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Coexpression cluster:C308: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.105186,0.118821,0.0230569,0.236097,0.184223,0.23426,0.0986544,1.49105,1.14315,0.0762605,0.201596,0.120169,0.00812929,0.0932869,0.597213,1.81284,0.227456,0.947923,0.176947,0.401914,0.245526,0.50361,0.0629663,1.22499,0.320763,0.132202,0.336628,0.223303,0.368776,0.602389,0.179289,0.703708,0.0835775,0.622421,0.139788,0.206628,0.00982223,0.870796,0.914299,0.750763,0.28228,0.0423329,0.974403,0.88791,0.480231,0.0301563,0.0991704,0.743826,0.872777,0.915671,0.139988,0.104833,0.941161,0.308256,0.428303,0.0946422,0.935089,0.0800554,1.3333,0.0796258,0.281871,0.100296,1.14679,0.601573,0.715752,0.187096,0.502307,0.834098,0.245481,0.684258,0.038443,0.14128,0.00549875,1.09169,0.0272645,0.121343,1.11674,0.575544,0.243236,0.895683,0.0947596,0.20839,0.352292,0.257386,0.385048,2.30075e-05,0.103998,1.28344,0.154748,0.927861,0.583373,0.363684,0.730982,0.558581,0.0153306,0.220227,1.19572,0.295343,1.48209,0.0634941,0.234239,0.260534,0.291245,0.229928,0.531603,0.0532312,0.21932,0.0917054,0.0339777,0.0611797,0.108159,0.289219,1.06978,0.0581562,0.541356,0.134126,0.00327021,0.0470551,0.185636,0.201231,1.07698,0.909353,0.858799,0.367143,0.639136,0.576709,1.08766,0.268089,0.45505,1.97078,0.364226,1.10786,0.467073,0.733045,0.594755,0.37041,2.02163,0.0623645,0.557426,1.36861,0.977798,1.30276,0.0964808,0.29275,0.181034,0.264331,0.170865,1.21274,0.160261,0.190291,0.458355,0.000663062,0.364525,0.0498676,0.328942,0.712168,0.446536,0.329911,0.0340611,0.0268425,0.523979,0.350068,0.242693,0.515263,1.67614,0.713157,0.310071,0.0980259,0.00556056
|tfbs_overrepresentation_for_novel_motifs=0.105186,0.118821,0.0230569,0.236097,0.184223,0.23426,0.0986544,1.49105,1.14315,0.0762605,0.201596,0.120169,0.00812929,0.0932869,0.597213,1.81284,0.227456,0.947923,0.176947,0.401914,0.245526,0.50361,0.0629663,1.22499,0.320763,0.132202,0.336628,0.223303,0.368776,0.602389,0.179289,0.703708,0.0835775,0.622421,0.139788,0.206628,0.00982223,0.870796,0.914299,0.750763,0.28228,0.0423329,0.974403,0.88791,0.480231,0.0301563,0.0991704,0.743826,0.872777,0.915671,0.139988,0.104833,0.941161,0.308256,0.428303,0.0946422,0.935089,0.0800554,1.3333,0.0796258,0.281871,0.100296,1.14679,0.601573,0.715752,0.187096,0.502307,0.834098,0.245481,0.684258,0.038443,0.14128,0.00549875,1.09169,0.0272645,0.121343,1.11674,0.575544,0.243236,0.895683,0.0947596,0.20839,0.352292,0.257386,0.385048,2.30075e-05,0.103998,1.28344,0.154748,0.927861,0.583373,0.363684,0.730982,0.558581,0.0153306,0.220227,1.19572,0.295343,1.48209,0.0634941,0.234239,0.260534,0.291245,0.229928,0.531603,0.0532312,0.21932,0.0917054,0.0339777,0.0611797,0.108159,0.289219,1.06978,0.0581562,0.541356,0.134126,0.00327021,0.0470551,0.185636,0.201231,1.07698,0.909353,0.858799,0.367143,0.639136,0.576709,1.08766,0.268089,0.45505,1.97078,0.364226,1.10786,0.467073,0.733045,0.594755,0.37041,2.02163,0.0623645,0.557426,1.36861,0.977798,1.30276,0.0964808,0.29275,0.181034,0.264331,0.170865,1.21274,0.160261,0.190291,0.458355,0.000663062,0.364525,0.0498676,0.328942,0.712168,0.446536,0.329911,0.0340611,0.0268425,0.523979,0.350068,0.242693,0.515263,1.67614,0.713157,0.310071,0.0980259,0.00556056
|tfbs_overrepresentation_jaspar=MA0003.1;4.20904e-06,MA0004.1;0.45503,MA0006.1;0.0696281,MA0007.1;0.418327,MA0009.1;1.58829,MA0014.1;2.22494e-05,MA0017.1;0.096641,MA0019.1;0.388744,MA0024.1;0.254518,MA0025.1;0.439186,MA0027.1;1.8466,MA0028.1;0.017688,MA0029.1;0.268301,MA0030.1;0.260095,MA0031.1;0.215562,MA0038.1;0.0999782,MA0040.1;0.272523,MA0041.1;0.227378,MA0042.1;0.428611,MA0043.1;0.332327,MA0046.1;2.36713,MA0048.1;0.0969338,MA0050.1;0.19388,MA0051.1;0.32328,MA0052.1;0.275327,MA0055.1;0.232674,MA0056.1;0,MA0057.1;0.527353,MA0058.1;0.279956,MA0059.1;0.823005,MA0060.1;0.00279011,MA0061.1;0.0923999,MA0063.1;0,MA0066.1;0.674802,MA0067.1;0.597968,MA0068.1;1.47322,MA0069.1;0.320777,MA0070.1;0.312273,MA0071.1;0.588101,MA0072.1;0.308875,MA0073.1;0.115655,MA0074.1;1.10102,MA0076.1;0.031919,MA0077.1;0.818719,MA0078.1;0.150427,MA0081.1;0.115503,MA0083.1;0.337888,MA0084.1;0.768496,MA0087.1;0.82764,MA0088.1;1.18096,MA0089.1;0,MA0090.1;0.332189,MA0091.1;0.799469,MA0092.1;0.386895,MA0093.1;0.606071,MA0095.1;0,MA0098.1;0,MA0100.1;0.106764,MA0101.1;0.190552,MA0103.1;0.564235,MA0105.1;0.0317322,MA0106.1;0.383434,MA0107.1;0.100362,MA0108.2;0.612085,MA0109.1;0,MA0111.1;0.640029,MA0113.1;0.406016,MA0114.1;0.205078,MA0115.1;0.530757,MA0116.1;0.88521,MA0117.1;0.36143,MA0119.1;1.11533,MA0122.1;0.382044,MA0124.1;1.23873,MA0125.1;0.42437,MA0130.1;0,MA0131.1;0.161082,MA0132.1;0,MA0133.1;0,MA0135.1;0.355725,MA0136.1;0.68982,MA0139.1;0.00855844,MA0140.1;0.276985,MA0141.1;0.0271979,MA0142.1;0.194761,MA0143.1;0.129619,MA0144.1;0.179407,MA0145.1;0.395589,MA0146.1;0.164987,MA0147.1;0.227969,MA0148.1;0.0660128,MA0149.1;1.42262,MA0062.2;0.00144723,MA0035.2;0.0807052,MA0039.2;0.0305413,MA0138.2;0.460666,MA0002.2;1.36777,MA0137.2;0.411378,MA0104.2;0.12844,MA0047.2;0.114453,MA0112.2;1.25197,MA0065.2;0.291904,MA0150.1;0.0342009,MA0151.1;0,MA0152.1;0.5966,MA0153.1;1.86059,MA0154.1;0.987789,MA0155.1;0.219362,MA0156.1;0.416987,MA0157.1;0.525632,MA0158.1;0,MA0159.1;0.630496,MA0160.1;0.537314,MA0161.1;0,MA0162.1;0.00057372,MA0163.1;0.430142,MA0164.1;0.837054,MA0080.2;0.606368,MA0018.2;0.121488,MA0099.2;0.0840507,MA0079.2;0.0078603,MA0102.2;0.803155,MA0258.1;0.484448,MA0259.1;0.116854,MA0442.1;0
}}
}}

Revision as of 19:02, 22 January 2013


Full id: C308_lung_Hepatocyte_liver_thyroid_heart_left_breast



Phase1 CAGE Peaks

Hg19::chr10:123886537..123886542,+p6@TACC2
Hg19::chr10:6018826..6018842,+p@chr10:6018826..6018842
+
Hg19::chr10:6018896..6018943,+p@chr10:6018896..6018943
+
Hg19::chr10:81316736..81316741,-p@chr10:81316736..81316741
-
Hg19::chr10:81374094..81374095,+p2@AK309522
Hg19::chr11:60524339..60524341,+p3@MS4A15
Hg19::chr11:60524471..60524476,+p2@MS4A15
Hg19::chr12:40619482..40619487,-p@chr12:40619482..40619487
-
Hg19::chr12:9268765..9268779,-p8@A2M
Hg19::chr13:107279210..107279243,+p@chr13:107279210..107279243
+
Hg19::chr15:49758548..49758563,+p@chr15:49758548..49758563
+
Hg19::chr17:53800009..53800012,-p11@TMEM100
Hg19::chr17:53809407..53809415,-p6@TMEM100
Hg19::chr1:111833472..111833476,+p1@CHIA
Hg19::chr1:27701307..27701322,-p1@FCN3
Hg19::chr20:15177480..15177528,+p2@MACROD2
Hg19::chr2:85886492..85886507,+p@chr2:85886492..85886507
+
Hg19::chr2:85886640..85886647,+p@chr2:85886640..85886647
+
Hg19::chr2:85886678..85886695,+p@chr2:85886678..85886695
+
Hg19::chr2:85886680..85886695,-p@chr2:85886680..85886695
-
Hg19::chr2:85886778..85886789,-p@chr2:85886778..85886789
-
Hg19::chr2:85890569..85890576,-p24@SFTPB
Hg19::chr2:85893765..85893801,-p2@SFTPB
Hg19::chr2:85895542..85895549,-p27@SFTPB
Hg19::chr3:150966924..150966933,-p13@P2RY14
Hg19::chr3:157221357..157221365,-p15@VEPH1
Hg19::chr3:157221380..157221399,-p7@VEPH1
Hg19::chr5:1548521..1548536,+p@chr5:1548521..1548536
+
Hg19::chr5:66787065..66787072,+p@chr5:66787065..66787072
+
Hg19::chr6:11291949..11291963,+p@chr6:11291949..11291963
+
Hg19::chr6:30905155..30905161,-p@chr6:30905155..30905161
-
Hg19::chr6:30905176..30905181,-p@chr6:30905176..30905181
-
Hg19::chr6:30905248..30905256,-p@chr6:30905248..30905256
-
Hg19::chr6:32152003..32152016,-p2@AGER
Hg19::chr6:32152020..32152040,-p1@AGER
Hg19::chr6:32152064..32152075,-p3@AGER
Hg19::chr6:41712177..41712188,-p@chr6:41712177..41712188
-
Hg19::chr6:41712545..41712551,-p@chr6:41712545..41712551
-
Hg19::chr8:69243711..69243722,-p4@LOC286189


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:0001101response to acid0.0102944784231565
GO:0010383cell wall polysaccharide metabolic process0.0102944784231565
GO:0006037cell wall chitin metabolic process0.0102944784231565
GO:0010037response to carbon dioxide0.0102944784231565
GO:0005615extracellular space0.0102944784231565
GO:0045029UDP-activated nucleotide receptor activity0.0155385513714468
GO:0019959interleukin-8 binding0.0155385513714468
GO:0015065uridine nucleotide receptor activity0.0155385513714468
GO:0017114wide-spectrum protease inhibitor activity0.0155385513714468
GO:0050828regulation of liquid surface tension0.0209143579160127
GO:0008061chitin binding0.0209143579160127
GO:0044421extracellular region part0.0209143579160127
GO:0043120tumor necrosis factor binding0.0279299039569851
GO:0019966interleukin-1 binding0.0279299039569851
GO:0051384response to glucocorticoid stimulus0.0279299039569851
GO:0019958C-X-C chemokine binding0.0279299039569851
GO:0003796lysozyme activity0.0279299039569851
GO:0031960response to corticosteroid stimulus0.0279299039569851
GO:0005529sugar binding0.0279299039569851
GO:0006032chitin catabolic process0.0279299039569851
GO:0006046N-acetylglucosamine catabolic process0.0279299039569851
GO:0006043glucosamine catabolic process0.0279299039569851
GO:0046348amino sugar catabolic process0.0279299039569851
GO:0006030chitin metabolic process0.0279299039569851
GO:0004568chitinase activity0.0279299039569851
GO:0009620response to fungus0.0325618814526327
GO:0010382cell wall metabolic process0.0325618814526327
GO:0007047cell wall organization and biogenesis0.0325618814526327
GO:0044247cellular polysaccharide catabolic process0.0325618814526327
GO:0000272polysaccharide catabolic process0.0325618814526327
GO:0045229external encapsulating structure organization and biogenesis0.03300816015487
GO:0030246carbohydrate binding0.0366394871563165
GO:0008320protein transmembrane transporter activity0.0394364418177486
GO:0007585respiratory gaseous exchange0.0396389005349773
GO:0006044N-acetylglucosamine metabolic process0.0416574366362695
GO:0006041glucosamine metabolic process0.0416574366362695
GO:0048545response to steroid hormone stimulus0.0416574366362695
GO:0042221response to chemical stimulus0.0416574366362695
GO:0019956chemokine binding0.0416574366362695
GO:0019965interleukin binding0.0416574366362695
GO:0006040amino sugar metabolic process0.0416574366362695
GO:0051260protein homooligomerization0.0416574366362695
GO:0007584response to nutrient0.0416574366362695
GO:0010035response to inorganic substance0.0416574366362695
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0416574366362695
GO:0001608nucleotide receptor activity, G-protein coupled0.0416574366362695
GO:0009605response to external stimulus0.0416574366362695
GO:0016502nucleotide receptor activity0.0416574366362695
GO:0001614purinergic nucleotide receptor activity0.0416574366362695



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><br>

Uber Anatomy
Ontology termp-valuen
lower lobe of right lung9.99e-301
right lung lobe9.99e-301
lower lobe of lung9.99e-301
lobe of lung9.99e-301
right lung9.99e-301
lung2.26e-1222
respiratory tube2.26e-1222
respiration organ2.26e-1222
pair of lungs2.26e-1222
lung primordium2.26e-1222
lung bud2.26e-1222
thoracic cavity element3.01e-0834
thoracic cavity3.01e-0834
thoracic segment organ4.96e-0835
epithelial bud1.25e-0737
respiratory primordium1.90e-0738
endoderm of foregut1.90e-0738
thyroid gland6.77e-075
pharyngeal pouch6.77e-075
thyroid diverticulum6.77e-075
pharyngeal pouch 26.77e-075
thyroid primordium6.77e-075


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)
MA0003.14.20904e-06
MA0004.10.45503
MA0006.10.0696281
MA0007.10.418327
MA0009.11.58829
MA0014.12.22494e-05
MA0017.10.096641
MA0019.10.388744
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.017688
MA0029.10.268301
MA0030.10.260095
MA0031.10.215562
MA0038.10.0999782
MA0040.10.272523
MA0041.10.227378
MA0042.10.428611
MA0043.10.332327
MA0046.12.36713
MA0048.10.0969338
MA0050.10.19388
MA0051.10.32328
MA0052.10.275327
MA0055.10.232674
MA0056.10
MA0057.10.527353
MA0058.10.279956
MA0059.10.823005
MA0060.10.00279011
MA0061.10.0923999
MA0063.10
MA0066.10.674802
MA0067.10.597968
MA0068.11.47322
MA0069.10.320777
MA0070.10.312273
MA0071.10.588101
MA0072.10.308875
MA0073.10.115655
MA0074.11.10102
MA0076.10.031919
MA0077.10.818719
MA0078.10.150427
MA0081.10.115503
MA0083.10.337888
MA0084.10.768496
MA0087.10.82764
MA0088.11.18096
MA0089.10
MA0090.10.332189
MA0091.10.799469
MA0092.10.386895
MA0093.10.606071
MA0095.10
MA0098.10
MA0100.10.106764
MA0101.10.190552
MA0103.10.564235
MA0105.10.0317322
MA0106.10.383434
MA0107.10.100362
MA0108.20.612085
MA0109.10
MA0111.10.640029
MA0113.10.406016
MA0114.10.205078
MA0115.10.530757
MA0116.10.88521
MA0117.10.36143
MA0119.11.11533
MA0122.10.382044
MA0124.11.23873
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.68982
MA0139.10.00855844
MA0140.10.276985
MA0141.10.0271979
MA0142.10.194761
MA0143.10.129619
MA0144.10.179407
MA0145.10.395589
MA0146.10.164987
MA0147.10.227969
MA0148.10.0660128
MA0149.11.42262
MA0062.20.00144723
MA0035.20.0807052
MA0039.20.0305413
MA0138.20.460666
MA0002.21.36777
MA0137.20.411378
MA0104.20.12844
MA0047.20.114453
MA0112.21.25197
MA0065.20.291904
MA0150.10.0342009
MA0151.10
MA0152.10.5966
MA0153.11.86059
MA0154.10.987789
MA0155.10.219362
MA0156.10.416987
MA0157.10.525632
MA0158.10
MA0159.10.630496
MA0160.10.537314
MA0161.10
MA0162.10.00057372
MA0163.10.430142
MA0164.10.837054
MA0080.20.606368
MA0018.20.121488
MA0099.20.0840507
MA0079.20.0078603
MA0102.20.803155
MA0258.10.484448
MA0259.10.116854
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

This analysis result is provided for C0 - C305 clusters.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C308&oldid=2568819"