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Coexpression cluster:C243: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0044421!extracellular region part!0.000205191071528448!1280;2331;176;1117;1302;11341$GO:0005583!fibrillar collagen!0.000978053245048239!1280;1302$GO:0005201!extracellular matrix structural constituent!0.00119181646855413!1280;176;1302$GO:0005578!proteinaceous extracellular matrix!0.00119181646855413!1280;2331;176;1302$GO:0001501!skeletal development!0.00359209545847259!1280;176;1302$GO:0030198!extracellular matrix organization and biogenesis!0.00608470421680022!176;1302$GO:0005581!collagen!0.00719737186271699!1280;1302$GO:0005585!collagen type II!0.0116419404215236!1280$GO:0043062!extracellular structure organization and biogenesis!0.0135409792303694!176;1302$GO:0005592!collagen type XI!0.0153553945672956!1302$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.0153553945672956!1302$GO:0005539!glycosaminoglycan binding!0.0153553945672956!176;26577$GO:0030247!polysaccharide binding!0.0153553945672956!176;26577$GO:0001871!pattern binding!0.0153553945672956!176;26577$GO:0005584!collagen type I!0.0153553945672956!1280$GO:0004700!atypical protein kinase C activity!0.0153553945672956!5590$GO:0044420!extracellular matrix part!0.0153553945672956!1280;1302$GO:0050954!sensory perception of mechanical stimulus!0.0153553945672956!1280;1302$GO:0007605!sensory perception of sound!0.0153553945672956!1280;1302$GO:0032502!developmental process!0.0153553945672956!1280;5590;176;2078;1302;11341$GO:0006817!phosphate transport!0.0165717751341296!1280;1302$GO:0007181!transforming growth factor beta receptor complex assembly!0.0165717751341296!2331$GO:0007275!multicellular organismal development!0.0165717751341296!1280;176;2078;1302;11341$GO:0030021!extracellular matrix structural constituent conferring compression resistance!0.0271333600942556!176$GO:0048731!system development!0.0300744875262851!1280;176;1302;11341$GO:0030199!collagen fibril organization!0.0300744875262851!1302$GO:0044409!entry into host!0.0300744875262851!11060$GO:0030260!entry into host cell!0.0300744875262851!11060$GO:0019059!initiation of viral infection!0.0300744875262851!11060$GO:0052192!movement in environment of other organism during symbiotic interaction!0.0300744875262851!11060$GO:0046718!entry of virus into host cell!0.0300744875262851!11060$GO:0052126!movement in host environment!0.0300744875262851!11060$GO:0051828!entry into other organism during symbiotic interaction!0.0300744875262851!11060$GO:0051806!entry into cell of other organism during symbiotic interaction!0.0300744875262851!11060$GO:0015698!inorganic anion transport!0.0316658241886977!1280;1302$GO:0004017!adenylate kinase activity!0.0316658241886977!203$GO:0006032!chitin catabolic process!0.0316658241886977!1117$GO:0006046!N-acetylglucosamine catabolic process!0.0316658241886977!1117$GO:0006043!glucosamine catabolic process!0.0316658241886977!1117$GO:0046348!amino sugar catabolic process!0.0316658241886977!1117$GO:0004697!protein kinase C activity!0.0316658241886977!5590$GO:0006030!chitin metabolic process!0.0316658241886977!1117$GO:0004568!chitinase activity!0.0316658241886977!1117$GO:0001565!phorbol ester receptor activity!0.0316658241886977!5590$GO:0048856!anatomical structure development!0.0373617123603633!1280;176;1302;11341$GO:0006820!anion transport!0.0373617123603633!1280;1302$GO:0044247!cellular polysaccharide catabolic process!0.0405912102693347!1117$GO:0000272!polysaccharide catabolic process!0.0405912102693347!1117$GO:0051701!interaction with host!0.0416483223058567!11060$GO:0048513!organ development!0.0471112555794051!1280;176;1302
|gostat_on_coexpression_clusters=GO:0044421!extracellular region part!0.000205191071528448!1280;2331;176;1117;1302;11341$GO:0005583!fibrillar collagen!0.000978053245048239!1280;1302$GO:0005201!extracellular matrix structural constituent!0.00119181646855413!1280;176;1302$GO:0005578!proteinaceous extracellular matrix!0.00119181646855413!1280;2331;176;1302$GO:0001501!skeletal development!0.00359209545847259!1280;176;1302$GO:0030198!extracellular matrix organization and biogenesis!0.00608470421680022!176;1302$GO:0005581!collagen!0.00719737186271699!1280;1302$GO:0005585!collagen type II!0.0116419404215236!1280$GO:0043062!extracellular structure organization and biogenesis!0.0135409792303694!176;1302$GO:0005592!collagen type XI!0.0153553945672956!1302$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.0153553945672956!1302$GO:0005539!glycosaminoglycan binding!0.0153553945672956!176;26577$GO:0030247!polysaccharide binding!0.0153553945672956!176;26577$GO:0001871!pattern binding!0.0153553945672956!176;26577$GO:0005584!collagen type I!0.0153553945672956!1280$GO:0004700!atypical protein kinase C activity!0.0153553945672956!5590$GO:0044420!extracellular matrix part!0.0153553945672956!1280;1302$GO:0050954!sensory perception of mechanical stimulus!0.0153553945672956!1280;1302$GO:0007605!sensory perception of sound!0.0153553945672956!1280;1302$GO:0032502!developmental process!0.0153553945672956!1280;5590;176;2078;1302;11341$GO:0006817!phosphate transport!0.0165717751341296!1280;1302$GO:0007181!transforming growth factor beta receptor complex assembly!0.0165717751341296!2331$GO:0007275!multicellular organismal development!0.0165717751341296!1280;176;2078;1302;11341$GO:0030021!extracellular matrix structural constituent conferring compression resistance!0.0271333600942556!176$GO:0048731!system development!0.0300744875262851!1280;176;1302;11341$GO:0030199!collagen fibril organization!0.0300744875262851!1302$GO:0044409!entry into host!0.0300744875262851!11060$GO:0030260!entry into host cell!0.0300744875262851!11060$GO:0019059!initiation of viral infection!0.0300744875262851!11060$GO:0052192!movement in environment of other organism during symbiotic interaction!0.0300744875262851!11060$GO:0046718!entry of virus into host cell!0.0300744875262851!11060$GO:0052126!movement in host environment!0.0300744875262851!11060$GO:0051828!entry into other organism during symbiotic interaction!0.0300744875262851!11060$GO:0051806!entry into cell of other organism during symbiotic interaction!0.0300744875262851!11060$GO:0015698!inorganic anion transport!0.0316658241886977!1280;1302$GO:0004017!adenylate kinase activity!0.0316658241886977!203$GO:0006032!chitin catabolic process!0.0316658241886977!1117$GO:0006046!N-acetylglucosamine catabolic process!0.0316658241886977!1117$GO:0006043!glucosamine catabolic process!0.0316658241886977!1117$GO:0046348!amino sugar catabolic process!0.0316658241886977!1117$GO:0004697!protein kinase C activity!0.0316658241886977!5590$GO:0006030!chitin metabolic process!0.0316658241886977!1117$GO:0004568!chitinase activity!0.0316658241886977!1117$GO:0001565!phorbol ester receptor activity!0.0316658241886977!5590$GO:0048856!anatomical structure development!0.0373617123603633!1280;176;1302;11341$GO:0006820!anion transport!0.0373617123603633!1280;1302$GO:0044247!cellular polysaccharide catabolic process!0.0405912102693347!1117$GO:0000272!polysaccharide catabolic process!0.0405912102693347!1117$GO:0051701!interaction with host!0.0416483223058567!11060$GO:0048513!organ development!0.0471112555794051!1280;176;1302
|id=C243
|id=C243
|ontology_enrichment_celltype=CL:0000055!1.35e-11!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.32e-32!115;UBERON:0000475!2.03e-23!365;UBERON:0001049!4.09e-22!57;UBERON:0005068!4.09e-22!57;UBERON:0006241!4.09e-22!57;UBERON:0007135!4.09e-22!57;UBERON:0001017!1.38e-20!82;UBERON:0005743!2.12e-20!86;UBERON:0002616!4.88e-20!59;UBERON:0003075!4.24e-19!86;UBERON:0007284!4.24e-19!86;UBERON:0000073!5.78e-19!94;UBERON:0001016!5.78e-19!94;UBERON:0000955!1.18e-17!69;UBERON:0006238!1.18e-17!69;UBERON:0003080!4.83e-17!42;UBERON:0002346!4.98e-17!90;UBERON:0004121!5.29e-17!169;UBERON:0000468!7.54e-17!659;UBERON:0002780!1.26e-16!41;UBERON:0001890!1.26e-16!41;UBERON:0006240!1.26e-16!41;UBERON:0000924!9.93e-16!173;UBERON:0006601!9.93e-16!173;UBERON:0000481!1.18e-15!347;UBERON:0000153!3.97e-14!129;UBERON:0007811!3.97e-14!129;UBERON:0000033!6.25e-14!123;UBERON:0002020!6.30e-14!34;UBERON:0003528!6.30e-14!34;UBERON:0001893!6.59e-14!34;UBERON:0002791!1.97e-13!33;UBERON:0001869!8.70e-13!32;UBERON:0000483!8.88e-13!309;UBERON:0003056!1.53e-12!61;UBERON:0000477!2.20e-12!286;UBERON:0000119!2.48e-12!312;UBERON:0000025!4.33e-12!194;UBERON:0000467!6.22e-12!625;UBERON:0000480!1.32e-11!626;UBERON:0004111!2.47e-11!241;UBERON:0000062!4.69e-11!511;UBERON:0000922!1.36e-10!612;UBERON:0002619!3.45e-10!22;UBERON:0000956!8.06e-10!25;UBERON:0000203!8.06e-10!25;UBERON:0001950!1.95e-09!20;UBERON:0002050!3.97e-09!605;UBERON:0005423!3.97e-09!605;UBERON:0000923!8.16e-09!604;UBERON:0005291!8.16e-09!604;UBERON:0006598!8.16e-09!604;UBERON:0002532!8.16e-09!604;UBERON:0000064!1.90e-08!219
}}
}}

Revision as of 14:24, 21 May 2012


Full id: C243_Chondrocyte_trachea_Synoviocyte_mesodermal_renal_Fibroblast_Ewing



Phase1 CAGE Peaks

Hg19::chr10:73730296..73730317,+p@chr10:73730296..73730317
+
Hg19::chr10:99790340..99790353,-p2@CRTAC1
Hg19::chr10:99790370..99790385,-p1@CRTAC1
Hg19::chr12:48367311..48367320,-p14@HNRNPM
Hg19::chr12:48398250..48398267,-p1@COL2A1
Hg19::chr12:53447073..53447087,+p@chr12:53447073..53447087
+
Hg19::chr12:57628783..57628814,+p@chr12:57628783..57628814
+
Hg19::chr12:57629169..57629214,-p@chr12:57629169..57629214
-
Hg19::chr12:57629234..57629249,-p@chr12:57629234..57629249
-
Hg19::chr12:57629315..57629334,-p@chr12:57629315..57629334
-
Hg19::chr12:57629562..57629589,-p@chr12:57629562..57629589
-
Hg19::chr12:57630410..57630437,-p@chr12:57630410..57630437
-
Hg19::chr12:57630458..57630470,-p@chr12:57630458..57630470
-
Hg19::chr12:57630873..57630895,-p1@NDUFA4L2
Hg19::chr12:57630900..57630911,-p2@NDUFA4L2
Hg19::chr15:89346657..89346673,+p1@ACAN
Hg19::chr15:89346682..89346691,+p4@ACAN
Hg19::chr15:89346699..89346715,+p2@ACAN
Hg19::chr15:89346739..89346750,+p3@ACAN
Hg19::chr15:89381951..89381962,+p@chr15:89381951..89381962
+
Hg19::chr15:89401833..89401842,+p10@ACAN
Hg19::chr15:89402048..89402061,+p8@ACAN
Hg19::chr15:89402148..89402159,+p6@ACAN
Hg19::chr15:89417758..89417770,+p@chr15:89417758..89417770
+
Hg19::chr16:69958887..69958927,+p3@WWP2
Hg19::chr16:69958930..69958953,+p2@WWP2
Hg19::chr16:69958959..69958971,+p6@WWP2
Hg19::chr17:26127550..26127556,-p1@NOS2
Hg19::chr19:41281416..41281445,+p1@MIA-RAB4B
Hg19::chr1:111770265..111770275,+p10@CHI3L2
Hg19::chr1:111770278..111770289,+p9@CHI3L2
Hg19::chr1:111770294..111770305,+p6@CHI3L2
Hg19::chr1:111770322..111770342,+p1@CHI3L2
Hg19::chr1:111773349..111773368,+p11@CHI3L2
Hg19::chr1:186273999..186274008,+p@chr1:186273999..186274008
+
Hg19::chr1:186276610..186276616,+p@chr1:186276610..186276616
+
Hg19::chr1:186277391..186277396,+p@chr1:186277391..186277396
+
Hg19::chr1:203316798..203316810,-p13@FMOD
Hg19::chr1:2066360..2066369,+p36@PRKCZ
Hg19::chr20:43936937..43936967,-p1@MATN4
Hg19::chr21:40033882..40033887,-p21@ERG
Hg19::chr2:216252918..216252935,-p@chr2:216252918..216252935
-
Hg19::chr2:216300502..216300517,+p4@ENST00000412951
Hg19::chr2:233734789..233734820,+p4@C2orf82
Hg19::chr2:233735030..233735044,+p3@C2orf82
Hg19::chr3:140981491..140981508,+p3@ACPL2
Hg19::chr3:142607876..142607887,-p7@PCOLCE2
Hg19::chr4:174320254..174320274,-p2@SCRG1
Hg19::chr4:174320281..174320304,-p3@SCRG1
Hg19::chr6:33160233..33160251,-p1@COL11A2
Hg19::chr8:57354045..57354055,-p@chr8:57354045..57354055
-
Hg19::chr9:130636920..130636950,-p5@AK1
Hg19::chr9:131168253..131168264,+p@chr9:131168253..131168264
+
Hg19::chr9:131168289..131168300,+p@chr9:131168289..131168300
+
Hg19::chrX:54824686..54824690,-p1@ITIH6


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:0044421extracellular region part0.000205191071528448
GO:0005583fibrillar collagen0.000978053245048239
GO:0005201extracellular matrix structural constituent0.00119181646855413
GO:0005578proteinaceous extracellular matrix0.00119181646855413
GO:0001501skeletal development0.00359209545847259
GO:0030198extracellular matrix organization and biogenesis0.00608470421680022
GO:0005581collagen0.00719737186271699
GO:0005585collagen type II0.0116419404215236
GO:0043062extracellular structure organization and biogenesis0.0135409792303694
GO:0005592collagen type XI0.0153553945672956
GO:0030020extracellular matrix structural constituent conferring tensile strength0.0153553945672956
GO:0005539glycosaminoglycan binding0.0153553945672956
GO:0030247polysaccharide binding0.0153553945672956
GO:0001871pattern binding0.0153553945672956
GO:0005584collagen type I0.0153553945672956
GO:0004700atypical protein kinase C activity0.0153553945672956
GO:0044420extracellular matrix part0.0153553945672956
GO:0050954sensory perception of mechanical stimulus0.0153553945672956
GO:0007605sensory perception of sound0.0153553945672956
GO:0032502developmental process0.0153553945672956
GO:0006817phosphate transport0.0165717751341296
GO:0007181transforming growth factor beta receptor complex assembly0.0165717751341296
GO:0007275multicellular organismal development0.0165717751341296
GO:0030021extracellular matrix structural constituent conferring compression resistance0.0271333600942556
GO:0048731system development0.0300744875262851
GO:0030199collagen fibril organization0.0300744875262851
GO:0044409entry into host0.0300744875262851
GO:0030260entry into host cell0.0300744875262851
GO:0019059initiation of viral infection0.0300744875262851
GO:0052192movement in environment of other organism during symbiotic interaction0.0300744875262851
GO:0046718entry of virus into host cell0.0300744875262851
GO:0052126movement in host environment0.0300744875262851
GO:0051828entry into other organism during symbiotic interaction0.0300744875262851
GO:0051806entry into cell of other organism during symbiotic interaction0.0300744875262851
GO:0015698inorganic anion transport0.0316658241886977
GO:0004017adenylate kinase activity0.0316658241886977
GO:0006032chitin catabolic process0.0316658241886977
GO:0006046N-acetylglucosamine catabolic process0.0316658241886977
GO:0006043glucosamine catabolic process0.0316658241886977
GO:0046348amino sugar catabolic process0.0316658241886977
GO:0004697protein kinase C activity0.0316658241886977
GO:0006030chitin metabolic process0.0316658241886977
GO:0004568chitinase activity0.0316658241886977
GO:0001565phorbol ester receptor activity0.0316658241886977
GO:0048856anatomical structure development0.0373617123603633
GO:0006820anion transport0.0373617123603633
GO:0044247cellular polysaccharide catabolic process0.0405912102693347
GO:0000272polysaccharide catabolic process0.0405912102693347
GO:0051701interaction with host0.0416483223058567
GO:0048513organ development0.0471112555794051



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
non-terminally differentiated cell1.35e-11180
Uber Anatomy
Ontology termp-valuen
adult organism8.32e-32115
organism subdivision2.03e-23365
neural tube4.09e-2257
neural rod4.09e-2257
future spinal cord4.09e-2257
neural keel4.09e-2257
central nervous system1.38e-2082
regional part of brain4.88e-2059
neural plate4.24e-1986
presumptive neural plate4.24e-1986
regional part of nervous system5.78e-1994
nervous system5.78e-1994
brain1.18e-1769
future brain1.18e-1769
anterior neural tube4.83e-1742
neurectoderm4.98e-1790
ectoderm-derived structure5.29e-17169
multi-cellular organism7.54e-17659
regional part of forebrain1.26e-1641
forebrain1.26e-1641
future forebrain1.26e-1641
ectoderm9.93e-16173
presumptive ectoderm9.93e-16173
multi-tissue structure1.18e-15347
anterior region of body3.97e-14129
craniocervical region3.97e-14129
head6.25e-14123
gray matter6.30e-1434
brain grey matter6.30e-1434
telencephalon6.59e-1434
regional part of telencephalon1.97e-1333
cerebral hemisphere8.70e-1332
epithelium8.88e-13309
pre-chordal neural plate1.53e-1261
anatomical cluster2.20e-12286
cell layer2.48e-12312
tube4.33e-12194
anatomical system6.22e-12625
anatomical group1.32e-11626
anatomical conduit2.47e-11241
organ4.69e-11511
embryo1.36e-10612
regional part of cerebral cortex3.45e-1022
cerebral cortex8.06e-1025
pallium8.06e-1025
neocortex1.95e-0920
embryonic structure3.97e-09605
developing anatomical structure3.97e-09605
germ layer8.16e-09604
embryonic tissue8.16e-09604
presumptive structure8.16e-09604
epiblast (generic)8.16e-09604
organ part1.90e-08219


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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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