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Coexpression cluster:C642: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.75e-28!115;UBERON:0001049!5.50e-21!57;UBERON:0005068!5.50e-21!57;UBERON:0006241!5.50e-21!57;UBERON:0007135!5.50e-21!57;UBERON:0002020!2.36e-18!34;UBERON:0003528!2.36e-18!34;UBERON:0001893!2.51e-18!34;UBERON:0002791!9.90e-18!33;UBERON:0005743!2.54e-17!86;UBERON:0002616!4.45e-17!59;UBERON:0001869!5.12e-17!32;UBERON:0002780!5.35e-17!41;UBERON:0001890!5.35e-17!41;UBERON:0006240!5.35e-17!41;UBERON:0003080!9.07e-17!42;UBERON:0001017!1.99e-16!82;UBERON:0000955!4.15e-16!69;UBERON:0006238!4.15e-16!69;UBERON:0000073!3.54e-15!94;UBERON:0001016!3.54e-15!94;UBERON:0003075!6.70e-14!86;UBERON:0007284!6.70e-14!86;UBERON:0002619!6.54e-13!22;UBERON:0000956!6.62e-13!25;UBERON:0000203!6.62e-13!25;UBERON:0002390!2.06e-12!102;UBERON:0003061!2.06e-12!102;UBERON:0001950!9.81e-12!20;UBERON:0002193!1.06e-11!112;UBERON:0002346!1.57e-11!90;UBERON:0003056!1.89e-10!61;UBERON:0002371!2.82e-07!80;UBERON:0002308!5.15e-07!9;UBERON:0000125!5.15e-07!9;UBERON:0002420!7.64e-07!9;UBERON:0007245!7.64e-07!9;UBERON:0010009!7.64e-07!9;UBERON:0010011!7.64e-07!9;UBERON:0000454!7.64e-07!9
|ontology_enrichment_uberon=UBERON:0007023!7.75e-28!115;UBERON:0001049!5.50e-21!57;UBERON:0005068!5.50e-21!57;UBERON:0006241!5.50e-21!57;UBERON:0007135!5.50e-21!57;UBERON:0002020!2.36e-18!34;UBERON:0003528!2.36e-18!34;UBERON:0001893!2.51e-18!34;UBERON:0002791!9.90e-18!33;UBERON:0005743!2.54e-17!86;UBERON:0002616!4.45e-17!59;UBERON:0001869!5.12e-17!32;UBERON:0002780!5.35e-17!41;UBERON:0001890!5.35e-17!41;UBERON:0006240!5.35e-17!41;UBERON:0003080!9.07e-17!42;UBERON:0001017!1.99e-16!82;UBERON:0000955!4.15e-16!69;UBERON:0006238!4.15e-16!69;UBERON:0000073!3.54e-15!94;UBERON:0001016!3.54e-15!94;UBERON:0003075!6.70e-14!86;UBERON:0007284!6.70e-14!86;UBERON:0002619!6.54e-13!22;UBERON:0000956!6.62e-13!25;UBERON:0000203!6.62e-13!25;UBERON:0002390!2.06e-12!102;UBERON:0003061!2.06e-12!102;UBERON:0001950!9.81e-12!20;UBERON:0002193!1.06e-11!112;UBERON:0002346!1.57e-11!90;UBERON:0003056!1.89e-10!61;UBERON:0002371!2.82e-07!80;UBERON:0002308!5.15e-07!9;UBERON:0000125!5.15e-07!9;UBERON:0002420!7.64e-07!9;UBERON:0007245!7.64e-07!9;UBERON:0010009!7.64e-07!9;UBERON:0010011!7.64e-07!9;UBERON:0000454!7.64e-07!9
|tf_chipseq_enrich=SRF#6722;4:4.24528561912856:0.0115903477001898:0.042349799652245
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}}
}}

Revision as of 12:45, 5 September 2012


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>


Cell Type
Ontology termp-valuen
hematopoietic stem cell7.14e-28172
angioblastic mesenchymal cell7.14e-28172
hematopoietic oligopotent progenitor cell9.99e-27165
hematopoietic multipotent progenitor cell9.99e-27165
leukocyte3.74e-23140
hematopoietic cell6.41e-23182
hematopoietic lineage restricted progenitor cell2.56e-19124
nongranular leukocyte7.93e-19119
myeloid cell4.29e-15112
common myeloid progenitor4.29e-15112
lymphoid lineage restricted progenitor cell1.54e-1152
myeloid leukocyte1.71e-1176
lymphocyte2.17e-1153
common lymphoid progenitor2.17e-1153
myeloid lineage restricted progenitor cell1.10e-0970
mature alpha-beta T cell2.80e-0918
alpha-beta T cell2.80e-0918
immature T cell2.80e-0918
mature T cell2.80e-0918
immature alpha-beta T cell2.80e-0918
granulocyte monocyte progenitor cell4.96e-0871
monopoietic cell2.73e-0763
monocyte2.73e-0763
monoblast2.73e-0763
promonocyte2.73e-0763
Uber Anatomy
Ontology termp-valuen
adult organism7.75e-28115
neural tube5.50e-2157
neural rod5.50e-2157
future spinal cord5.50e-2157
neural keel5.50e-2157
gray matter2.36e-1834
brain grey matter2.36e-1834
telencephalon2.51e-1834
regional part of telencephalon9.90e-1833
regional part of brain4.45e-1759
cerebral hemisphere5.12e-1732
regional part of forebrain5.35e-1741
forebrain5.35e-1741
future forebrain5.35e-1741
anterior neural tube9.07e-1742
central nervous system1.99e-1682
brain4.15e-1669
future brain4.15e-1669
regional part of nervous system3.54e-1594
nervous system3.54e-1594
neural plate6.70e-1486
presumptive neural plate6.70e-1486
regional part of cerebral cortex6.54e-1322
cerebral cortex6.62e-1325
pallium6.62e-1325
hematopoietic system2.06e-12102
blood island2.06e-12102
neocortex9.81e-1220
hemolymphoid system1.06e-11112
neurectoderm1.57e-1190
pre-chordal neural plate1.89e-1061
bone marrow2.82e-0780
nucleus of brain5.15e-079
neural nucleus5.15e-079
basal ganglion7.64e-079
nuclear complex of neuraxis7.64e-079
aggregate regional part of brain7.64e-079
collection of basal ganglia7.64e-079
cerebral subcortex7.64e-079


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


(#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.