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Coexpression cluster:C259: Difference between revisions

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{{Coexpression_clusters
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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 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3,0.0383074,0.066475,0.387325,5.35558e-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-05,0.0944398,0.00219358,0.0047045,0.00180728,1.00448e-05,0.000439939,0.00208433,1.08076e-05,0.330828,0.0108574,0.180904,0.000643645,0.0138113,0.608051,0.609235,0.0638467,0.00299483,0.000819799,0.608967,0.48201,0.0379449,0.0224533,0.0104721,0.171966,9.29605e-05,0.422345,0.101674,0.105083,3.73745e-06,0.104056,0.560052,4.4797e-07,0.00266744,0.0888295,0.313919,0.179366,0.69213,0.0234613,0.13404,0.00024838,1.43918e-05,1.31633e-06,0.000105385,2.37636e-06,6.57815e-07,0.0175132,0.0698133,0.000586097,6.94242e-15,0.155244,1.84572e-05,1.67905e-08,2.28211e-06,0.00752566,0.0357874,1.49389e-05,0.000229919,0.181102,0.000925339,0.000303574,0.230917,0.15995,0.0626787,0.0319965,6.46425e-05,0.00473554,0.000373142,0.00206287,0.0134709,0.122095,0.00126888,7.06664e-09,0.8118,2.04755e-07,2.42747e-13,1.77762e-05,0.510905,0.0691245,9.92996e-08,0.00573768,0.0306069,0.623449,0.356804,3.79172e-06,1.03686e-09,6.09772e-09,9.47215e-06,0.000225961,0.00036915,0.00020547,0.202563,4.52128e-13|tfbs_overrepresentation_for_novel_motifs=0.0498264,0.00431179,0.0463794,0.936202,2.69255,1.33367,0.0577192,0.10658,0.00445934,0.000812944,0.115229,1.92317,0.00164781,0.0538303,1.09403,0.230197,0.160738,1.37557,0.0657141,0.890665,1.74919,0.00482005,0.132971,0.18453,0.0701155,0.282393,0.335122,0.309568,0.00556544,0.00972811,0.0229604,0.182397,0.00852379,0.29989,0.00318612,0.000230319,0.00302679,0.140372,0.532811,0.0800087,0.427529,0.0198612,0.0339689,1.4224,0.00136666,0.327431,0.0580955,0.0252168,0.0466274,0.0307669,0.299055,0.0622518,0.0850714,0.231144,0.3402,0.201607,0.366102,0.385211,0.0551006,0.0441561,0.207824,0.0589178,0.0481821,0.145212,0.232623,0.126911,1.05375,0.727856,1.59153,0.58255,0.0796588,1.83305,0.000124334,1.6116,0.000164418,0.00102972,0.0293575,0.136087,0.517685,0.0665908,0.230583,0.872544,2.37848,0.0518815,0.300427,4.18982e-07,0.0478677,0.0500263,0.100673,1.91699,0.485902,0.280966,0.562326,1.83657,0.0891866,0.508421,0.213178,0.219696,0.102812,0.12193,0.209354,1.05563,0.618126,0.162843,0.384166,0.0265728,0.153835,0.0526935,0.0150007,0.00424303,0.288058,0.214289,0.123301,0.0297234,4.00534,0.134123,4.58886e-05,0.242979,0.125708,0.918784,2.40971,0.327579,0.321239,0.895026,0.539181,0.136492,0.0555538,0.569761,0.365014,0.0121187,0.281458,0.46874,0.376217,0.240788,1.2425,0.019372,0.0950578,0.896382,0.461248,1.25501,0.868564,1.92878,0.205577,0.621264,0.773946,0.0419814,0.364875,1.10041,0.68118,0.0324854,0.00047371,0.000202453,0.28173,0.00377142,0.809038,0.609476,1.58288,0.0250763,0.896494,0.0110894,0.429612,0.740387,0.17377,0.0114913,0.407726,2.37361,0.14284,0.208912,4.48458e-09|tfbs_overrepresentation_jaspar=MA0003.1;2.1823e-10,MA0004.1;0.840732,MA0006.1;0.0290142,MA0007.1;0.105058,MA0009.1;0.252434,MA0014.1;3.1363e-08,MA0017.1;0.124978,MA0019.1;0.262257,MA0024.1;0.183969,MA0025.1;0.350278,MA0027.1;1.73105,MA0028.1;0.00648135,MA0029.1;0.195946,MA0030.1;0.55303,MA0031.1;0.459469,MA0038.1;0.0586854,MA0040.1;1.09698,MA0041.1;0.315593,MA0042.1;0.793334,MA0043.1;0.252653,MA0046.1;0.24494,MA0048.1;0.000159464,MA0050.1;0.109642,MA0051.1;0.208758,MA0052.1;0.584895,MA0055.1;1.08018e-05,MA0056.1;0,MA0057.1;0.00863949,MA0058.1;0.795613,MA0059.1;0.790284,MA0060.1;0.00449395,MA0061.1;0.225128,MA0063.1;0,MA0066.1;0.0588357,MA0067.1;0.49981,MA0068.1;0.000847657,MA0069.1;0.242306,MA0070.1;0.661924,MA0071.1;1.52405,MA0072.1;0.231695,MA0073.1;4.82164e-16,MA0074.1;0.0569489,MA0076.1;0.0138475,MA0077.1;1.20132,MA0078.1;1.09854,MA0081.1;0.306407,MA0083.1;0.715135,MA0084.1;0.664025,MA0087.1;0.651017,MA0088.1;5.48782e-05,MA0089.1;0,MA0090.1;0.373396,MA0091.1;0.121304,MA0092.1;0.232478,MA0093.1;0.555641,MA0095.1;0,MA0098.1;0,MA0100.1;0.227752,MA0101.1;0.200267,MA0103.1;0.0259301,MA0105.1;0.000432825,MA0106.1;0.0741862,MA0107.1;0.188877,MA0108.2;0.45517,MA0109.1;0,MA0111.1;0.209449,MA0113.1;0.0808928,MA0114.1;0.475868,MA0115.1;0.436009,MA0116.1;0.041195,MA0117.1;0.27892,MA0119.1;0.00956314,MA0122.1;0.806534,MA0124.1;1.83257,MA0125.1;0.336564,MA0130.1;0,MA0131.1;0.10574,MA0132.1;0,MA0133.1;0,MA0135.1;1.37811,MA0136.1;0.220509,MA0139.1;0.00176573,MA0140.1;0.389168,MA0141.1;0.783113,MA0142.1;0.41554,MA0143.1;0.982274,MA0144.1;0.00117372,MA0145.1;0.00493127,MA0146.1;1.39205e-06,MA0147.1;0.342831,MA0148.1;0.592302,MA0149.1;0.0422402,MA0062.2;0.000249738,MA0035.2;1.50746,MA0039.2;3.80668e-13,MA0138.2;0.322872,MA0002.2;0.0875896,MA0137.2;0.00705641,MA0104.2;0.187993,MA0047.2;1.34586,MA0112.2;0.00375503,MA0065.2;0.00194477,MA0150.1;0.0704527,MA0151.1;0,MA0152.1;2.05334,MA0153.1;1.55891,MA0154.1;0.013285,MA0155.1;0.0028753,MA0156.1;0.110132,MA0157.1;0.378956,MA0158.1;0,MA0159.1;0.0435583,MA0160.1;0.35201,MA0161.1;0,MA0162.1;3.26153e-10,MA0163.1;4.66278e-10,MA0164.1;0.607782,MA0080.2;0.555957,MA0018.2;0.259418,MA0099.2;0.0472524,MA0079.2;0,MA0102.2;0.697711,MA0258.1;0.000958209,MA0259.1;0.220187,MA0442.1;0}}
|full_id=C259_Preadipocyte_Adipocyte_Fibroblast_Chondrocyte_tenocyte_normal_Ewing
|id=C259
}}

Latest revision as of 11:08, 17 September 2013


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)
MA0003.12.1823e-10
MA0004.10.840732
MA0006.10.0290142
MA0007.10.105058
MA0009.10.252434
MA0014.13.1363e-08
MA0017.10.124978
MA0019.10.262257
MA0024.10.183969
MA0025.10.350278
MA0027.11.73105
MA0028.10.00648135
MA0029.10.195946
MA0030.10.55303
MA0031.10.459469
MA0038.10.0586854
MA0040.11.09698
MA0041.10.315593
MA0042.10.793334
MA0043.10.252653
MA0046.10.24494
MA0048.10.000159464
MA0050.10.109642
MA0051.10.208758
MA0052.10.584895
MA0055.11.08018e-05
MA0056.10
MA0057.10.00863949
MA0058.10.795613
MA0059.10.790284
MA0060.10.00449395
MA0061.10.225128
MA0063.10
MA0066.10.0588357
MA0067.10.49981
MA0068.10.000847657
MA0069.10.242306
MA0070.10.661924
MA0071.11.52405
MA0072.10.231695
MA0073.14.82164e-16
MA0074.10.0569489
MA0076.10.0138475
MA0077.11.20132
MA0078.11.09854
MA0081.10.306407
MA0083.10.715135
MA0084.10.664025
MA0087.10.651017
MA0088.15.48782e-05
MA0089.10
MA0090.10.373396
MA0091.10.121304
MA0092.10.232478
MA0093.10.555641
MA0095.10
MA0098.10
MA0100.10.227752
MA0101.10.200267
MA0103.10.0259301
MA0105.10.000432825
MA0106.10.0741862
MA0107.10.188877
MA0108.20.45517
MA0109.10
MA0111.10.209449
MA0113.10.0808928
MA0114.10.475868
MA0115.10.436009
MA0116.10.041195
MA0117.10.27892
MA0119.10.00956314
MA0122.10.806534
MA0124.11.83257
MA0125.10.336564
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.11.37811
MA0136.10.220509
MA0139.10.00176573
MA0140.10.389168
MA0141.10.783113
MA0142.10.41554
MA0143.10.982274
MA0144.10.00117372
MA0145.10.00493127
MA0146.11.39205e-06
MA0147.10.342831
MA0148.10.592302
MA0149.10.0422402
MA0062.20.000249738
MA0035.21.50746
MA0039.23.80668e-13
MA0138.20.322872
MA0002.20.0875896
MA0137.20.00705641
MA0104.20.187993
MA0047.21.34586
MA0112.20.00375503
MA0065.20.00194477
MA0150.10.0704527
MA0151.10
MA0152.12.05334
MA0153.11.55891
MA0154.10.013285
MA0155.10.0028753
MA0156.10.110132
MA0157.10.378956
MA0158.10
MA0159.10.0435583
MA0160.10.35201
MA0161.10
MA0162.13.26153e-10
MA0163.14.66278e-10
MA0164.10.607782
MA0080.20.555957
MA0018.20.259418
MA0099.20.0472524
MA0079.20
MA0102.20.697711
MA0258.10.000958209
MA0259.10.220187
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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