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Coexpression cluster:C259: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.00100082420817143!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.00100082420817144!1303$GO:0005593!FACIT collagen!0.00200164841634287!1303$GO:0030934!anchoring collagen!0.00200164841634287!1303$GO:0030199!collagen fibril organization!0.00200164841634287!1303$GO:0030198!extracellular matrix organization and biogenesis!0.007672985595981!1303$GO:0005581!collagen!0.00772064389160821!1303$GO:0043062!extracellular structure organization and biogenesis!0.0105086541858001!1303$GO:0005201!extracellular matrix structural constituent!0.0130107147062286!1303$GO:0044420!extracellular matrix part!0.0130107147062286!1303$GO:0006817!phosphate transport!0.0130107147062286!1303$GO:0001501!skeletal development!0.0174310216256525!1303$GO:0015698!inorganic anion transport!0.0200164841634287!1303$GO:0006820!anion transport!0.0230904442313838!1303$GO:0005578!proteinaceous extracellular matrix!0.0280897994426783!1303
|gostat_on_coexpression_clusters=GO:0005595!collagen type XII!0.00100082420817143!1303$GO:0030020!extracellular matrix structural constituent conferring tensile strength!0.00100082420817144!1303$GO:0005593!FACIT collagen!0.00200164841634287!1303$GO:0030934!anchoring collagen!0.00200164841634287!1303$GO:0030199!collagen fibril organization!0.00200164841634287!1303$GO:0030198!extracellular matrix organization and biogenesis!0.007672985595981!1303$GO:0005581!collagen!0.00772064389160821!1303$GO:0043062!extracellular structure organization and biogenesis!0.0105086541858001!1303$GO:0005201!extracellular matrix structural constituent!0.0130107147062286!1303$GO:0044420!extracellular matrix part!0.0130107147062286!1303$GO:0006817!phosphate transport!0.0130107147062286!1303$GO:0001501!skeletal development!0.0174310216256525!1303$GO:0015698!inorganic anion transport!0.0200164841634287!1303$GO:0006820!anion transport!0.0230904442313838!1303$GO:0005578!proteinaceous extracellular matrix!0.0280897994426783!1303
|id=C259
|id=C259
|ontology_enrichment_celltype=CL:0000055!8.27e-26!180;CL:0000057!4.02e-19!75;CL:0002620!1.19e-08!23;CL:0000680!9.17e-08!57;CL:0000056!9.17e-08!57;CL:0000355!9.17e-08!57;CL:0000499!1.71e-07!27;CL:0000183!3.90e-07!59;CL:0000187!3.98e-07!54;CL:0002334!4.54e-07!12
|ontology_enrichment_celltype=CL:0000057!2.34e-16!76;CL:0002620!2.95e-12!23;CL:0000499!4.62e-11!28;CL:0002334!2.59e-09!12;CL:0000723!1.36e-08!433;CL:0000048!2.62e-08!427;CL:0000034!5.43e-08!441;CL:0002320!9.15e-08!361;CL:0000134!4.02e-07!354
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:17!1.94e-08!5;DOID:450!1.94e-08!5;DOID:66!1.94e-08!5;DOID:423!1.94e-08!5;DOID:0080000!1.94e-08!5;DOID:11722!1.94e-08!5
|ontology_enrichment_uberon=UBERON:0003102!5.28e-12!95;UBERON:0000914!3.90e-11!83;UBERON:0002329!3.90e-11!83;UBERON:0003077!3.90e-11!83;UBERON:0003059!3.90e-11!83;UBERON:0007282!3.90e-11!83;UBERON:0009618!3.90e-11!83;UBERON:0007285!3.90e-11!83;UBERON:0000475!3.89e-10!365;UBERON:0000468!1.82e-09!659;UBERON:0000481!6.49e-09!347;UBERON:0002199!6.93e-09!45;UBERON:0002416!6.93e-09!45;UBERON:0005256!1.09e-08!143;UBERON:0004290!1.59e-08!70;UBERON:0002385!3.33e-08!63;UBERON:0001015!3.33e-08!63;UBERON:0000383!3.33e-08!63;UBERON:0001134!4.73e-08!61;UBERON:0002036!4.73e-08!61;UBERON:0003082!4.73e-08!61;UBERON:0000486!5.82e-08!82;UBERON:0002097!1.03e-07!40;UBERON:0002100!4.66e-07!216;UBERON:0004923!7.43e-07!57
|ontology_enrichment_uberon=UBERON:0002097!1.05e-10!41;UBERON:0003688!1.70e-10!6;UBERON:0002358!1.70e-10!6;UBERON:0003684!1.70e-10!6;UBERON:0001178!1.70e-10!6;UBERON:0002199!8.38e-10!46;UBERON:0002416!8.38e-10!46;UBERON:0003102!2.29e-08!99;UBERON:0004457!4.30e-08!12;UBERON:0000042!4.30e-08!12;UBERON:0002384!1.82e-07!371
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02e-08,0.000171268,0.764119,0.000117289,0.19343,0.0121001,0.0172473,0.327738,0.131872,0.0167625,0.064659,0.000796685,0.00157213,4.47301e-05,0.869799,0.568047,0.183384,0.998594,0.410237,0.115506,0.000265679,0.210876,0.789717,7.20873e-05,0.17505,0.0307997,0.000861144,0.0523711,0.0787487,0.407201,0.260981,0.379295,0.404896,1.11442e-10,0.00812791,5.39665e-06,4.64118e-06,0.0025886,0.014797,0.0021496,0.179226,0.0269334,0.00140968,0.0175634,0.664856,0.998315,0.014505,0.221221,0.110952,0.00874312,0.252686,0.000676265,0.152164,0.00380695,2.91656e-05,0.0730856,0.401259,0.00340593,0.000918536,0.449866,0.00504751,0.959467,0.0161155,0.00595781,0.573534,0.961944,0.796176,0.000317218,0.851925,0.249176,0.150466,0.0888576,0.0865219,0.000502194,0.135652,2.6169e-08,0.887572,0.389411,0.997489,0.275906,0.146677,0.788967,7.84212e-08,0.0058816,0.2341,0.00126968,0.0300838,0.0944606,0.616575,0.674407,0.925921,0.00264474,3.30199e-05,2.16242e-05,0.133244,0.54085,0.00199429,0.0169461,0.00143983,0.0164264,0.0766033,0.873468,0.354136,0.000215421,0.241381,0.782061,0.696736,0.00288421,0.00413501,0.903616,8.31136e-06,0.999914,0.877572,0.0636676,0.00241538,0.0584275,0.00513652,0.385441,1.03792e-05,0.00166716,0.444791,0.73026,0.107008,0.999894,0.947659,8.00542e-06,0.133365,0.172456,0.30013,0.0530812,0.99998,0.0194832,0.0516724,0.990614,0.000124154,0.0066195,0.00974072,0.0390073,0.0048939,9.82019e-07,0.459867,0.0089924,1.3212e-08,1,1,0.0193836,0.407156,0.309307,0.00736977,0.000957195,0.0116356,0.00195542,0.00707415,0.0467749,0.189194,0.051327,0.35133,0.27317,3.08455e-11,4.60635e-07,0.0982306,0.0012839,0.00284793,0.00533122,0.49378,0.107395,0.0428605,0.00154282,1.1218e-07,3.42834e-07,0.739052,0.978468,0.310361,0.000455284,0.78793,0.112188,0.903263,0.000140218,0.000151701,0.151513,2.0165e-05,2.59611e-05,0.757503,0.999916,0.027801,0.135649,0.226723,0.0909186,0.00594178,0.0234247,0.824787,0.779553,0.39161,0.033371,4.38146e-07,0.156637,0.000603345,0.0694153,0.171764,0.774508,0.0878821,0.150397,0.055566,9.58805e-07,0.0187277,0.0922994,0.00103136,0.000171309,7.96152e-05,0.0354664,0.743801,0.00069417,2.58258e-07,0.0726157,0.0970249,0.0245532,0.123215,0.0949359,0.0695296,0.763828,0.270135,0.00966978,0.305974,0.857129,0.000103071,0.213412,0.964574,0.0629397,0.65209,0.941267,0.999716,0.130129,0.946136,0.0944719,0.530158,0.699797,0.896264,0.999604,1.05997e-07,0.941358,9.29182e-11,0.684086,0.043519,8.53546e-07,0.0576636,0.432732,0.0145858,0.00736039,0.000948811,0.658902,5.11138e-06,0.957734,0.583947,0.493312,0.916205,0.0857685,0.114481,0.94891,0.661965,0.602959,1,1,0.0349281,0.472797,0.933873,0.0230472,0.000291752,0.90811,0.70916,0.379299,0.830044,0.36378,0.041357,0.225229,0.691796,0.00049798,0.266761,0.956302,0.39771,0.0864675,0.000419637,0.999996,0.0487041,0.994383,0.920423,0.0333265,0.999808,0.892359,0.282027,0.999985,0.108433,0.999997,0.858762,1,0.784301,0.993959,0.741638,0.977717,0.354062,0.405856,0.878673,0.724646,0.201433,0.20623,7.40048e-08,0.00521706,0.979157,0.820669,0.00263073,0.864177,0.00121974,0.0160964,8.18028e-08,0.00579935,0.744143,0.198726,0.256382,0.207945,0.999086,0.825248,0.0205978,0.464492,6.29757e-05,0.9486,0.000141618,0.342606,0.000416269,0.0874615,0.99996,0.65723,0.423426,0.0469376,0.0251421,0.0121537,0.997419,0.920713,0.900507,6.76106e-05,1.9846e-09,0.787032,0.202561,2.1773e-06,0.772397,0.119872,0.100153,5.71303e-11,0.0482129,0.400593,0.137523,0.668669,0.00110633,0.537747,0.922369,0.644933,0.00750349,0.74186,0.0997485,0.00377008,0.0283322,0.977298,0.000190447,0.152809,0.174858,1.28772e-07,0.392492,2.8779e-05,0.0949177,0.0831125,0.989187,0.992711,1.08765e-06,0.00211425,0.893597,0.0360161,2.50183e-08,0.662598,0.511943,0.000383233,4.52248e-05,0.783212,9.27617e-05,0.110035,2.25603e-06,0.0507046,0.757856,0.000680545,3.02817e-07,0.0547914,8.40079e-08,1.83671e-05,0.00971576,0.143529,1.5458e-06,0.515584,0.869421,0.0115687,0.000295397,0.511928,1.19119e-13,0.066684,1.78488e-07,6.53017e-11,1.96672e-06,1.49528e-06,0.548034,0.441789,0.000348472,0.143207,1.40564e-09,0.71884,2.66633e-06,1.33138e-07,0.294344,0.000314042,5.14616e-07,0.000251785,0.00135775,0.00189844,3.71165e-13,1.47839e-08,0.0186833,8.54463e-08,6.75777e-17,0.00774532,0.000739714,0.000425799,0.418633,0.00163115,5.71624e-06,6.46128e-08,0.0108033,0.0383074,0.066475,0.387325,5.35558e-07,0.109972,0.233635,0.657826,0.125865,0.000189712,0.322526,0.19633,0.219049,0.561086,0.00050788,0.0692087,0.0073627,0.0206108,4.48272e-08,0.334213,0.0197516,0.454672,0.578484,0.000210584,0.0152723,0.144536,0.323797,0.0647424,0.547321,0.0450072,0.00608495,4.86132e-09,0.00280651,0.176134,0.260317,1.06365e-06,0.000741278,2.89908e-05,9.21136e-08,0.00145894,3.2965e-05,0.0276065,0.000283766,5.3239e-08,1.58867e-11,0.0316127,9.74197e-08,1.41934e-06,7.92545e-06,0.0083533,1.61413e-07,0.0261511,0.000362146,2.44147e-05,2.18899e-06,0.000697944,0.0241551,4.25403e-06,0.0172,0.00140316,0.219097,0.0616845,0.0326398,0.00400804,0.0060517,0.00193905,0.922675,0.000506797,0.192155,1.10904e-05,0.0944398,0.00219358,0.0047045,0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}}
}}

Revision as of 14:12, 19 October 2012


Full id: C259_Preadipocyte_Adipocyte_Fibroblast_Chondrocyte_tenocyte_normal_Ewing



Phase1 CAGE Peaks

Hg19::chr13:102344930..102344943,+p@chr13:102344930..102344943
+
Hg19::chr15:68595092..68595106,-p@chr15:68595092..68595106
-
Hg19::chr15:68595149..68595169,-p@chr15:68595149..68595169
-
Hg19::chr15:68603386..68603397,-p@chr15:68603386..68603397
-
Hg19::chr15:68612587..68612601,-p@chr15:68612587..68612601
-
Hg19::chr15:68650846..68650865,-p@chr15:68650846..68650865
-
Hg19::chr6:75794403..75794415,-p5@AL359627
Hg19::chr6:75794532..75794555,-p3@AL359627
Hg19::chr6:75794584..75794598,-p8@AL359627
Hg19::chr6:75794631..75794646,-p4@AL359627
Hg19::chr6:75794856..75794875,-p1@AL359627
Hg19::chr6:75795263..75795278,-p4@COL12A1
Hg19::chr6:75796064..75796066,-p15@COL12A1
Hg19::chr6:75796102..75796109,-p8@COL12A1
Hg19::chr6:75796121..75796128,-p12@COL12A1
Hg19::chr6:75822973..75822991,-p@chr6:75822973..75822991
-
Hg19::chr6:75825549..75825569,-p@chr6:75825549..75825569
-
Hg19::chr6:75825624..75825638,-p@chr6:75825624..75825638
-
Hg19::chr6:75827153..75827189,-p@chr6:75827153..75827189
-
Hg19::chr6:75827226..75827242,-p@chr6:75827226..75827242
-
Hg19::chr6:75827251..75827265,-p@chr6:75827251..75827265
-
Hg19::chr6:75831042..75831053,-p@chr6:75831042..75831053
-
Hg19::chr6:75831090..75831097,-p@chr6:75831090..75831097
-
Hg19::chr6:75831122..75831147,-p@chr6:75831122..75831147
-
Hg19::chr6:75833794..75833805,-p1@AK022029
Hg19::chr6:75834940..75834995,-p@chr6:75834940..75834995
-
Hg19::chr6:75836108..75836130,-p@chr6:75836108..75836130
-
Hg19::chr6:75843119..75843139,-p@chr6:75843119..75843139
-
Hg19::chr6:75848596..75848625,-p@chr6:75848596..75848625
-
Hg19::chr6:75851774..75851789,-p@chr6:75851774..75851789
-
Hg19::chr6:75855077..75855098,-p@chr6:75855077..75855098
-
Hg19::chr6:75855104..75855124,-p@chr6:75855104..75855124
-
Hg19::chr6:75855152..75855173,-p@chr6:75855152..75855173
-
Hg19::chr6:75855870..75855893,-p6@COL12A1
Hg19::chr6:75862119..75862155,-p7@COL12A1
Hg19::chr6:75865417..75865433,-p@chr6:75865417..75865433
-
Hg19::chr6:75866149..75866182,+p@chr6:75866149..75866182
+
Hg19::chr6:75866153..75866165,-p@chr6:75866153..75866165
-
Hg19::chr6:75875248..75875260,-p@chr6:75875248..75875260
-
Hg19::chr6:75875403..75875417,-p@chr6:75875403..75875417
-
Hg19::chr6:75875426..75875445,-p@chr6:75875426..75875445
-
Hg19::chr6:75884784..75884798,-p@chr6:75884784..75884798
-
Hg19::chr6:75887466..75887531,+p@chr6:75887466..75887531
+
Hg19::chr6:75890763..75890818,-p@chr6:75890763..75890818
-
Hg19::chr6:75893016..75893037,-p@chr6:75893016..75893037
-
Hg19::chr6:75893192..75893204,-p@chr6:75893192..75893204
-
Hg19::chr6:75893613..75893629,+p@chr6:75893613..75893629
+
Hg19::chr6:75893699..75893714,-p@chr6:75893699..75893714
-
Hg19::chr6:75898243..75898255,-p9@COL12A1
Hg19::chr6:75899015..75899053,-p@chr6:75899015..75899053
-
Hg19::chr6:75904655..75904670,-p@chr6:75904655..75904670
-


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:0005595collagen type XII0.00100082420817143
GO:0030020extracellular matrix structural constituent conferring tensile strength0.00100082420817144
GO:0005593FACIT collagen0.00200164841634287
GO:0030934anchoring collagen0.00200164841634287
GO:0030199collagen fibril organization0.00200164841634287
GO:0030198extracellular matrix organization and biogenesis0.007672985595981
GO:0005581collagen0.00772064389160821
GO:0043062extracellular structure organization and biogenesis0.0105086541858001
GO:0005201extracellular matrix structural constituent0.0130107147062286
GO:0044420extracellular matrix part0.0130107147062286
GO:0006817phosphate transport0.0130107147062286
GO:0001501skeletal development0.0174310216256525
GO:0015698inorganic anion transport0.0200164841634287
GO:0006820anion transport0.0230904442313838
GO:0005578proteinaceous extracellular matrix0.0280897994426783



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>disease_data<br>

Cell Type
Ontology termp-valuen
fibroblast2.34e-1676
skin fibroblast2.95e-1223
stromal cell4.62e-1128
preadipocyte2.59e-0912
somatic stem cell1.36e-08433
multi fate stem cell2.62e-08427
stem cell5.43e-08441
connective tissue cell9.15e-08361
mesenchymal cell4.02e-07354
Uber Anatomy
Ontology termp-valuen
skin of body1.05e-1041
omentum1.70e-106
peritoneum1.70e-106
abdominal cavity1.70e-106
visceral peritoneum1.70e-106
integument8.38e-1046
integumental system8.38e-1046
surface structure2.29e-0899
cavity lining4.30e-0812
serous membrane4.30e-0812
connective tissue1.82e-07371
Disease
Ontology termp-valuen
musculoskeletal system disease1.94e-085
myotonic disease1.94e-085
muscle tissue disease1.94e-085
myopathy1.94e-085
muscular disease1.94e-085
myotonic dystrophy1.94e-085


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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