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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.00730054797818,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0249805434194815,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0300822291072195,0,0,0,0,0,0,0,0,0,0,0|full_id=C346_gall_ductus_seminal_temporal_duodenum_Hepatocyte_liver|gostat_on_coexpression_clusters=GO:0030277!maintenance of gastrointestinal epithelium!0.0207089471839206!4588$GO:0001517!N-acetylglucosamine 6-O-sulfotransferase activity!0.0207089471839206!10164$GO:0006928!cell motility!0.0207089471839206!10164;476$GO:0051674!localization of cell!0.0207089471839206!10164;476$GO:0031532!actin cytoskeleton reorganization!0.0207089471839206!9578$GO:0051923!sulfation!0.0207089471839206!10164$GO:0006477!protein amino acid sulfation!0.0207089471839206!10164$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0207089471839206!476$GO:0000287!magnesium ion binding!0.0207089471839206!476;9578$GO:0030641!cellular hydrogen ion homeostasis!0.0258440314808478!476$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0269172999760724!476$GO:0055067!monovalent inorganic cation homeostasis!0.0269172999760724!476$GO:0005391!sodium:potassium-exchanging ATPase activity!0.0281571499812529!476$GO:0022600!digestive system process!0.0282556773832283!4588$GO:0030317!sperm 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1,0.752901,0.649361,0.610856,0.756592,0.91664,0.0946158,0.616475,0.225059,0.8659,0.841997,0.850361,0.544718,0.653605,0.314113,0.931789,0.873062,0.544621,0.925106,0.95533,0.914555,0.951645|tfbs_overrepresentation_for_novel_motifs=0.0423165,0.317335,0.358286,0.0978295,1.20717,0.320799,0.13697,0.109043,0.397494,0.120027,0.082933,0.16234,0.145892,0.8119,0.518813,0.585005,0.283109,0.193671,1.00792,0.227958,0.156113,0.696425,0.0933127,0.273486,0.0554737,0.176305,0.218248,0.0922862,0.287673,0.689974,0.543916,0.310643,0.299308,0.065937,0.0203044,0.379547,0.0196487,0.322308,0.602389,0.343301,0.0886746,0.236364,0.208384,0.2773,0.186318,0.187401,0.426563,0.078127,0.0568324,0.287898,0.185267,0.871226,0.467335,0.370484,0.497309,0.412789,0.29535,0.114516,0.937932,0.365802,0.342179,0.138926,0.899466,0.262912,0.455994,0.238513,0.574343,0.913986,0.818079,0.761456,0.481218,0.242354,0.0464599,1.24004,0.426911,0.812382,1.6133,0.250834,0.300348,1.16619,0.754548,0.725474,0.149063,0.23628,0.451923,0.0200528,0.346514,0.0851193,0.20212,1.00897,0.65804,0.429389,0.323471,0.81031,0.0284506,1.61366,0.302557,0.356655,0.592226,1.32488,0.186412,0.319139,1.6593,0.285815,0.652132,0.0809099,0.27418,0.403765,0.0553809,0.104272,0.67607,0.350081,0.150691,0.612889,0.614737,0.417004,0.172834,0.541317,0.236884,0.0125651,0.488501,0.581168,0.0957026,0.155712,0.715288,0.251373,0.415941,0.327313,0.525232,0.0675538,0.429962,1.39974,0.537753,0.467143,0.669744,2.51568,0.530997,0.0925536,0.631317,1.45283,1.05945,0.597865,0.418402,1.66496,0.654968,0.110137,0.220337,1.29622,0.232508,0.308357,1.01248,0.059744,0.430278,0.587749,0.429264,0.789951,0.559715,0.484298,1.67118,0.391014,0.596781,0.414981,0.299757,0.397308,0.242939,0.454322,0.280756,0.423097,0.757819|tfbs_overrepresentation_jaspar=MA0003.1;0.976439,MA0004.1;0.085298,MA0006.1;1.19779,MA0007.1;0.0768943,MA0009.1;0.395891,MA0014.1;0.0274348,MA0017.1;1.40477,MA0019.1;0.165418,MA0024.1;0.312615,MA0025.1;0.508683,MA0027.1;1.93196,MA0028.1;0.032054,MA0029.1;0.327543,MA0030.1;0.318663,MA0031.1;0.270046,MA0038.1;0.138548,MA0040.1;0.332103,MA0041.1;0.0940493,MA0042.1;0.272024,MA0043.1;0.39615,MA0046.1;0.386991,MA0048.1;0.326644,MA0050.1;0.273123,MA0051.1;0.422881,MA0052.1;0.335128,MA0055.1;0.034896,MA0056.1;0,MA0057.1;0.046597,MA0058.1;0.177816,MA0059.1;0.397441,MA0060.1;0.00694078,MA0061.1;0.314844,MA0063.1;0,MA0066.1;0.138793,MA0067.1;0.673046,MA0068.1;0.355309,MA0069.1;0.998321,MA0070.1;0.374777,MA0071.1;2.43217,MA0072.1;0.371146,MA0073.1;4.28678e-05,MA0074.1;0.421793,MA0076.1;0.194815,MA0077.1;0.364942,MA0078.1;0.197204,MA0081.1;0.397764,MA0083.1;1.83165,MA0084.1;0.847335,MA0087.1;0.369175,MA0088.1;0.124262,MA0089.1;0,MA0090.1;1.70642,MA0091.1;0.0865076,MA0092.1;0.245507,MA0093.1;0.118655,MA0095.1;0,MA0098.1;0,MA0100.1;0.449302,MA0101.1;0.290288,MA0103.1;0.789368,MA0105.1;0.557127,MA0106.1;0.163029,MA0107.1;0.340081,MA0108.2;0.267801,MA0109.1;0,MA0111.1;0.0631734,MA0113.1;0.991329,MA0114.1;2.45242,MA0115.1;0.603788,MA0116.1;2.5408,MA0117.1;0.427006,MA0119.1;0.654601,MA0122.1;0.44876,MA0124.1;0.566745,MA0125.1;0.493194,MA0130.1;0,MA0131.1;0.2093,MA0132.1;0,MA0133.1;0,MA0135.1;0.420972,MA0136.1;0.142619,MA0139.1;0.676418,MA0140.1;1.22262,MA0141.1;2.02973,MA0142.1;0.247045,MA0143.1;0.173319,MA0144.1;1.44648,MA0145.1;0.0869984,MA0146.1;2.58166,MA0147.1;0.35727,MA0148.1;0.0971411,MA0149.1;0.110599,MA0062.2;0.714667,MA0035.2;2.41286,MA0039.2;0.0128887,MA0138.2;1.71493,MA0002.2;0.8313,MA0137.2;0.581971,MA0104.2;0.105762,MA0047.2;0.155654,MA0112.2;0.338487,MA0065.2;0.734628,MA0150.1;0.204231,MA0151.1;0,MA0152.1;0.761762,MA0153.1;3.09544,MA0154.1;2.17367,MA0155.1;2.12369,MA0156.1;0.138397,MA0157.1;0.227782,MA0158.1;0,MA0159.1;1.64881,MA0160.1;2.2963,MA0161.1;0,MA0162.1;0.00415725,MA0163.1;0.0896127,MA0164.1;0.181076,MA0080.2;0.284607,MA0018.2;0.163878,MA0099.2;0.762621,MA0079.2;0.00289224,MA0102.2;0.88257,MA0258.1;1.02444,MA0259.1;0.626372,MA0442.1;0}}
|full_id=C346_gall_ductus_seminal_temporal_duodenum_Hepatocyte_liver
|gostat_on_coexpression_clusters=GO:0030277!maintenance of gastrointestinal epithelium!0.0207089471839206!4588$GO:0001517!N-acetylglucosamine 6-O-sulfotransferase activity!0.0207089471839206!10164$GO:0006928!cell motility!0.0207089471839206!10164;476$GO:0051674!localization of cell!0.0207089471839206!10164;476$GO:0031532!actin cytoskeleton reorganization!0.0207089471839206!9578$GO:0051923!sulfation!0.0207089471839206!10164$GO:0006477!protein amino acid sulfation!0.0207089471839206!10164$GO:0005890!sodium:potassium-exchanging ATPase complex!0.0207089471839206!476$GO:0000287!magnesium ion binding!0.0207089471839206!476;9578$GO:0030641!cellular hydrogen ion homeostasis!0.0258440314808478!476$GO:0030004!cellular monovalent inorganic cation homeostasis!0.0269172999760724!476$GO:0055067!monovalent inorganic cation homeostasis!0.0269172999760724!476$GO:0005391!sodium:potassium-exchanging ATPase activity!0.0281571499812529!476$GO:0022600!digestive system process!0.0282556773832283!4588$GO:0030317!sperm motility!0.0282556773832283!476$GO:0005802!trans-Golgi network!0.0282556773832283!10164$GO:0007163!establishment and/or maintenance of cell polarity!0.0367114937127861!9578$GO:0006044!N-acetylglucosamine metabolic process!0.0396325799223194!10164$GO:0006041!glucosamine metabolic process!0.0396325799223194!10164$GO:0006040!amino sugar metabolic process!0.0440937139326096!10164
|id=C346
}}

Latest revision as of 11:20, 17 September 2013


Full id: C346_gall_ductus_seminal_temporal_duodenum_Hepatocyte_liver



Phase1 CAGE Peaks

Hg19::chr11:1036824..1036834,-p12@MUC6
Hg19::chr11:1036870..1036877,-p19@MUC6
Hg19::chr11:1247434..1247435,+p@chr11:1247434..1247435
+
Hg19::chr11:1247439..1247442,+p@chr11:1247439..1247442
+
Hg19::chr11:1247457..1247468,+p@chr11:1247457..1247468
+
Hg19::chr11:1248306..1248342,+p@chr11:1248306..1248342
+
Hg19::chr11:1248537..1248548,+p@chr11:1248537..1248548
+
Hg19::chr11:69832005..69832020,+p2@ENST00000534086
Hg19::chr11:69906080..69906083,+p@chr11:69906080..69906083
+
Hg19::chr14:103470614..103470619,-p17@CDC42BPB
Hg19::chr16:71560034..71560052,+p2@CHST4
Hg19::chr16:71560158..71560170,+p3@CHST4
Hg19::chr16:71560178..71560189,+p4@CHST4
Hg19::chr16:71560323..71560348,+p1@CHST4
Hg19::chr17:79429043..79429051,-p@chr17:79429043..79429051
-
Hg19::chr18:3215101..3215129,-p@chr18:3215101..3215129
-
Hg19::chr18:3215174..3215185,-p@chr18:3215174..3215185
-
Hg19::chr18:3215199..3215210,-p@chr18:3215199..3215210
-
Hg19::chr18:55095211..55095224,+p@chr18:55095211..55095224
+
Hg19::chr19:40433829..40433855,-p@chr19:40433829..40433855
-
Hg19::chr19:40434104..40434122,-p@chr19:40434104..40434122
-
Hg19::chr1:116915270..116915282,+p53@ATP1A1
Hg19::chr1:187929602..187929615,+p@chr1:187929602..187929615
+
Hg19::chr1:22836627..22836645,+p@chr1:22836627..22836645
+
Hg19::chr20:35983148..35983193,+p@chr20:35983148..35983193
+
Hg19::chr21:43783664..43783667,+p@chr21:43783664..43783667
+
Hg19::chr22:50732337..50732349,-p@chr22:50732337..50732349
-
Hg19::chr3:193561585..193561593,-p2@ENST00000439074
Hg19::chr3:193561605..193561612,-p3@ENST00000439074
Hg19::chr3:193561630..193561644,-p1@ENST00000439074
Hg19::chr4:26491064..26491072,-p@chr4:26491064..26491072
-
Hg19::chr5:111570472..111570478,-p@chr5:111570472..111570478
-


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:0030277maintenance of gastrointestinal epithelium0.0207089471839206
GO:0001517N-acetylglucosamine 6-O-sulfotransferase activity0.0207089471839206
GO:0006928cell motility0.0207089471839206
GO:0051674localization of cell0.0207089471839206
GO:0031532actin cytoskeleton reorganization0.0207089471839206
GO:0051923sulfation0.0207089471839206
GO:0006477protein amino acid sulfation0.0207089471839206
GO:0005890sodium:potassium-exchanging ATPase complex0.0207089471839206
GO:0000287magnesium ion binding0.0207089471839206
GO:0030641cellular hydrogen ion homeostasis0.0258440314808478
GO:0030004cellular monovalent inorganic cation homeostasis0.0269172999760724
GO:0055067monovalent inorganic cation homeostasis0.0269172999760724
GO:0005391sodium:potassium-exchanging ATPase activity0.0281571499812529
GO:0022600digestive system process0.0282556773832283
GO:0030317sperm motility0.0282556773832283
GO:0005802trans-Golgi network0.0282556773832283
GO:0007163establishment and/or maintenance of cell polarity0.0367114937127861
GO:0006044N-acetylglucosamine metabolic process0.0396325799223194
GO:0006041glucosamine metabolic process0.0396325799223194
GO:0006040amino sugar metabolic process0.0440937139326096



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
open tracheal system trachea5.04e-342
gallbladder2.62e-233
gall bladder primordium2.62e-233
trachea8.99e-117
respiratory airway8.99e-117
biliary system1.04e-089
biliary tree1.04e-089
biliary bud1.04e-089
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma7.05e-342


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)
MA0003.10.976439
MA0004.10.085298
MA0006.11.19779
MA0007.10.0768943
MA0009.10.395891
MA0014.10.0274348
MA0017.11.40477
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.032054
MA0029.10.327543
MA0030.10.318663
MA0031.10.270046
MA0038.10.138548
MA0040.10.332103
MA0041.10.0940493
MA0042.10.272024
MA0043.10.39615
MA0046.10.386991
MA0048.10.326644
MA0050.10.273123
MA0051.10.422881
MA0052.10.335128
MA0055.10.034896
MA0056.10
MA0057.10.046597
MA0058.10.177816
MA0059.10.397441
MA0060.10.00694078
MA0061.10.314844
MA0063.10
MA0066.10.138793
MA0067.10.673046
MA0068.10.355309
MA0069.10.998321
MA0070.10.374777
MA0071.12.43217
MA0072.10.371146
MA0073.14.28678e-05
MA0074.10.421793
MA0076.10.194815
MA0077.10.364942
MA0078.10.197204
MA0081.10.397764
MA0083.11.83165
MA0084.10.847335
MA0087.10.369175
MA0088.10.124262
MA0089.10
MA0090.11.70642
MA0091.10.0865076
MA0092.10.245507
MA0093.10.118655
MA0095.10
MA0098.10
MA0100.10.449302
MA0101.10.290288
MA0103.10.789368
MA0105.10.557127
MA0106.10.163029
MA0107.10.340081
MA0108.20.267801
MA0109.10
MA0111.10.0631734
MA0113.10.991329
MA0114.12.45242
MA0115.10.603788
MA0116.12.5408
MA0117.10.427006
MA0119.10.654601
MA0122.10.44876
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.10.676418
MA0140.11.22262
MA0141.12.02973
MA0142.10.247045
MA0143.10.173319
MA0144.11.44648
MA0145.10.0869984
MA0146.12.58166
MA0147.10.35727
MA0148.10.0971411
MA0149.10.110599
MA0062.20.714667
MA0035.22.41286
MA0039.20.0128887
MA0138.21.71493
MA0002.20.8313
MA0137.20.581971
MA0104.20.105762
MA0047.20.155654
MA0112.20.338487
MA0065.20.734628
MA0150.10.204231
MA0151.10
MA0152.10.761762
MA0153.13.09544
MA0154.12.17367
MA0155.12.12369
MA0156.10.138397
MA0157.10.227782
MA0158.10
MA0159.11.64881
MA0160.12.2963
MA0161.10
MA0162.10.00415725
MA0163.10.0896127
MA0164.10.181076
MA0080.20.284607
MA0018.20.163878
MA0099.20.762621
MA0079.20.00289224
MA0102.20.88257
MA0258.11.02444
MA0259.10.626372
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
POU5F1#5460441.92990018148822.62936373879147e-069.22432379965209e-05



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.

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