cell differentiation0.0489034391672832



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><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.54e-35114
neural tube1.24e-2856
neural rod1.24e-2856
future spinal cord1.24e-2856
neural keel1.24e-2856
regional part of nervous system3.22e-2653
regional part of brain3.22e-2653
brain grey matter1.96e-2334
gray matter1.96e-2334
telencephalon2.50e-2334
brain1.04e-2268
future brain1.04e-2268
regional part of forebrain5.65e-2241
forebrain5.65e-2241
anterior neural tube5.65e-2241
future forebrain5.65e-2241
central nervous system6.37e-2281
regional part of telencephalon1.10e-2132
cerebral hemisphere1.46e-2132
nervous system4.85e-2089
neural plate9.17e-1982
presumptive neural plate9.17e-1982
neurectoderm6.74e-1786
cerebral cortex7.08e-1625
pallium7.08e-1625
regional part of cerebral cortex5.59e-1522
pre-chordal neural plate3.53e-1461
neocortex2.64e-1320
ecto-epithelium8.32e-12104
hematopoietic system1.01e-1098
blood island1.01e-1098
neural nucleus3.21e-099
nucleus of brain3.21e-099
hemolymphoid system4.45e-09108
basal ganglion5.13e-099
nuclear complex of neuraxis5.13e-099
aggregate regional part of brain5.13e-099
collection of basal ganglia5.13e-099
cerebral subcortex5.13e-099
blood1.62e-0815
haemolymphatic fluid1.62e-0815
organism substance1.62e-0815
structure with developmental contribution from neural crest2.32e-08132
posterior neural tube8.02e-0815
chordal neural plate8.02e-0815
telencephalic nucleus1.81e-077
brainstem9.96e-076


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)
MA0003.13.61585
MA0004.10.297884
MA0006.11.55315
MA0007.10.282081
MA0009.10.724811
MA0014.13.58868
MA0017.10.57848
MA0019.11.09485
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.11.39986
MA0038.11.00626
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.11.28679
MA0050.12.18586
MA0051.10.997995
MA0052.10.652145
MA0055.12.63233
MA0056.10
MA0057.10.294933
MA0058.10.219229
MA0059.10.218203
MA0060.10.0892161
MA0061.10.255087
MA0063.10
MA0066.10.387854
MA0067.11.03434
MA0068.10.196125
MA0069.10.710614
MA0070.10.69985
MA0071.10.35315
MA0072.10.695528
MA0073.12.119
MA0074.11.76626
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.10.170244
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.171791
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.162663
MA0105.10.26318
MA0106.10.424592
MA0107.10.385539
MA0108.20.568002
MA0109.10
MA0111.10.254772
MA0113.10.439505
MA0114.10.376635
MA0115.10.959312
MA0116.10.391626
MA0117.10.76111
MA0119.10.205526
MA0122.10.786181
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.12.9791
MA0136.10.393782
MA0139.10.870578
MA0140.10.350813
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.35188
MA0145.11.29615
MA0146.10.191696
MA0147.10.793354
MA0148.10.855011
MA0149.10.342334
MA0062.21.35421
MA0035.20.350194
MA0039.20.809044
MA0138.20.474787
MA0002.20.0821804
MA0137.20.186529
MA0104.20.620335
MA0047.20.413608
MA0112.20.0689988
MA0065.20.0781722
MA0150.10.238884
MA0151.10
MA0152.10.356591
MA0153.10.820317
MA0154.10.257061
MA0155.10.560882
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.398903
MA0160.10.332385
MA0161.10
MA0162.11.67029
MA0163.10.390307
MA0164.10.450848
MA0080.20.511865
MA0018.20.425847
MA0099.20.356906
MA0079.23.42699
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SRF#672244.245285619128560.01159034770018980.042349799652245



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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