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Coexpression cluster:C243: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:04, 17 September 2013


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

p.valueFDRnGenesnPathwayName
3.89935446244208e-050.02468291374725843106Amoebiasis (KEGG):05146
0.0001206750088461360.03819364029980213155IL-1 up reg. targets (Netpath):NetPath_13



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
GAG secreting cell1.20e-199
carbohydrate secreting cell1.20e-199
collagen secreting cell1.21e-156
chondroblast1.21e-156
chondrocyte1.21e-156
extracellular matrix secreting cell2.58e-1115
stromal cell3.62e-0728
Uber Anatomy
Ontology termp-valuen
adult organism1.37e-38114
neural tube1.13e-1756
neural rod1.13e-1756
future spinal cord1.13e-1756
neural keel1.13e-1756
central nervous system6.42e-1581
regional part of nervous system8.54e-1553
regional part of brain8.54e-1553
neural plate2.32e-1382
presumptive neural plate2.32e-1382
nervous system6.55e-1389
brain grey matter1.46e-1234
gray matter1.46e-1234
neurectoderm1.67e-1286
telencephalon1.85e-1234
brain7.78e-1268
future brain7.78e-1268
regional part of forebrain1.14e-1141
forebrain1.14e-1141
anterior neural tube1.14e-1141
future forebrain1.14e-1141
regional part of telencephalon2.42e-1132
structure with developmental contribution from neural crest4.96e-11132
ecto-epithelium1.22e-10104
neocortex1.24e-1020
regional part of cerebral cortex1.43e-0922
cerebral hemisphere2.18e-0932
organ system subdivision4.00e-09223
brainstem5.42e-096
open tracheal system trachea1.82e-082
cerebral cortex2.76e-0825
pallium2.76e-0825
throat3.09e-082
meninx4.09e-082
membrane organ4.09e-082
meningeal cluster4.09e-082
pre-chordal neural plate4.26e-0861
ectoderm-derived structure8.02e-08171
ectoderm8.02e-08171
presumptive ectoderm8.02e-08171
posterior neural tube1.59e-0715
chordal neural plate1.59e-0715


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)
MA0003.10.104049
MA0004.10.0230278
MA0006.10.0678065
MA0007.10.419216
MA0009.10.231637
MA0014.10.262247
MA0017.10.214918
MA0019.10.231029
MA0024.10.166016
MA0025.10.326531
MA0027.11.69857
MA0028.10.00464806
MA0029.10.177433
MA0030.10.508845
MA0031.10.134441
MA0038.10.414012
MA0040.10.534038
MA0041.10.0269039
MA0042.10.0902904
MA0043.10.231848
MA0046.10.224416
MA0048.10.253558
MA0050.10.433405
MA0051.10.406356
MA0052.10.183297
MA0055.10.456123
MA0056.10
MA0057.12.77018
MA0058.10.00874589
MA0059.10.00861211
MA0060.10.0341282
MA0061.13.67698
MA0063.10
MA0066.10.414788
MA0067.10.473069
MA0068.12.53538
MA0069.10.631819
MA0070.10.214581
MA0071.10.149709
MA0072.10.211675
MA0073.119.8878
MA0074.10.180446
MA0076.10.0105149
MA0077.10.206727
MA0078.10.286718
MA0081.10.124224
MA0083.10.666474
MA0084.10.635217
MA0087.10.2101
MA0088.10.295537
MA0089.10
MA0090.11.14668
MA0091.10.0235515
MA0092.11.30555
MA0093.10.0224819
MA0095.10
MA0098.10
MA0100.10.439549
MA0101.11.30631
MA0103.10.262976
MA0105.13.81045
MA0106.10.491621
MA0107.14.27636
MA0108.20.41444
MA0109.10
MA0111.10.0668683
MA0113.10.895397
MA0114.10.795623
MA0115.10.410377
MA0116.11.11423
MA0117.10.257218
MA0119.10.628913
MA0122.10.755856
MA0124.10.377376
MA0125.10.313172
MA0130.10
MA0131.10.308252
MA0132.10
MA0133.10
MA0135.10.252217
MA0136.10.0516336
MA0139.10.498759
MA0140.10.616386
MA0141.10.0434582
MA0142.10.376423
MA0143.10.244737
MA0144.12.21595
MA0145.13.22682
MA0146.10.100846
MA0147.10.00128417
MA0148.10.282682
MA0149.10.0347551
MA0062.20.00579851
MA0035.20.962029
MA0039.21.06381
MA0138.20.288154
MA0002.20.877966
MA0137.20.78833
MA0104.20.00280437
MA0047.20.468253
MA0112.21.65985
MA0065.20.807979
MA0150.10.0115619
MA0151.10
MA0152.10.352609
MA0153.10.300753
MA0154.11.84504
MA0155.12.27433
MA0156.10.0876463
MA0157.10.341461
MA0158.10
MA0159.10.637066
MA0160.10.0318984
MA0161.10
MA0162.10.177466
MA0163.15.77335
MA0164.10.258285
MA0080.20.0701428
MA0018.20.0638918
MA0099.20.0391796
MA0079.25.49102
MA0102.20.668584
MA0258.10.466579
MA0259.10.0356699
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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