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Coexpression cluster:C367: Difference between revisions

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{{Coexpression_clusters
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activity!0.00579560515052357!5653$GO:0030163!protein catabolic process!0.00592419392120253!4316;5653$GO:0007130!synaptonemal complex assembly!0.00602716320831794!10734$GO:0007129!synapsis!0.00659191867090141!10734$GO:0043285!biopolymer catabolic process!0.00790864191242954!4316;5653$GO:0042577!lipid phosphatase activity!0.0100426108972329!8821$GO:0000795!synaptonemal complex!0.0103064350029073!10734$GO:0042982!amyloid precursor protein metabolic process!0.0105438101975185!5653$GO:0042246!tissue regeneration!0.0111317409286778!5653$GO:0009057!macromolecule catabolic process!0.0111317409286778!4316;5653$GO:0050435!beta-amyloid metabolic process!0.0111317409286778!5653$GO:0031099!regeneration!0.0112949442082651!5653$GO:0042552!myelination!0.015656790337173!5653$GO:0004175!endopeptidase activity!0.0159698035176525!4316;5653$GO:0000794!condensed nuclear chromosome!0.0165549481747521!10734$GO:0007272!ensheathment of neurons!0.0165549481747521!5653$GO:0008366!axon 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04817,0.913504,0.733651,0.86962,0.871237,0.528003,0.0829875,0.951908,0.897594,0.909798,0.902351,0.783457,0.882896,0.779734,0.708487,0.921397,0.313635,0.566201,0.893204,0.778145,0.888685,0.760387,0.817598,0.754642,0.0010241,0.716895,0.848783,0.857075,0.639262,0.895459,0.8853,0.841177,0.704619,0.57606,0.895366,0.676566,0.423601,0.424626,0.805726,0.195627,0.34016,0.424394,0.0173642,0.805928,0.685876,0.344759,0.00609198,0.62084,0.571658,0.643948,0.000616949,0.373209,0.483153,0.668749,0.496554,0.547588,0.747943,0.685267,0.363089,0.49992,0.608908,0.312282,0.76541,0.898378,0.969998,0.656077,0.422271,0.451619,0.952822,0.794268,0.892767,0.728946,0.472723,0.00322314,0.311431,0.845713,0.953619,0.75656,0.826465,0.900712,0.650746,0.25233,0.750968,0.903359,0.707973,0.1035,0.920648,0.706194,0.368938,0.879906,0.963449,0.844996,0.943652,0.83452,0.921082,0.257803,0.75737,0.116792,0.902637,0.635009,0.592801,0.977866,0.561571,0.0977004,0.824124,0.521768,0.957378,0.655258,0.919325,0.855583,0.819339,0.911936,0.78766,0.900355,0.824763|tfbs_overrepresentation_for_novel_motifs=0.185567,1.97104,0.177713,0.718077,0.581353,0.351855,0.150903,0.130777,0.263726,0.0928516,0.643771,0.525567,0.17587,0.144149,0.577363,0.15742,0.302324,1.85328,1.47436,0.0911091,0.0469504,0.463268,0.104721,0.13133,0.494587,0.560796,1.19319,0.338447,0.324953,0.367225,0.594031,0.330539,0.01399,0.0818183,0.257682,0.0239089,0.0239955,0.35343,0.213908,0.106313,0.771457,0.0760943,0.950691,0.133382,0.0658445,0.211277,0.461692,0.088465,0.227373,0.590796,0.201351,0.158611,0.550796,0.391649,0.52046,0.447445,0.946371,0.400151,0.0478488,0.126682,0.951935,0.465205,0.705633,0.28158,0.492088,0.712388,0.598376,0.940287,0.322501,0.786982,0.0704501,0.282337,0.00084636,0.518722,0.3069,0.0636748,0.590817,0.269153,1.54537,0.481486,0.587852,0.280786,0.163587,0.474327,0.474452,0.0017363,0.0888608,0.349311,0.624655,1.03562,0.682835,0.451575,0.909593,0.184466,0.136766,1.33811,0.560576,0.37755,0.63208,0.00961202,0.216047,0.339232,0.373064,0.305101,0.248225,0.0914534,0.293159,0.438102,1.79043,0.0294273,0.422457,0.370843,0.388815,0.323972,0.63916,0.249597,0.0485938,0.591331,0.254779,0.188737,0.511538,0.620753,1.70994,0.980472,0.740513,0.269709,0.147159,0.34759,0.548727,0.0808203,1.14682,1.50019,0.561391,0.168477,0.694633,0.0397976,0.276014,1.6799,0.655888,1.48038,1.08626,0.62213,0.148175,0.97824,0.249475,1.26744,0.668871,1.32355,0.55032,0.0686645,0.0500352,0.000113697,0.452479,0.246299,0.152669,0.815647,0.598763,1.24112,0.228587,0.195988,0.621036,0.436936,1.54321,0.770033,0.261021,0.949932,0.0608031,0.458109,0.668919|tfbs_overrepresentation_jaspar=MA0003.1;0.0907022,MA0004.1;0.0961566,MA0006.1;0.0332857,MA0007.1;0.293913,MA0009.1;1.07184,MA0014.1;0.0731518,MA0017.1;0.173605,MA0019.1;0.533378,MA0024.1;0.332558,MA0025.1;0.531977,MA0027.1;1.95983,MA0028.1;0.0380705,MA0029.1;0.347825,MA0030.1;0.898657,MA0031.1;0.288912,MA0038.1;0.15256,MA0040.1;0.352485,MA0041.1;0.105506,MA0042.1;0.300789,MA0043.1;0.417784,MA0046.1;0.408463,MA0048.1;0.0261535,MA0050.1;0.0900741,MA0051.1;0.150026,MA0052.1;0.936014,MA0055.1;0.790605,MA0056.1;0,MA0057.1;0.227938,MA0058.1;0.0546193,MA0059.1;0.0541371,MA0060.1;0.705082,MA0061.1;0.205567,MA0063.1;0,MA0066.1;2.79646,MA0067.1;0.697961,MA0068.1;1.86673,MA0069.1;0.405267,MA0070.1;0.396023,MA0071.1;0.12997,MA0072.1;0.392323,MA0073.1;0.000699327,MA0074.1;0.89351,MA0076.1;0.060743,MA0077.1;0.386,MA0078.1;2.54007,MA0081.1;0.441387,MA0083.1;0.423797,MA0084.1;0.873335,MA0087.1;0.390315,MA0088.1;0.384887,MA0089.1;0,MA0090.1;0.508642,MA0091.1;0.0974512,MA0092.1;0.272882,MA0093.1;0.0341631,MA0095.1;0,MA0098.1;0,MA0100.1;0.161006,MA0101.1;0.327739,MA0103.1;1.69832,MA0105.1;0.103391,MA0106.1;0.178189,MA0107.1;0.387848,MA0108.2;0.781414,MA0109.1;0,MA0111.1;0.252572,MA0113.1;1.05411,MA0114.1;0.0161389,MA0115.1;0.62811,MA0116.1;0.0805087,MA0117.1;0.449155,MA0119.1;1.10716,MA0122.1;0.471243,MA0124.1;0.590699,MA0125.1;0.516292,MA0130.1;0,MA0131.1;0.226279,MA0132.1;0,MA0133.1;0,MA0135.1;0.443024,MA0136.1;0.156833,MA0139.1;1.05851,MA0140.1;0.403323,MA0141.1;0.197657,MA0142.1;0.265252,MA0143.1;0.553308,MA0144.1;0.338277,MA0145.1;0.833844,MA0146.1;0.0820453,MA0147.1;0.0184972,MA0148.1;0.1088,MA0149.1;0.123091,MA0062.2;0.00542453,MA0035.2;0.402308,MA0039.2;0.379307,MA0138.2;0.214585,MA0002.2;1.26293,MA0137.2;0.156367,MA0104.2;0.00891586,MA0047.2;0.508505,MA0112.2;1.52564,MA0065.2;0.00887985,MA0150.1;0.229194,MA0151.1;0,MA0152.1;0.412817,MA0153.1;0.501603,MA0154.1;1.10983,MA0155.1;0.253174,MA0156.1;0.15867,MA0157.1;0.686763,MA0158.1;0,MA0159.1;0.991097,MA0160.1;0.116872,MA0161.1;0,MA0162.1;2.4905e-05,MA0163.1;0.00234709,MA0164.1;0.572716,MA0080.2;0.321686,MA0018.2;0.179075,MA0099.2;0.413335,MA0079.2;0.000269655,MA0102.2;0.908736,MA0258.1;0.0584056,MA0259.1;0.0202561,MA0442.1;0}}
|full_id=C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular
|id=C367
}}

Latest revision as of 11:21, 17 September 2013


Full id: C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular



Phase1 CAGE Peaks

Hg19::chr11:102401469..102401488,-p1@MMP7
Hg19::chr13:107026326..107026335,-p@chr13:107026326..107026335
-
Hg19::chr15:20093569..20093572,+p@chr15:20093569..20093572
+
Hg19::chr17:70636802..70636818,+p@chr17:70636802..70636818
+
Hg19::chr19:15923954..15923958,-p@chr19:15923954..15923958
-
Hg19::chr19:49522727..49522759,-p@chr19:49522727..49522759
-
Hg19::chr19:49545646..49545652,+p@chr19:49545646..49545652
+
Hg19::chr19:49545660..49545673,+p@chr19:49545660..49545673
+
Hg19::chr19:49545674..49545685,+p@chr19:49545674..49545685
+
Hg19::chr19:49545691..49545692,+p@chr19:49545691..49545692
+
Hg19::chr19:49553696..49553725,-p@chr19:49553696..49553725
-
Hg19::chr19:49553788..49553818,-p@chr19:49553788..49553818
-
Hg19::chr19:51472014..51472030,-p2@KLK6
Hg19::chr1:218785863..218785866,+p@chr1:218785863..218785866
+
Hg19::chr1:222159603..222159607,+p@chr1:222159603..222159607
+
Hg19::chr20:56283735..56283746,+p@chr20:56283735..56283746
+
Hg19::chr2:106016186..106016205,+p@chr2:106016186..106016205
+
Hg19::chr2:30440814..30440823,+p@chr2:30440814..30440823
+
Hg19::chr3:139035972..139036016,-p@chr3:139035972..139036016
-
Hg19::chr4:143369478..143369483,-p@chr4:143369478..143369483
-
Hg19::chr4:143395551..143395584,-p3@INPP4B
Hg19::chr4:143395591..143395600,-p16@INPP4B
Hg19::chr4:143395603..143395614,-p14@INPP4B
Hg19::chr6:1054763..1054800,-p@chr6:1054763..1054800
-
Hg19::chr7:98796685..98796688,-p@chr7:98796685..98796688
-
Hg19::chr7:98807901..98807908,-p@chr7:98807901..98807908
-
Hg19::chr7:98822527..98822533,+p@chr7:98822527..98822533
+
Hg19::chr7:99779265..99779276,+p15@STAG3
Hg19::chr9:132337683..132337714,+p1@ENST00000443993
p1@uc004bya.1
Hg19::chrX:46121582..46121588,-p@chrX:46121582..46121588
-


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:0030574collagen catabolic process3.49113901529097e-05
GO:0044256protein digestion3.49113901529097e-05
GO:0044254multicellular organismal protein catabolic process3.49113901529097e-05
GO:0044266multicellular organismal macromolecule catabolic process3.49113901529097e-05
GO:0044259multicellular organismal macromolecule metabolic process3.49113901529097e-05
GO:0044268multicellular organismal protein metabolic process3.49113901529097e-05
GO:0044243multicellular organismal catabolic process3.49113901529097e-05
GO:0032963collagen metabolic process3.49113901529097e-05
GO:0044236multicellular organismal metabolic process3.738365344664e-05
GO:0007586digestion0.000592102168167378
GO:0004235matrilysin activity0.00137011228498335
GO:0016316phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity0.00251176160996224
GO:0004293tissue kallikrein activity0.00579560515052357
GO:0030163protein catabolic process0.00592419392120253
GO:0007130synaptonemal complex assembly0.00602716320831794
GO:0007129synapsis0.00659191867090141
GO:0043285biopolymer catabolic process0.00790864191242954
GO:0042577lipid phosphatase activity0.0100426108972329
GO:0000795synaptonemal complex0.0103064350029073
GO:0042982amyloid precursor protein metabolic process0.0105438101975185
GO:0042246tissue regeneration0.0111317409286778
GO:0009057macromolecule catabolic process0.0111317409286778
GO:0050435beta-amyloid metabolic process0.0111317409286778
GO:0031099regeneration0.0112949442082651
GO:0042552myelination0.015656790337173
GO:0004175endopeptidase activity0.0159698035176525
GO:0000794condensed nuclear chromosome0.0165549481747521
GO:0007272ensheathment of neurons0.0165549481747521
GO:0008366axon ensheathment0.0165549481747521
GO:0007127meiosis I0.0165549481747521
GO:0048589developmental growth0.0179596740625052
GO:0001508regulation of action potential0.0183529399737562
GO:0009056catabolic process0.0183529399737562
GO:0016540protein autoprocessing0.0203500138822008
GO:0016787hydrolase activity0.0207309052081313
GO:0000793condensed chromosome0.0217205866203829
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0231604999529081
GO:0007059chromosome segregation0.0233402148347696
GO:0008233peptidase activity0.0246856409289252
GO:0044454nuclear chromosome part0.0246856409289252
GO:0051327M phase of meiotic cell cycle0.0246856409289252
GO:0007126meiosis0.0246856409289252
GO:0051321meiotic cell cycle0.0248082502336922
GO:0006508proteolysis0.0248798947491532
GO:0042445hormone metabolic process0.0293596090777808
GO:0016485protein processing0.0316086834367993
GO:0000228nuclear chromosome0.0316086834367993
GO:0042060wound healing0.0408964047267248
GO:0045595regulation of cell differentiation0.0440120927780186



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
bladder cell2.30e-211
lower urinary tract cell2.30e-211
epithelial cell of gall bladder3.70e-112
epithelial cell2.35e-07253
Uber Anatomy
Ontology termp-valuen
hepatopancreatic ampulla1.53e-211
extrahepatic bile duct1.53e-211
common bile duct1.53e-211
duodenal papilla1.53e-211
urinary bladder urothelium2.30e-211
wall of urinary bladder2.30e-211
mucosa of urinary bladder2.30e-211
mammalian vulva5.16e-211
external female genitalia5.16e-211
biliary system1.24e-209
biliary tree1.24e-209
biliary bud1.24e-209
bile duct1.90e-146
digestive system duct1.90e-146
urinary bladder2.23e-112
lower urinary tract2.23e-112
endoderm-derived structure1.47e-09160
endoderm1.47e-09160
presumptive endoderm1.47e-09160
endo-epithelium1.16e-0882
digestive system2.47e-08145
digestive tract2.47e-08145
primitive gut2.47e-08145
duodenum4.52e-082
gallbladder7.26e-083
gall bladder primordium7.26e-083
epithelium of foregut-midgut junction7.66e-0825
anatomical boundary7.66e-0825
hepatobiliary system7.66e-0825
foregut-midgut junction7.66e-0825
septum transversum7.66e-0825
Disease
Ontology termp-valuen
carcinoma9.81e-15106
squamous cell carcinoma2.67e-1314
tubular adenocarcinoma1.82e-112
cell type cancer8.27e-11143
disease of anatomical entity1.65e-0839


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)
MA0003.10.0907022
MA0004.10.0961566
MA0006.10.0332857
MA0007.10.293913
MA0009.11.07184
MA0014.10.0731518
MA0017.10.173605
MA0019.10.533378
MA0024.10.332558
MA0025.10.531977
MA0027.11.95983
MA0028.10.0380705
MA0029.10.347825
MA0030.10.898657
MA0031.10.288912
MA0038.10.15256
MA0040.10.352485
MA0041.10.105506
MA0042.10.300789
MA0043.10.417784
MA0046.10.408463
MA0048.10.0261535
MA0050.10.0900741
MA0051.10.150026
MA0052.10.936014
MA0055.10.790605
MA0056.10
MA0057.10.227938
MA0058.10.0546193
MA0059.10.0541371
MA0060.10.705082
MA0061.10.205567
MA0063.10
MA0066.12.79646
MA0067.10.697961
MA0068.11.86673
MA0069.10.405267
MA0070.10.396023
MA0071.10.12997
MA0072.10.392323
MA0073.10.000699327
MA0074.10.89351
MA0076.10.060743
MA0077.10.386
MA0078.12.54007
MA0081.10.441387
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.10.384887
MA0089.10
MA0090.10.508642
MA0091.10.0974512
MA0092.10.272882
MA0093.10.0341631
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.327739
MA0103.11.69832
MA0105.10.103391
MA0106.10.178189
MA0107.10.387848
MA0108.20.781414
MA0109.10
MA0111.10.252572
MA0113.11.05411
MA0114.10.0161389
MA0115.10.62811
MA0116.10.0805087
MA0117.10.449155
MA0119.11.10716
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.226279
MA0132.10
MA0133.10
MA0135.10.443024
MA0136.10.156833
MA0139.11.05851
MA0140.10.403323
MA0141.10.197657
MA0142.10.265252
MA0143.10.553308
MA0144.10.338277
MA0145.10.833844
MA0146.10.0820453
MA0147.10.0184972
MA0148.10.1088
MA0149.10.123091
MA0062.20.00542453
MA0035.20.402308
MA0039.20.379307
MA0138.20.214585
MA0002.21.26293
MA0137.20.156367
MA0104.20.00891586
MA0047.20.508505
MA0112.21.52564
MA0065.20.00887985
MA0150.10.229194
MA0151.10
MA0152.10.412817
MA0153.10.501603
MA0154.11.10983
MA0155.10.253174
MA0156.10.15867
MA0157.10.686763
MA0158.10
MA0159.10.991097
MA0160.10.116872
MA0161.10
MA0162.12.4905e-05
MA0163.10.00234709
MA0164.10.572716
MA0080.20.321686
MA0018.20.179075
MA0099.20.413335
MA0079.20.000269655
MA0102.20.908736
MA0258.10.0584056
MA0259.10.0202561
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
ESR1#209966.15372065923090.000356321486410390.00356591220000141
NR3C1#290862.994604666234610.01309398003524260.0464480056008663



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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