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Coexpression cluster:C228: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.170607,0.003076,0.294927,0.425275,0.761616,1.83527,0.0359272,0.165731,0.540017,0.0279423,0.181565,1.10319,0.0188501,0.0330751,2.42989,0.623234,0.119289,0.945366,0.0539391,0.125359,0.706587,0.119838,0.0826628,0.996303,0.230909,0.05514,0.161338,0.0813416,0.0138209,0.0715735,0.058039,0.427666,0.0763427,0.0198489,0.00110025,0.00732902,0.0693209,0.0198935,0.197543,0.12402,1.07381,0.484274,0.3124,0.202395,0.00866791,0.0325416,0.143887,0.0636843,0.339889,0.110749,0.0599013,0.153799,0.0868378,0.181106,0.28077,0.319102,2.11586,0.269003,0.121184,0.267523,0.160351,0.145852,0.0909001,0.106053,0.0416222,0.0906885,0.34542,0.652367,0.820863,0.511132,0.00866623,0.41949,0.13103,0.27936,0.00614077,0.0291699,0.0816133,0.0983574,0.409614,0.390276,0.283204,0.105556,0.367592,0.172085,0.244004,2.36761e-06,0.00549601,0.174968,0.243676,0.742187,0.418256,0.226174,0.4503,1.58596,0.0133656,0.184867,0.167625,0.170887,0.0709247,1.72617,0.912823,0.44264,0.5016,1.25776,0.0858223,0.873821,0.113383,0.130938,0.00716698,0.0104338,0.176209,0.166081,0.282595,0.37674,0.380274,1.05053,0.000118673,0.154594,0.0896888,0.272381,0.273551,0.517587,0.680308,0.170883,0.469328,0.325276,0.322633,0.457107,0.303903,1.73077,0.64297,0.538896,0.314391,0.381084,0.428622,0.0962988,0.513391,0.659481,0.394746,1.17283,0.79037,0.365644,1.33257,0.504498,0.0865557,0.774647,0.273413,1.0194,0.134653,0.0126941,0.0181463,3.09866e-07,0.226872,0.00102919,0.337645,0.537178,0.226742,0.0374225,0.63435,0.0279811,0.364708,0.214937,0.811807,0.0869393,1.07191,0.160183,0.0677044,0.599435,1.09562e-08
|tfbs_overrepresentation_for_novel_motifs=0.170607,0.003076,0.294927,0.425275,0.761616,1.83527,0.0359272,0.165731,0.540017,0.0279423,0.181565,1.10319,0.0188501,0.0330751,2.42989,0.623234,0.119289,0.945366,0.0539391,0.125359,0.706587,0.119838,0.0826628,0.996303,0.230909,0.05514,0.161338,0.0813416,0.0138209,0.0715735,0.058039,0.427666,0.0763427,0.0198489,0.00110025,0.00732902,0.0693209,0.0198935,0.197543,0.12402,1.07381,0.484274,0.3124,0.202395,0.00866791,0.0325416,0.143887,0.0636843,0.339889,0.110749,0.0599013,0.153799,0.0868378,0.181106,0.28077,0.319102,2.11586,0.269003,0.121184,0.267523,0.160351,0.145852,0.0909001,0.106053,0.0416222,0.0906885,0.34542,0.652367,0.820863,0.511132,0.00866623,0.41949,0.13103,0.27936,0.00614077,0.0291699,0.0816133,0.0983574,0.409614,0.390276,0.283204,0.105556,0.367592,0.172085,0.244004,2.36761e-06,0.00549601,0.174968,0.243676,0.742187,0.418256,0.226174,0.4503,1.58596,0.0133656,0.184867,0.167625,0.170887,0.0709247,1.72617,0.912823,0.44264,0.5016,1.25776,0.0858223,0.873821,0.113383,0.130938,0.00716698,0.0104338,0.176209,0.166081,0.282595,0.37674,0.380274,1.05053,0.000118673,0.154594,0.0896888,0.272381,0.273551,0.517587,0.680308,0.170883,0.469328,0.325276,0.322633,0.457107,0.303903,1.73077,0.64297,0.538896,0.314391,0.381084,0.428622,0.0962988,0.513391,0.659481,0.394746,1.17283,0.79037,0.365644,1.33257,0.504498,0.0865557,0.774647,0.273413,1.0194,0.134653,0.0126941,0.0181463,3.09866e-07,0.226872,0.00102919,0.337645,0.537178,0.226742,0.0374225,0.63435,0.0279811,0.364708,0.214937,0.811807,0.0869393,1.07191,0.160183,0.0677044,0.599435,1.09562e-08
|tfbs_overrepresentation_jaspar=MA0003.1;2.01395e-09,MA0004.1;0.187985,MA0006.1;0.01288,MA0007.1;0.0622008,MA0009.1;0.580521,MA0014.1;1.26609e-05,MA0017.1;0.95842,MA0019.1;0.185705,MA0024.1;0.139391,MA0025.1;0.290149,MA0027.1;1.6471,MA0028.1;0.0161707,MA0029.1;5.22435,MA0030.1;0.4418,MA0031.1;1.18963,MA0038.1;1.3666,MA0040.1;0.153121,MA0041.1;0.0836142,MA0042.1;0.570278,MA0043.1;0.200452,MA0046.1;4.91912,MA0048.1;0.00221814,MA0050.1;0.0654993,MA0051.1;0.141769,MA0052.1;0.470992,MA0055.1;0.00898435,MA0056.1;0,MA0057.1;0.196801,MA0058.1;0.345438,MA0059.1;0.0869946,MA0060.1;0.0184268,MA0061.1;0.0100955,MA0063.1;0,MA0066.1;0.036752,MA0067.1;0.431554,MA0068.1;0.0035579,MA0069.1;0.191124,MA0070.1;0.184309,MA0071.1;0.512993,MA0072.1;0.535604,MA0073.1;6.8693e-05,MA0074.1;1.34346,MA0076.1;0.00650833,MA0077.1;0.176993,MA0078.1;0.0664432,MA0081.1;0.342679,MA0083.1;0.204972,MA0084.1;0.59013,MA0087.1;0.180133,MA0088.1;0.00689518,MA0089.1;0,MA0090.1;0.943138,MA0091.1;0.924293,MA0092.1;0.506239,MA0093.1;0.210231,MA0095.1;0,MA0098.1;0,MA0100.1;1.00592,MA0101.1;0.112324,MA0103.1;0.319263,MA0105.1;0.00101018,MA0106.1;0.182034,MA0107.1;0.0444677,MA0108.2;0.353256,MA0109.1;0,MA0111.1;0.26631,MA0113.1;0.43762,MA0114.1;1.96954,MA0115.1;0.96956,MA0116.1;0.00433934,MA0117.1;0.224307,MA0119.1;0.0742602,MA0122.1;0.241483,MA0124.1;0.338933,MA0125.1;0.277393,MA0130.1;0,MA0131.1;0.0732939,MA0132.1;0,MA0133.1;0,MA0135.1;0.219593,MA0136.1;0.0385053,MA0139.1;0.0200299,MA0140.1;3.16255,MA0141.1;0.338045,MA0142.1;0.317961,MA0143.1;0.437943,MA0144.1;0.0112872,MA0145.1;0.0113224,MA0146.1;0.000398195,MA0147.1;0.0493222,MA0148.1;2.83921,MA0149.1;0.0247918,MA0062.2;0.00885881,MA0035.2;4.39685,MA0039.2;0.000212024,MA0138.2;0.066895,MA0002.2;0.222403,MA0137.2;0.412022,MA0104.2;0.0181429,MA0047.2;3.16016,MA0112.2;0.0317112,MA0065.2;1.79567,MA0150.1;0.40763,MA0151.1;0,MA0152.1;1.20696,MA0153.1;3.78682,MA0154.1;0.0154681,MA0155.1;0.00284875,MA0156.1;0.00298728,MA0157.1;1.00572,MA0158.1;0,MA0159.1;0.106727,MA0160.1;0.241572,MA0161.1;0,MA0162.1;6.68437e-06,MA0163.1;0.00273499,MA0164.1;2.24841,MA0080.2;0.00210053,MA0018.2;0.0487634,MA0099.2;0.117814,MA0079.2;4.66309e-08,MA0102.2;0.622942,MA0258.1;0.124014,MA0259.1;0.00545353,MA0442.1;0
}}
}}

Revision as of 18:47, 22 January 2013


Full id: C228_colon_Intestinal_Prostate_hepatoblastoma_hepatocellular_testis_adult



Phase1 CAGE Peaks

Hg19::chr10:104629450..104629461,+p3@AS3MT
Hg19::chr10:104629528..104629542,+p6@AS3MT
Hg19::chr10:24726425..24726450,+p@chr10:24726425..24726450
+
Hg19::chr10:24726466..24726472,+p@chr10:24726466..24726472
+
Hg19::chr10:71850931..71850940,+p@chr10:71850931..71850940
+
Hg19::chr11:118082912..118082938,-p@chr11:118082912..118082938
-
Hg19::chr11:13994430..13994436,+p@chr11:13994430..13994436
+
Hg19::chr11:9878820..9878833,-p@chr11:9878820..9878833
-
Hg19::chr12:102437910..102437918,-p@chr12:102437910..102437918
-
Hg19::chr12:69726073..69726089,-p@chr12:69726073..69726089
-
Hg19::chr12:93399748..93399757,+p@chr12:93399748..93399757
+
Hg19::chr12:93399816..93399825,+p@chr12:93399816..93399825
+
Hg19::chr12:93399852..93399859,+p@chr12:93399852..93399859
+
Hg19::chr12:93399866..93399909,+p@chr12:93399866..93399909
+
Hg19::chr12:93399913..93399929,+p@chr12:93399913..93399929
+
Hg19::chr13:32790605..32790619,+p@chr13:32790605..32790619
+
Hg19::chr13:32790683..32790693,+p@chr13:32790683..32790693
+
Hg19::chr13:42179573..42179585,-p@chr13:42179573..42179585
-
Hg19::chr13:46093155..46093164,+p@chr13:46093155..46093164
+
Hg19::chr13:46093198..46093203,+p@chr13:46093198..46093203
+
Hg19::chr14:22850283..22850310,-p@chr14:22850283..22850310
-
Hg19::chr15:60749901..60749904,-p@chr15:60749901..60749904
-
Hg19::chr15:71003168..71003184,-p@chr15:71003168..71003184
-
Hg19::chr15:89540938..89540967,-p@chr15:89540938..89540967
-
Hg19::chr16:19661585..19661596,+p@chr16:19661585..19661596
+
Hg19::chr16:19661615..19661621,+p@chr16:19661615..19661621
+
Hg19::chr16:78274724..78274726,+p@chr16:78274724..78274726
+
Hg19::chr18:24722967..24722980,-p4@CHST9
Hg19::chr18:24722995..24723030,-p3@CHST9
Hg19::chr18:6929797..6929812,-p1@uc002kng.1
Hg19::chr18:7034928..7034943,-p@chr18:7034928..7034943
-
Hg19::chr18:7133714..7133725,-p@chr18:7133714..7133725
-
Hg19::chr19:56653064..56653103,+p1@AK124209
Hg19::chr1:111023361..111023366,+p1@CYMP
Hg19::chr1:19522637..19522659,-p@chr1:19522637..19522659
-
Hg19::chr1:19522690..19522704,-p@chr1:19522690..19522704
-
Hg19::chr21:42694732..42694744,+p3@FAM3B
Hg19::chr21:42694788..42694804,+p@chr21:42694788..42694804
+
Hg19::chr2:127873614..127873626,+p@chr2:127873614..127873626
+
Hg19::chr2:137966134..137966139,+p@chr2:137966134..137966139
+
Hg19::chr2:176484786..176484791,+p@chr2:176484786..176484791
+
Hg19::chr2:28340333..28340358,+p@chr2:28340333..28340358
+
Hg19::chr2:62189730..62189756,+p@chr2:62189730..62189756
+
Hg19::chr3:139373728..139373733,+p@chr3:139373728..139373733
+
Hg19::chr4:107237136..107237147,+p10@AIMP1
Hg19::chr5:142213315..142213336,+p@chr5:142213315..142213336
+
Hg19::chr6:26500524..26500540,+p@chr6:26500524..26500540
+
Hg19::chr6:41492615..41492636,-p@chr6:41492615..41492636
-
Hg19::chr6:80382928..80382946,+p@chr6:80382928..80382946
+
Hg19::chr6:8446968..8446983,+p@chr6:8446968..8446983
+
Hg19::chr7:117329764..117329777,+p1@ENST00000429014
Hg19::chr7:97958802..97958804,-p@chr7:97958802..97958804
-
Hg19::chr8:55331615..55331618,+p@chr8:55331615..55331618
+
Hg19::chr8:99425711..99425716,-p1@ENST00000518956
Hg19::chr9:129830560..129830568,+p@chr9:129830560..129830568
+
Hg19::chr9:138591341..138591346,-p3@SOHLH1
Hg19::chr9:35801527..35801540,+p@chr9:35801527..35801540
+
Hg19::chr9:71347655..71347671,+p@chr9:71347655..71347671
+
Hg19::chrX:21849506..21849512,-p@chrX:21849506..21849512
-
Hg19::chrX:24690735..24690744,-p10@PCYT1B
Hg19::chrX:32583949..32583951,-p@chrX:32583949..32583951
-
Hg19::chrX:75367265..75367270,-p@chrX:75367265..75367270
-


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:0004105choline-phosphate cytidylyltransferase activity0.020116143791594
GO:0001537N-acetylgalactosamine 4-O-sulfotransferase activity0.020116143791594
GO:0006656phosphatidylcholine biosynthetic process0.020116143791594
GO:0046470phosphatidylcholine metabolic process0.020116143791594
GO:0043231intracellular membrane-bound organelle0.020116143791594
GO:0043227membrane-bound organelle0.020116143791594
GO:0030073insulin secretion0.0271777219978296
GO:0030072peptide hormone secretion0.0271777219978296
GO:0002790peptide secretion0.0271777219978296
GO:0030166proteoglycan biosynthetic process0.0271777219978296
GO:0043229intracellular organelle0.0271777219978296
GO:0043226organelle0.0271777219978296
GO:0005794Golgi apparatus0.0310458162510283
GO:0006029proteoglycan metabolic process0.0310458162510283
GO:0046879hormone secretion0.0339619745399327
GO:0015833peptide transport0.0353773819092401
GO:0042446hormone biosynthetic process0.0353773819092401
GO:0005783endoplasmic reticulum0.0353773819092401
GO:0046474glycerophospholipid biosynthetic process0.0353773819092401
GO:0030203glycosaminoglycan metabolic process0.0353773819092401
GO:0006022aminoglycan metabolic process0.0353773819092401
GO:0008146sulfotransferase activity0.0353773819092401
GO:0044424intracellular part0.0357889772004106
GO:0016782transferase activity, transferring sulfur-containing groups0.0386429063395159
GO:0003001generation of a signal involved in cell-cell signaling0.0418642014843719
GO:0006790sulfur metabolic process0.0486792011353691
GO:0042445hormone metabolic process0.0486792011353691
GO:0008654phospholipid biosynthetic process0.0490627688252635



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>


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)
MA0003.12.01395e-09
MA0004.10.187985
MA0006.10.01288
MA0007.10.0622008
MA0009.10.580521
MA0014.11.26609e-05
MA0017.10.95842
MA0019.10.185705
MA0024.10.139391
MA0025.10.290149
MA0027.11.6471
MA0028.10.0161707
MA0029.15.22435
MA0030.10.4418
MA0031.11.18963
MA0038.11.3666
MA0040.10.153121
MA0041.10.0836142
MA0042.10.570278
MA0043.10.200452
MA0046.14.91912
MA0048.10.00221814
MA0050.10.0654993
MA0051.10.141769
MA0052.10.470992
MA0055.10.00898435
MA0056.10
MA0057.10.196801
MA0058.10.345438
MA0059.10.0869946
MA0060.10.0184268
MA0061.10.0100955
MA0063.10
MA0066.10.036752
MA0067.10.431554
MA0068.10.0035579
MA0069.10.191124
MA0070.10.184309
MA0071.10.512993
MA0072.10.535604
MA0073.16.8693e-05
MA0074.11.34346
MA0076.10.00650833
MA0077.10.176993
MA0078.10.0664432
MA0081.10.342679
MA0083.10.204972
MA0084.10.59013
MA0087.10.180133
MA0088.10.00689518
MA0089.10
MA0090.10.943138
MA0091.10.924293
MA0092.10.506239
MA0093.10.210231
MA0095.10
MA0098.10
MA0100.11.00592
MA0101.10.112324
MA0103.10.319263
MA0105.10.00101018
MA0106.10.182034
MA0107.10.0444677
MA0108.20.353256
MA0109.10
MA0111.10.26631
MA0113.10.43762
MA0114.11.96954
MA0115.10.96956
MA0116.10.00433934
MA0117.10.224307
MA0119.10.0742602
MA0122.10.241483
MA0124.10.338933
MA0125.10.277393
MA0130.10
MA0131.10.0732939
MA0132.10
MA0133.10
MA0135.10.219593
MA0136.10.0385053
MA0139.10.0200299
MA0140.13.16255
MA0141.10.338045
MA0142.10.317961
MA0143.10.437943
MA0144.10.0112872
MA0145.10.0113224
MA0146.10.000398195
MA0147.10.0493222
MA0148.12.83921
MA0149.10.0247918
MA0062.20.00885881
MA0035.24.39685
MA0039.20.000212024
MA0138.20.066895
MA0002.20.222403
MA0137.20.412022
MA0104.20.0181429
MA0047.23.16016
MA0112.20.0317112
MA0065.21.79567
MA0150.10.40763
MA0151.10
MA0152.11.20696
MA0153.13.78682
MA0154.10.0154681
MA0155.10.00284875
MA0156.10.00298728
MA0157.11.00572
MA0158.10
MA0159.10.106727
MA0160.10.241572
MA0161.10
MA0162.16.68437e-06
MA0163.10.00273499
MA0164.12.24841
MA0080.20.00210053
MA0018.20.0487634
MA0099.20.117814
MA0079.24.66309e-08
MA0102.20.622942
MA0258.10.124014
MA0259.10.00545353
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BHLHE40#855375.066172497239390.0004575513181554810.00421729786575239
EP300#2033202.185142492330060.000407507046013120.00388565948859347
FOXA1#3169193.395918955456831.31164976046539e-065.20271133054482e-05
FOXA2#3170187.150779799160882.92438537022645e-113.40870405894063e-09
HDAC2#3066143.029333601818830.0001535939249195960.00195791479612812
HNF4A#3172134.850318947070942.06524670596649e-067.53641861371189e-05
HNF4G#3174104.637648794588195.28001062848442e-050.000896357330995261
MAFF#2376454.541561007253640.00492837480357720.0230328248136573
TCF7L2#6934183.126825453814078.66135227406049e-060.00023501765917137



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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