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Difference between revisions of "Coexpression cluster:C470"

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|ontology_enrichment_uberon=UBERON:0003102!3.81e-14!99;UBERON:0002199!3.36e-13!46;UBERON:0002416!3.36e-13!46;UBERON:0007524!1.36e-12!73;UBERON:0002329!2.27e-12!71;UBERON:0003059!2.27e-12!71;UBERON:0007282!2.27e-12!71;UBERON:0004290!2.27e-12!71;UBERON:0009618!2.27e-12!71;UBERON:0003077!5.59e-12!72;UBERON:0007285!5.59e-12!72;UBERON:0002097!2.37e-10!41;UBERON:0002385!4.58e-10!64;UBERON:0001015!4.58e-10!64;UBERON:0000383!4.58e-10!64;UBERON:0007503!6.89e-10!78;UBERON:0000486!7.99e-10!83;UBERON:0000475!1.37e-09!264;UBERON:0001134!1.45e-09!62;UBERON:0002036!1.45e-09!62;UBERON:0003082!1.45e-09!62;UBERON:0001013!1.35e-08!14;UBERON:0005256!1.84e-08!122;UBERON:0004923!1.02e-07!66;UBERON:0000479!2.06e-07!773;UBERON:0003104!2.29e-07!160;UBERON:0009142!2.29e-07!160;UBERON:0003688!3.03e-07!6;UBERON:0002358!3.03e-07!6;UBERON:0003684!3.03e-07!6;UBERON:0001178!3.03e-07!6;UBERON:0004457!4.46e-07!12;UBERON:0000042!4.46e-07!12;UBERON:0002100!5.56e-07!199
 
|ontology_enrichment_uberon=UBERON:0003102!3.81e-14!99;UBERON:0002199!3.36e-13!46;UBERON:0002416!3.36e-13!46;UBERON:0007524!1.36e-12!73;UBERON:0002329!2.27e-12!71;UBERON:0003059!2.27e-12!71;UBERON:0007282!2.27e-12!71;UBERON:0004290!2.27e-12!71;UBERON:0009618!2.27e-12!71;UBERON:0003077!5.59e-12!72;UBERON:0007285!5.59e-12!72;UBERON:0002097!2.37e-10!41;UBERON:0002385!4.58e-10!64;UBERON:0001015!4.58e-10!64;UBERON:0000383!4.58e-10!64;UBERON:0007503!6.89e-10!78;UBERON:0000486!7.99e-10!83;UBERON:0000475!1.37e-09!264;UBERON:0001134!1.45e-09!62;UBERON:0002036!1.45e-09!62;UBERON:0003082!1.45e-09!62;UBERON:0001013!1.35e-08!14;UBERON:0005256!1.84e-08!122;UBERON:0004923!1.02e-07!66;UBERON:0000479!2.06e-07!773;UBERON:0003104!2.29e-07!160;UBERON:0009142!2.29e-07!160;UBERON:0003688!3.03e-07!6;UBERON:0002358!3.03e-07!6;UBERON:0003684!3.03e-07!6;UBERON:0001178!3.03e-07!6;UBERON:0004457!4.46e-07!12;UBERON:0000042!4.46e-07!12;UBERON:0002100!5.56e-07!199
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.685475,0.0268426,1.10719,0.18689,0.563528,0.185775,0.239567,0.124268,0.852063,0.337519,0.960665,0.272066,0.0182787,1.21892,0.949723,0.296747,0.416635,0.0529639,0.0212388,0.28395,0.324802,0.416615,1.02103,0.259643,0.392149,3.04992,0.574586,0.529528,1.44162,0.509878,0.462061,0.448071,0.157997,0.0842136,0.0614574,0.095179,2.89773,0.547612,0.188523,0.772449,0.478015,0.859404,0.941543,0.0758747,0.206188,0.369625,0.675098,0.479472,0.278107,0.078811,0.813183,0.695343,0.361765,1.28171,0.653159,0.233295,0.276619,1.13675,0.147749,0.60157,0.483605,0.679156,0.29166,0.393294,0.255455,0.956236,0.73513,1.08739,0.43915,0.930562,0.133532,0.0320016,0.816595,0.651319,2.20591,0.0686019,0.0588919,0.379205,0.436366,0.382881,0.737888,0.392395,0.25519,0.127139,0.604277,0.020244,0.02106,0.140525,0.321213,1.18432,0.823081,0.579812,0.462581,0.166137,0.267495,0.181399,0.229209,0.499768,0.324895,0.952027,0.0509974,0.45769,2.14397,0.419744,0.355282,0.16277,0.406348,0.228655,0.391767,0.0697646,0.104554,0.492438,0.0955593,0.171884,0.777703,0.814512,3.23817,0.460172,0.362802,0.0442476,0.64371,0.319278,0.183912,0.263675,0.882719,0.989505,0.234914,0.466912,0.683004,0.182525,2.42443,0.910031,0.696335,1.33164,0.835304,1.01534,0.886598,0.179476,0.795107,1.6331,1.23566,0.759951,1.23799,0.496668,0.356718,0.20386,0.343142,1.4753,1.3737,0.0420132,0.0781321,0.885079,0.58078,0.274841,1.25907,0.959994,0.308372,0.529975,0.392237,0.107739,0.758809,0.564094,0.435692,0.109525,0.36994,0.254599,0.344454,0.238589,0.207986
 
}}
 
}}

Revision as of 05:14, 26 November 2012


Full id: C470_Adipocyte_Preadipocyte_Smooth_Fibroblast_aorta_normal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:92336119..92336144,-p18@FBLN5
Hg19::chr14:92336334..92336351,-p22@FBLN5
Hg19::chr14:92336363..92336402,-p17@FBLN5
Hg19::chr14:92343879..92343891,-p@chr14:92343879..92343891
-
Hg19::chr14:92347684..92347698,-p@chr14:92347684..92347698
-
Hg19::chr14:92349351..92349365,-p@chr14:92349351..92349365
-
Hg19::chr14:92361339..92361353,-p@chr14:92361339..92361353
-
Hg19::chr14:92403359..92403409,+p@chr14:92403359..92403409
+
Hg19::chr14:92403378..92403403,-p@chr14:92403378..92403403
-
Hg19::chr14:92403405..92403440,-p@chr14:92403405..92403440
-
Hg19::chr14:92403450..92403483,-p@chr14:92403450..92403483
-
Hg19::chr14:92413677..92413688,-p12@FBLN5
Hg19::chr14:92413727..92413738,-p7@FBLN5
Hg19::chr14:92413748..92413762,-p1@FBLN5
Hg19::chr14:92413764..92413794,-p2@FBLN5
Hg19::chr14:92413800..92413837,-p4@FBLN5
Hg19::chr14:92414294..92414355,-p9@FBLN5
Hg19::chr15:89442263..89442298,-p@chr15:89442263..89442298
-
Hg19::chr19:38812519..38812533,-p@chr19:38812519..38812533
-
Hg19::chr4:88928828..88928841,+p3@PKD2
Hg19::chr5:151047146..151047178,-p4@SPARC


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:0007160cell-matrix adhesion0.00182617469241869
GO:0031589cell-substrate adhesion0.00182617469241869
GO:0005509calcium ion binding0.00352400893404339
GO:0050982detection of mechanical stimulus0.0088744333492283
GO:0005932basal body0.0101810085027996
GO:0005578proteinaceous extracellular matrix0.0101810085027996
GO:0009612response to mechanical stimulus0.0204284640188069
GO:0007368determination of left/right symmetry0.0204284640188069
GO:0009799determination of symmetry0.0204284640188069
GO:0009855determination of bilateral symmetry0.0204284640188069
GO:0005518collagen binding0.0204284640188069
GO:0005248voltage-gated sodium channel activity0.0209774322652129
GO:0044421extracellular region part0.0209774322652129
GO:0022610biological adhesion0.0209774322652129
GO:0007155cell adhesion0.0209774322652129
GO:0048513organ development0.0241483101232616
GO:0007259JAK-STAT cascade0.0241483101232616
GO:0005247voltage-gated chloride channel activity0.0241483101232616
GO:0005178integrin binding0.0241483101232616
GO:0005929cilium0.0241483101232616
GO:0022844voltage-gated anion channel activity0.0241483101232616
GO:0009582detection of abiotic stimulus0.0241483101232616
GO:0044463cell projection part0.0241483101232616
GO:0009581detection of external stimulus0.0246171127198746
GO:0005272sodium channel activity0.0269354144139597
GO:0048731system development0.0305550245877575
GO:0008022protein C-terminus binding0.0305550245877575
GO:0005604basement membrane0.0305550245877575
GO:0043169cation binding0.0305550245877575
GO:0051606detection of stimulus0.0305550245877575
GO:0005254chloride channel activity0.0305550245877575
GO:0001503ossification0.0305550245877575
GO:0031214biomineral formation0.0305550245877575
GO:0046872metal ion binding0.0305550245877575
GO:0046849bone remodeling0.0305550245877575
GO:0043167ion binding0.0305550245877575
GO:0005253anion channel activity0.0305550245877575
GO:0007050cell cycle arrest0.0305550245877575
GO:0032403protein complex binding0.0305550245877575
GO:0048771tissue remodeling0.030967346229515
GO:0048856anatomical structure development0.0311067998750359
GO:0006874cellular calcium ion homeostasis0.0311067998750359
GO:0055074calcium ion homeostasis0.0311067998750359
GO:0005507copper ion binding0.0311067998750359
GO:0006875cellular metal ion homeostasis0.0311067998750359
GO:0055065metal ion homeostasis0.0311067998750359
GO:0007389pattern specification process0.0311067998750359
GO:0044420extracellular matrix part0.0321715484447625
GO:0005815microtubule organizing center0.0351465779076556
GO:0007275multicellular organismal development0.0351465779076556
GO:0009628response to abiotic stimulus0.0380995966342028
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0398871888862169
GO:0055066di-, tri-valent inorganic cation homeostasis0.0398871888862169
GO:0006816calcium ion transport0.0398871888862169
GO:0030003cellular cation homeostasis0.0415848374287668
GO:0055080cation homeostasis0.0415848374287668
GO:0001501skeletal development0.0415848374287668
GO:0008509anion transmembrane transporter activity0.0415848374287668
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0415848374287668
GO:0005515protein binding0.0415848374287668
GO:0045786negative regulation of progression through cell cycle0.0433601492881494
GO:0005625soluble fraction0.0435163738114841
GO:0055082cellular chemical homeostasis0.0435163738114841
GO:0006873cellular ion homeostasis0.0435163738114841
GO:0015674di-, tri-valent inorganic cation transport0.0446416026002452
GO:0022843voltage-gated cation channel activity0.0453784752599863
GO:0050801ion homeostasis0.0467881969022059



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
fibroblast2.41e-3276
skin fibroblast2.81e-1523
preadipocyte2.48e-1012
muscle precursor cell7.68e-0958
myoblast7.68e-0958
multi-potent skeletal muscle stem cell7.68e-0958
fat cell7.88e-0915
multi fate stem cell6.70e-08427
muscle cell1.20e-0755
somatic stem cell2.96e-07433
contractile cell6.54e-0759
Uber Anatomy
Ontology termp-valuen
surface structure3.81e-1499
integument3.36e-1346
integumental system3.36e-1346
dense mesenchyme tissue1.36e-1273
somite2.27e-1271
presomitic mesoderm2.27e-1271
presumptive segmental plate2.27e-1271
dermomyotome2.27e-1271
trunk paraxial mesoderm2.27e-1271
paraxial mesoderm5.59e-1272
presumptive paraxial mesoderm5.59e-1272
skin of body2.37e-1041
muscle tissue4.58e-1064
musculature4.58e-1064
musculature of body4.58e-1064
epithelial vesicle6.89e-1078
multilaminar epithelium7.99e-1083
organism subdivision1.37e-09264
skeletal muscle tissue1.45e-0962
striated muscle tissue1.45e-0962
myotome1.45e-0962
adipose tissue1.35e-0814
trunk mesenchyme1.84e-08122
organ component layer1.02e-0766
tissue2.06e-07773
mesenchyme2.29e-07160
entire embryonic mesenchyme2.29e-07160
omentum3.03e-076
peritoneum3.03e-076
abdominal cavity3.03e-076
visceral peritoneum3.03e-076
cavity lining4.46e-0712
serous membrane4.46e-0712
trunk5.56e-07199


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


This analysis result is provided for C0 - C305 clusters.