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Coexpression cluster:C283: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0006032!chitin catabolic process!0.00331155068880254!1116$GO:0006046!N-acetylglucosamine catabolic process!0.00331155068880254!1116$GO:0006043!glucosamine catabolic process!0.00331155068880254!1116$GO:0046348!amino sugar catabolic process!0.00331155068880254!1116$GO:0006030!chitin metabolic process!0.00331155068880254!1116$GO:0004568!chitinase activity!0.00331155068880254!1116$GO:0044247!cellular polysaccharide catabolic process!0.00347712822324267!1116$GO:0000272!polysaccharide catabolic process!0.00347712822324267!1116$GO:0006044!N-acetylglucosamine metabolic process!0.00463617096432356!1116$GO:0006041!glucosamine metabolic process!0.00463617096432356!1116$GO:0006040!amino sugar metabolic process!0.00493722102694197!1116$GO:0044264!cellular polysaccharide metabolic process!0.00876287259190826!1116$GO:0005976!polysaccharide metabolic process!0.00876287259190826!1116$GO:0005201!extracellular matrix structural constituent!0.0116377352777918!1116$GO:0044275!cellular carbohydrate catabolic process!0.0149604172294138!1116$GO:0004553!hydrolase activity, hydrolyzing O-glycosyl compounds!0.0149604172294138!1116$GO:0016052!carbohydrate catabolic process!0.0149604172294138!1116$GO:0016798!hydrolase activity, acting on glycosyl bonds!0.0161898033674791!1116$GO:0005529!sugar binding!0.0241917492424101!1116$GO:0005578!proteinaceous extracellular matrix!0.0278832567997174!1116$GO:0043285!biopolymer catabolic process!0.0279759802190039!1116$GO:0030246!carbohydrate binding!0.0279759802190039!1116$GO:0044262!cellular carbohydrate metabolic process!0.0279759802190039!1116$GO:0044265!cellular macromolecule catabolic process!0.0279759802190039!1116$GO:0005615!extracellular space!0.0279759802190039!1116$GO:0009057!macromolecule catabolic process!0.0312021664900506!1116$GO:0009308!amine metabolic process!0.0312021664900506!1116$GO:0006807!nitrogen compound metabolic process!0.0320747338144018!1116$GO:0005975!carbohydrate metabolic process!0.0357205934298834!1116$GO:0044248!cellular catabolic process!0.0357205934298834!1116$GO:0044421!extracellular region part!0.0388840145394879!1116$GO:0009056!catabolic process!0.0402767352525609!1116
|gostat_on_coexpression_clusters=GO:0006032!chitin catabolic process!0.00331155068880254!1116$GO:0006046!N-acetylglucosamine catabolic process!0.00331155068880254!1116$GO:0006043!glucosamine catabolic process!0.00331155068880254!1116$GO:0046348!amino sugar catabolic process!0.00331155068880254!1116$GO:0006030!chitin metabolic process!0.00331155068880254!1116$GO:0004568!chitinase activity!0.00331155068880254!1116$GO:0044247!cellular polysaccharide catabolic process!0.00347712822324267!1116$GO:0000272!polysaccharide catabolic process!0.00347712822324267!1116$GO:0006044!N-acetylglucosamine metabolic process!0.00463617096432356!1116$GO:0006041!glucosamine metabolic process!0.00463617096432356!1116$GO:0006040!amino sugar metabolic process!0.00493722102694197!1116$GO:0044264!cellular polysaccharide metabolic process!0.00876287259190826!1116$GO:0005976!polysaccharide metabolic process!0.00876287259190826!1116$GO:0005201!extracellular matrix structural constituent!0.0116377352777918!1116$GO:0044275!cellular carbohydrate catabolic process!0.0149604172294138!1116$GO:0004553!hydrolase activity, hydrolyzing O-glycosyl compounds!0.0149604172294138!1116$GO:0016052!carbohydrate catabolic process!0.0149604172294138!1116$GO:0016798!hydrolase activity, acting on glycosyl bonds!0.0161898033674791!1116$GO:0005529!sugar binding!0.0241917492424101!1116$GO:0005578!proteinaceous extracellular matrix!0.0278832567997174!1116$GO:0043285!biopolymer catabolic process!0.0279759802190039!1116$GO:0030246!carbohydrate binding!0.0279759802190039!1116$GO:0044262!cellular carbohydrate metabolic process!0.0279759802190039!1116$GO:0044265!cellular macromolecule catabolic process!0.0279759802190039!1116$GO:0005615!extracellular space!0.0279759802190039!1116$GO:0009057!macromolecule catabolic process!0.0312021664900506!1116$GO:0009308!amine metabolic process!0.0312021664900506!1116$GO:0006807!nitrogen compound metabolic process!0.0320747338144018!1116$GO:0005975!carbohydrate metabolic process!0.0357205934298834!1116$GO:0044248!cellular catabolic process!0.0357205934298834!1116$GO:0044421!extracellular region part!0.0388840145394879!1116$GO:0009056!catabolic process!0.0402767352525609!1116
|id=C283
|id=C283
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000153!5.51e-21!9;CL:0000447!5.51e-21!9;CL:0000667!1.89e-16!6;CL:0000058!1.89e-16!6;CL:0000138!1.89e-16!6;CL:0000235!1.95e-16!6;CL:0000135!1.20e-12!3;CL:0000386!1.20e-12!3;CL:0000388!1.20e-12!3;CL:0000499!2.88e-12!28;CL:0000327!3.75e-12!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.41e-29!115;UBERON:0001049!2.67e-15!57;UBERON:0005068!2.67e-15!57;UBERON:0006241!2.67e-15!57;UBERON:0007135!2.67e-15!57;UBERON:0005743!3.42e-14!86;UBERON:0001017!5.95e-14!82;UBERON:0002616!3.09e-12!59;UBERON:0003080!3.15e-12!42;UBERON:0000955!4.41e-12!69;UBERON:0006238!4.41e-12!69;UBERON:0000073!4.42e-12!94;UBERON:0001016!4.42e-12!94;UBERON:0002780!5.92e-12!41;UBERON:0001890!5.92e-12!41;UBERON:0006240!5.92e-12!41;UBERON:0003075!6.65e-10!86;UBERON:0007284!6.65e-10!86;UBERON:0002020!9.06e-10!34;UBERON:0003528!9.06e-10!34;UBERON:0001893!2.23e-09!34;UBERON:0002791!4.13e-09!33;UBERON:0002346!6.14e-09!90;UBERON:0001869!1.44e-08!32;UBERON:0000479!1.16e-07!787;UBERON:0003056!6.77e-07!61
|ontology_enrichment_uberon=UBERON:0007846!1.20e-12!3;UBERON:0000043!1.20e-12!3;UBERON:0007845!1.20e-12!3
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887,0.967978,0.536371,0.947568,0.999171,0.0949991,0.485414,0.731268,0.460694,0.610541,0.99976,0.0166837,0.82923,0.265955,0.990408,0.359154,0.999995,0.000847868,0.455315,0.754195,0.580153,0.907939,0.085505,0.17744,0.96052,0.884044,0.880645,0.0605474,0.994409,0.703009,0.945149,0.730142,0.373707,0.986087,0.913749,0.90355,0.939593,0.902091,0.760349,0.996588,0.760539,0.524331,0.783153,0.54994,0.887669,0.709417,0.830173,0.0208715,0.0683428,0.999632,0.892137,0.557888,0.799172,0.544831,0.624171,0.699978,0.778593,0.907951,0.411821,0.693285,0.993093,0.999998,0.151096,0.976627,0.96683,0.85722,0.962296,0.801589,0.999995,0.597147,0.526529,0.98201,0.618236,0.947954,0.995839,0.678434,0.979474,0.896722,0.426246,0.872304,0.947736,0.999998,1,0.971153,0.89041,0.101931,0.0235204,0.103197,0.540181,0.786683,0.010421,0.70032,0.511547,0.00249659,0.672839,0.980387,0.922282,0.445179,0.887138,0.506413,0.572503,0.118558,0.775968,0.945083,0.506771,0.737838,0.594498,0.120633,0.702317,0.994394,0.465084,0.964023,0.890544,0.806587,0.997697,0.0753297,0.311665,0.919604,0.62933,0.961471,3.58153e-07,0.999979,0.925527,0.681442,0.771943,0.614274,0.908329,0.243136,0.792162,0.0166335,0.942875,0.841447,0.193196,0.210305,0.935889,0.994541,0.856758,0.739055,0.863652,0.00290639,0.840001,0.957893,0.340567,0.783021,0.690583,0.813869,0.205165,0.800453,0.942176,0.0899452,0.841153,0.327634,0.940304,0.767117,0.992293,0.939258,0.829521,0.727933,0.820226,0.92612,0.219856,0.856571,0.607018,0.987177,0.802759,0.977062,0.982207,0.999671,0.999994,0.430806,0.99971,0.884053,0.494044,0.88911,0.997696,0.279657,0.0461782,0.017635,0.98234,0.992746,0.0678947,0.999163,0.998098,0.430154,0.655098,0.0527655,0.99897,0.545258,0.935023,0.461849,0.324562,0.500687,0.188939,0.633825,0.885833,0.121467,0.94429,0.0412374,0.998606,1,0.980746,0.999835,0.999994,0.867298,0.96391,0.994178,0.98327,0.999983,0.893536,0.760309,0.0181196,9.24317e-06,0.989991,0.970235,0.998136,1.31148e-07,0.310808,0.888561,0.926699,0.999993,0.769711,0.999987,0.893704,0.93297,0.999685,0.989186,0.258765,0.999256,0.720677,0.999996,0.0136382,0.999999,0.999993,1,0.862754,0.967645,0.280017,0.467659,0.000881298,1.01665e-05,0.00333212,0.937319,0.925909,0.0880306,0.70353,0.78776,0.0157344,0.235042,0.935652,0.217872,0.85971,9.18325e-05,5.81483e-05,0.35975,0.0134745,0.882394,0.775662,0.502421,0.00394554,0.00537205,0.387831,0.0055029,0.952217,0.14391,0.0798801,0.00320465,1,0.00055516,0.739057,0.13187,0.582,0.0181306,0.999944,0.353828,0.865598,0.443479,0.898986,0.999837,0.152321,0.850873,0.736853,0.0361285,0.872737,0.947838,0.997986,0.720639,0.969992,0.903796,0.992544,0.00922922,0.000131816,0.0117111,0.396108,0.000993257,0.720233,0.846648,0.553838,0.49392,0.127007,0.39016,0.114188,0.0290601,0.419011,0.660208,0.000221177,0.361573,0.757735,0.0515577,0.0371391,0.861322,0.340916,0.0146297,0.977946,0.850818,0.433685,0.410765,0.034957,0.94156,0.33458,0.725113,0.96315,0.144627,0.042767,0.791874,0.0614324,0.83047,0.992794,0.00430002,0.412774,3.14854e-05,0.452105,0.0563986,0.0592431,4.18215e-06,0.985442,0.0145841,0.909533,0.3774,0.145793,0.948981,0.0376724,0.0307718,0.970502,0.408953,0.402957,0.094462,0.105205,0.681597,0.0227288,0.755011,0.961255,0.934737,0.730861,0.692963,0.764802,0.454401,0.766462,0.936655,0.000214369,0.829139,0.02939,0.0444049,0.359919,0.963094,0.188527,0.19465,0.197887,0.673465,0.8901,0.128826,0.102093,0.867098,0.854439,0.398349,0.777315,0.602276,0.952206,0.753782,1.44163e-06,0.746269,0.884106,0.0300644,0.00187122,0.978843,0.656594,0.290647,0.852957,0.549021,0.910597,0.56579,0.933638,0.981441,0.0681097,0.452239,0.000758223,0.560458,0.510744,0.348845,0.00025587,0.998661,0.0476774,0.859637,0.796674,0.0022741,0.61,0.0366536,0.492976,0.529785,0.000686256,0.869149,0.183206,5.62478e-07,0.0894863,0.930838,0.667887,0.243534,0.0377708,0.86847,0.956013,0.821217,0.683743,0.671973,0.990468,0.00327687,0.882765,0.971762,0.904243,0.115748,0.447426,0.848943,0.900799,0.986855,0.0754081,1.49406e-05,0.000148373,0.0554693,0.79209,0.926394,0.884026,2.33618e-05,0.979034,0.3296,0.57299,0.790575,0.96865,0.0647377,0.394068,0.977032,0.378783,0.968607,0.0978455,0.570356,2.44495e-08,0.918922,0.712199,0.000517963,0.571262,0.997292,0.990464,0.878215,0.0165032,0.773383,0.960153,0.727471,0.794732,0.638148,0.863778,0.26866,0.816245,0.28347,0.00817491,0.0634325,0.830106,0.499288,0.287248,0.762956,0.11343,2.11771e-09,9.38543e-07,0.783922,0.41563,0.998549,0.209549,0.68756,0.989256,0.260204,0.3629,0.303526,0.824504,0.800745,0.993994,0.848568,0.0689152,0.00642043,8.52774e-05,0.966859,0.890052,0.592801,0.559131,0.848534,0.0386775,0.0181394,0.042323,0.964051,0.835194,8.15197e-05,0.57786,0.00204538,0.936602,0.900313,0.778315,0.997726,0.980223,0.871489,0.00513201,0.00296091,0.980154,0.327734,0.130089,0.0112102,0.677315,0.992079,0.804645,0.0432267,0.948547,0.269171,0.718863,0.00634551,0.281386,0.91162
}}
}}

Revision as of 14:28, 19 October 2012


Full id: C283_tenocyte_Chondrocyte_mesenchymal_Macrophage_pleomorphic_Synoviocyte_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr1:203148057..203148072,+p@chr1:203148057..203148072
+
Hg19::chr1:203148146..203148212,+p1@CU678996
Hg19::chr1:203148270..203148291,-p@chr1:203148270..203148291
-
Hg19::chr1:203148271..203148296,+p7@CU678996
Hg19::chr1:203148336..203148348,-p@chr1:203148336..203148348
-
Hg19::chr1:203148357..203148383,-p@chr1:203148357..203148383
-
Hg19::chr1:203148373..203148396,+p3@CU678996
Hg19::chr1:203148394..203148401,-p10@CHI3L1
Hg19::chr1:203148408..203148431,+p2@CU678996
Hg19::chr1:203148428..203148437,-p11@CHI3L1
Hg19::chr1:203148455..203148477,-p5@CHI3L1
Hg19::chr1:203148495..203148505,-p13@CHI3L1
Hg19::chr1:203148522..203148550,-p4@CHI3L1
Hg19::chr1:203148531..203148567,+p4@CU678996
Hg19::chr1:203148907..203148922,+p@chr1:203148907..203148922
+
Hg19::chr1:203148919..203148937,-p16@CHI3L1
Hg19::chr1:203148938..203148988,-p6@CHI3L1
Hg19::chr1:203149716..203149729,-p19@CHI3L1
Hg19::chr1:203149741..203149762,-p14@CHI3L1
Hg19::chr1:203149809..203149816,-p@chr1:203149809..203149816
-
Hg19::chr1:203150031..203150040,-p@chr1:203150031..203150040
-
Hg19::chr1:203150041..203150049,-p@chr1:203150041..203150049
-
Hg19::chr1:203150369..203150408,-p@chr1:203150369..203150408
-
Hg19::chr1:203151897..203151908,-p15@CHI3L1
Hg19::chr1:203151934..203151947,-p7@CHI3L1
Hg19::chr1:203151964..203151973,-p21@CHI3L1
Hg19::chr1:203152777..203152814,+p@chr1:203152777..203152814
+
Hg19::chr1:203152791..203152804,-p@chr1:203152791..203152804
-
Hg19::chr1:203152808..203152846,-p@chr1:203152808..203152846
-
Hg19::chr1:203152845..203152866,+p@chr1:203152845..203152866
+
Hg19::chr1:203152849..203152863,-p@chr1:203152849..203152863
-
Hg19::chr1:203152872..203152879,-p@chr1:203152872..203152879
-
Hg19::chr1:203152908..203152924,-p@chr1:203152908..203152924
-
Hg19::chr1:203153416..203153419,-p@chr1:203153416..203153419
-
Hg19::chr1:203153711..203153722,+p@chr1:203153711..203153722
+
Hg19::chr1:203154299..203154330,+p@chr1:203154299..203154330
+
Hg19::chr1:203154334..203154339,+p@chr1:203154334..203154339
+
Hg19::chr1:203154342..203154363,-p9@CHI3L1
Hg19::chr1:203154349..203154356,+p@chr1:203154349..203154356
+
Hg19::chr1:203154383..203154466,-p3@CHI3L1
Hg19::chr1:203154393..203154416,+p@chr1:203154393..203154416
+
Hg19::chr1:203154486..203154506,-p8@CHI3L1
Hg19::chr1:203154508..203154518,-p20@CHI3L1
Hg19::chr1:203155464..203155497,-p@chr1:203155464..203155497
-
Hg19::chr1:203155823..203155838,-p1@CHI3L1
Hg19::chr1:203155868..203155882,-p2@CHI3L1


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:0006032chitin catabolic process0.00331155068880254
GO:0006046N-acetylglucosamine catabolic process0.00331155068880254
GO:0006043glucosamine catabolic process0.00331155068880254
GO:0046348amino sugar catabolic process0.00331155068880254
GO:0006030chitin metabolic process0.00331155068880254
GO:0004568chitinase activity0.00331155068880254
GO:0044247cellular polysaccharide catabolic process0.00347712822324267
GO:0000272polysaccharide catabolic process0.00347712822324267
GO:0006044N-acetylglucosamine metabolic process0.00463617096432356
GO:0006041glucosamine metabolic process0.00463617096432356
GO:0006040amino sugar metabolic process0.00493722102694197
GO:0044264cellular polysaccharide metabolic process0.00876287259190826
GO:0005976polysaccharide metabolic process0.00876287259190826
GO:0005201extracellular matrix structural constituent0.0116377352777918
GO:0044275cellular carbohydrate catabolic process0.0149604172294138
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0149604172294138
GO:0016052carbohydrate catabolic process0.0149604172294138
GO:0016798hydrolase activity, acting on glycosyl bonds0.0161898033674791
GO:0005529sugar binding0.0241917492424101
GO:0005578proteinaceous extracellular matrix0.0278832567997174
GO:0043285biopolymer catabolic process0.0279759802190039
GO:0030246carbohydrate binding0.0279759802190039
GO:0044262cellular carbohydrate metabolic process0.0279759802190039
GO:0044265cellular macromolecule catabolic process0.0279759802190039
GO:0005615extracellular space0.0279759802190039
GO:0009057macromolecule catabolic process0.0312021664900506
GO:0009308amine metabolic process0.0312021664900506
GO:0006807nitrogen compound metabolic process0.0320747338144018
GO:0005975carbohydrate metabolic process0.0357205934298834
GO:0044248cellular catabolic process0.0357205934298834
GO:0044421extracellular region part0.0388840145394879
GO:0009056catabolic process0.0402767352525609



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 cell5.51e-219
carbohydrate secreting cell5.51e-219
collagen secreting cell1.89e-166
chondroblast1.89e-166
chondrocyte1.89e-166
macrophage1.95e-166
fibrocyte1.20e-123
attachment cell1.20e-123
tendon cell1.20e-123
stromal cell2.88e-1228
extracellular matrix secreting cell3.75e-1215
Uber Anatomy
Ontology termp-valuen
dense regular connective tissue1.20e-123
tendon1.20e-123
regular connective tissue1.20e-123


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

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