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Coexpression cluster:C251: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0468178,7.85406,0.254443,0.03346,0.0832486,0.03305,0.447288,1.70864,1.08982,0.282956,0.0260597,0.0708735,0.405603,7.05428,2.16804,2.86616,0.156337,1.02635,0.46522,2.58767,0.12245,4.56482,0.127317,0.511161,0.577546,0.0798892,5.42788,0.548335,0.0858599,1.61342,0.234882,0.177715,0.147158,0.281571,0.00289222,0.964449,0.00274487,0.134535,0.331307,0.00268858,0.24711,0.40838,0.632913,0.0266229,1.21026,1.13385,0.055621,0.102164,2.99892,0.187931,0.0858169,0.471573,1.10712,0.225925,0.888308,1.15659,0.194765,0.372713,3.67981,0.0420799,1.1096,0.206418,2.02595,0.141031,0.0626973,0.123014,0.402704,0.720274,0.171563,0.575342,0.194618,0.195207,0.19417,0.332593,0.0905317,0.329822,6.11812,0.132044,0.50648,0.558564,0.215987,0.140452,0.0625703,0.0477361,0.294608,0.00602688,0.00352721,0.00213962,0.0972405,0.811794,0.479041,0.2753,0.18786,0.00875162,0.778207,0.00163642,0.00191532,0.214593,0.0993381,0.529983,0.1011,0.184422,1.78653,0.158413,2.43369,0.0250991,0.149529,0.188223,0.0140223,0.00387289,0.275528,0.209243,0.0411446,0.028131,2.91557,0.00267409,0.0129981,0.0214019,0.121831,0.645138,0.326377,3.55486,2.24093,0.236477,0.532117,0.820161,0.0531479,0.19092,0.358758,1.56601,0.275788,0.096454,1.72079,0.0654612,1.22774,0.441743,1.42584,0.0307756,0.454492,1.24681,0.860735,0.423988,0.0537169,0.212326,0.376564,0.0399727,3.03754,1.09233,0.0816112,0.07578,2.18717,4.10603e-06,0.276058,0.16026,0.056257,0.602187,0.0900541,0.480738,4.8034,1.82764,0.423004,1.33871,0.169196,0.0528958,0.126241,0.0622867,0.0644748,0.0548093,3.52264
|tfbs_overrepresentation_for_novel_motifs=0.0468178,7.85406,0.254443,0.03346,0.0832486,0.03305,0.447288,1.70864,1.08982,0.282956,0.0260597,0.0708735,0.405603,7.05428,2.16804,2.86616,0.156337,1.02635,0.46522,2.58767,0.12245,4.56482,0.127317,0.511161,0.577546,0.0798892,5.42788,0.548335,0.0858599,1.61342,0.234882,0.177715,0.147158,0.281571,0.00289222,0.964449,0.00274487,0.134535,0.331307,0.00268858,0.24711,0.40838,0.632913,0.0266229,1.21026,1.13385,0.055621,0.102164,2.99892,0.187931,0.0858169,0.471573,1.10712,0.225925,0.888308,1.15659,0.194765,0.372713,3.67981,0.0420799,1.1096,0.206418,2.02595,0.141031,0.0626973,0.123014,0.402704,0.720274,0.171563,0.575342,0.194618,0.195207,0.19417,0.332593,0.0905317,0.329822,6.11812,0.132044,0.50648,0.558564,0.215987,0.140452,0.0625703,0.0477361,0.294608,0.00602688,0.00352721,0.00213962,0.0972405,0.811794,0.479041,0.2753,0.18786,0.00875162,0.778207,0.00163642,0.00191532,0.214593,0.0993381,0.529983,0.1011,0.184422,1.78653,0.158413,2.43369,0.0250991,0.149529,0.188223,0.0140223,0.00387289,0.275528,0.209243,0.0411446,0.028131,2.91557,0.00267409,0.0129981,0.0214019,0.121831,0.645138,0.326377,3.55486,2.24093,0.236477,0.532117,0.820161,0.0531479,0.19092,0.358758,1.56601,0.275788,0.096454,1.72079,0.0654612,1.22774,0.441743,1.42584,0.0307756,0.454492,1.24681,0.860735,0.423988,0.0537169,0.212326,0.376564,0.0399727,3.03754,1.09233,0.0816112,0.07578,2.18717,4.10603e-06,0.276058,0.16026,0.056257,0.602187,0.0900541,0.480738,4.8034,1.82764,0.423004,1.33871,0.169196,0.0528958,0.126241,0.0622867,0.0644748,0.0548093,3.52264
|tfbs_overrepresentation_jaspar=MA0003.1;0.374947,MA0004.1;0.510805,MA0006.1;0.522608,MA0007.1;10.1928,MA0009.1;0.247013,MA0014.1;3.6815e-05,MA0017.1;0.957254,MA0019.1;2.50228,MA0024.1;0.179268,MA0025.1;0.344113,MA0027.1;1.7227,MA0028.1;0.206267,MA0029.1;0.558569,MA0030.1;0.184045,MA0031.1;0.146399,MA0038.1;0.0561953,MA0040.1;0.194748,MA0041.1;0.0315298,MA0042.1;0.0243105,MA0043.1;0.24723,MA0046.1;0.239588,MA0048.1;0.0837579,MA0050.1;0.0244947,MA0051.1;0.0547588,MA0052.1;0.197173,MA0055.1;0.85053,MA0056.1;0,MA0057.1;1.55379,MA0058.1;2.31311,MA0059.1;5.06651,MA0060.1;0.000516773,MA0061.1;0.122917,MA0063.1;0,MA0066.1;0.20618,MA0067.1;1.23427,MA0068.1;0.594877,MA0069.1;0.236979,MA0070.1;0.229464,MA0071.1;1.48939,MA0072.1;0.22647,MA0073.1;24.0992,MA0074.1;0.443106,MA0076.1;0.552661,MA0077.1;1.18148,MA0078.1;2.17157,MA0081.1;0.0107166,MA0083.1;0.252183,MA0084.1;0.656589,MA0087.1;0.224848,MA0088.1;1.33898,MA0089.1;0,MA0090.1;1.64916,MA0091.1;0.115952,MA0092.1;0.426145,MA0093.1;1.07299,MA0095.1;0,MA0098.1;0,MA0100.1;1.25551,MA0101.1;0.0290862,MA0103.1;1.67902,MA0105.1;0.323545,MA0106.1;5.31261,MA0107.1;0.30552,MA0108.2;0.144705,MA0109.1;0,MA0111.1;1.32154,MA0113.1;0.959234,MA0114.1;0.453617,MA0115.1;0.42937,MA0116.1;2.30531,MA0117.1;0.273271,MA0119.1;0.996978,MA0122.1;0.291885,MA0124.1;0.395861,MA0125.1;0.330489,MA0130.1;0,MA0131.1;0.684278,MA0132.1;0,MA0133.1;0,MA0135.1;0.268144,MA0136.1;0.0586412,MA0139.1;0.583451,MA0140.1;0.16556,MA0141.1;0.756874,MA0142.1;0.129252,MA0143.1;0.0779387,MA0144.1;0.0698001,MA0145.1;5.09337,MA0146.1;3.48773,MA0147.1;2.34686,MA0148.1;0.314662,MA0149.1;0.0402234,MA0062.2;0.196268,MA0035.2;0.0428087,MA0039.2;3.12449,MA0138.2;5.07114,MA0002.2;4.81045,MA0137.2;0.00650365,MA0104.2;1.36674,MA0047.2;0.0666578,MA0112.2;5.22272,MA0065.2;0.269935,MA0150.1;0.0141424,MA0151.1;0,MA0152.1;0.0449747,MA0153.1;0.317813,MA0154.1;13.1065,MA0155.1;0.192339,MA0156.1;0.00670135,MA0157.1;1.2199,MA0158.1;0,MA0159.1;0.72134,MA0160.1;0.340065,MA0161.1;0,MA0162.1;0.319829,MA0163.1;1.80066,MA0164.1;0.0830315,MA0080.2;0.533766,MA0018.2;0.25124,MA0099.2;0.0450826,MA0079.2;0.148297,MA0102.2;0.690195,MA0258.1;1.92676,MA0259.1;2.04356,MA0442.1;0
}}
}}

Revision as of 18:52, 22 January 2013


Full id: C251_gall_tonsil_trachea_CD14_salivary_throat_tongue



Phase1 CAGE Peaks

Hg19::chr11:1244263..1244268,+p18@MUC5B
Hg19::chr11:1244288..1244302,+p1@MUC5B
Hg19::chr11:1246908..1246942,+p@chr11:1246908..1246942
+
Hg19::chr11:1248582..1248591,+p@chr11:1248582..1248591
+
Hg19::chr11:1249793..1249803,+p25@MUC5B
Hg19::chr11:1249994..1249999,+p30@MUC5B
Hg19::chr11:1251248..1251255,+p@chr11:1251248..1251255
+
Hg19::chr11:1252161..1252166,+p@chr11:1252161..1252166
+
Hg19::chr11:1260725..1260734,+p@chr11:1260725..1260734
+
Hg19::chr11:1262722..1262737,+p@chr11:1262722..1262737
+
Hg19::chr11:1262749..1262754,+p@chr11:1262749..1262754
+
Hg19::chr11:1262797..1262805,+p@chr11:1262797..1262805
+
Hg19::chr11:1262879..1262886,+p@chr11:1262879..1262886
+
Hg19::chr11:1262959..1262968,-p@chr11:1262959..1262968
-
Hg19::chr11:1263220..1263227,+p@chr11:1263220..1263227
+
Hg19::chr11:1263382..1263385,+p@chr11:1263382..1263385
+
Hg19::chr11:1263439..1263454,-p@chr11:1263439..1263454
-
Hg19::chr11:1263446..1263456,+p@chr11:1263446..1263456
+
Hg19::chr11:1263486..1263491,+p@chr11:1263486..1263491
+
Hg19::chr11:1263559..1263572,+p@chr11:1263559..1263572
+
Hg19::chr11:1263601..1263611,+p@chr11:1263601..1263611
+
Hg19::chr11:1263622..1263627,+p@chr11:1263622..1263627
+
Hg19::chr11:1263636..1263653,+p@chr11:1263636..1263653
+
Hg19::chr11:1263666..1263677,+p@chr11:1263666..1263677
+
Hg19::chr11:1263705..1263748,+p@chr11:1263705..1263748
+
Hg19::chr11:1263750..1263761,+p@chr11:1263750..1263761
+
Hg19::chr11:1263767..1263777,+p@chr11:1263767..1263777
+
Hg19::chr11:1263870..1263886,+p@chr11:1263870..1263886
+
Hg19::chr11:1265985..1265990,+p@chr11:1265985..1265990
+
Hg19::chr11:1267070..1267081,+p9@MUC5B
Hg19::chr11:1267131..1267141,+p20@MUC5B
Hg19::chr11:1267642..1267655,+p17@MUC5B
Hg19::chr11:1267665..1267678,+p7@MUC5B
Hg19::chr11:1267685..1267693,+p26@MUC5B
Hg19::chr11:1267694..1267708,+p10@MUC5B
Hg19::chr11:1267812..1267847,+p15@MUC5B
Hg19::chr11:1270881..1270911,+p13@MUC5B
Hg19::chr11:1271068..1271087,+p11@MUC5B
Hg19::chr11:1272208..1272220,+p2@MUC5B
Hg19::chr11:1272233..1272254,+p3@MUC5B
Hg19::chr11:1272348..1272371,+p5@MUC5B
Hg19::chr11:1272387..1272410,+p6@MUC5B
Hg19::chr11:1272505..1272518,+p22@MUC5B
Hg19::chr11:1272548..1272559,+p8@MUC5B
Hg19::chr11:1275337..1275348,+p16@MUC5B
Hg19::chr11:1275383..1275393,+p27@MUC5B
Hg19::chr11:1276056..1276069,+p@chr11:1276056..1276069
+
Hg19::chr11:1276071..1276078,+p@chr11:1276071..1276078
+
Hg19::chr20:31611160..31611167,+p5@BPIFB6
Hg19::chr20:31611175..31611184,+p6@BPIFB6
Hg19::chr9:140331458..140331471,-p@chr9:140331458..140331471
-
Hg19::chr9:140331478..140331491,-p@chr9:140331478..140331491
-


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:0005201extracellular matrix structural constituent0.0217237725185447
GO:0030414protease inhibitor activity0.023489932885906
GO:0004857enzyme inhibitor activity0.0236076769103968
GO:0007155cell adhesion0.033910279053338
GO:0022610biological adhesion0.033910279053338



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 trachea5.58e-252
tongue1.61e-163
gustatory system1.61e-163
future tongue1.61e-163
tonsil1.82e-131
mucosa-associated lymphoid tissue1.82e-131
lymphoid tissue1.82e-131
tonsillar ring1.82e-131
oral opening2.42e-1322
submandibular gland6.06e-131
submandibular gland primordium6.06e-131
foregut3.11e-1287
orifice2.11e-1136
chordate pharynx3.15e-1110
pharyngeal region of foregut3.15e-1110
subdivision of digestive tract1.79e-10118
pharynx2.94e-1011
mouth4.17e-1029
stomodeum4.17e-1029
digestive system5.46e-10145
digestive tract5.46e-10145
primitive gut5.46e-10145
respiratory system2.30e-0974
adult organism4.61e-09114
endoderm-derived structure6.67e-09160
endoderm6.67e-09160
presumptive endoderm6.67e-09160
saliva-secreting gland8.57e-096
gland of oral region8.57e-096
gland of foregut8.57e-096
oral gland8.57e-096
oral cavity8.57e-096
segment of respiratory tract1.01e-0847
trachea8.35e-087
respiratory airway8.35e-087
respiratory tract1.54e-0754
major salivary gland4.17e-072
throat4.69e-072
Disease
Ontology termp-valuen
signet ring cell adenocarcinoma5.28e-072


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)
MA0003.10.374947
MA0004.10.510805
MA0006.10.522608
MA0007.110.1928
MA0009.10.247013
MA0014.13.6815e-05
MA0017.10.957254
MA0019.12.50228
MA0024.10.179268
MA0025.10.344113
MA0027.11.7227
MA0028.10.206267
MA0029.10.558569
MA0030.10.184045
MA0031.10.146399
MA0038.10.0561953
MA0040.10.194748
MA0041.10.0315298
MA0042.10.0243105
MA0043.10.24723
MA0046.10.239588
MA0048.10.0837579
MA0050.10.0244947
MA0051.10.0547588
MA0052.10.197173
MA0055.10.85053
MA0056.10
MA0057.11.55379
MA0058.12.31311
MA0059.15.06651
MA0060.10.000516773
MA0061.10.122917
MA0063.10
MA0066.10.20618
MA0067.11.23427
MA0068.10.594877
MA0069.10.236979
MA0070.10.229464
MA0071.11.48939
MA0072.10.22647
MA0073.124.0992
MA0074.10.443106
MA0076.10.552661
MA0077.11.18148
MA0078.12.17157
MA0081.10.0107166
MA0083.10.252183
MA0084.10.656589
MA0087.10.224848
MA0088.11.33898
MA0089.10
MA0090.11.64916
MA0091.10.115952
MA0092.10.426145
MA0093.11.07299
MA0095.10
MA0098.10
MA0100.11.25551
MA0101.10.0290862
MA0103.11.67902
MA0105.10.323545
MA0106.15.31261
MA0107.10.30552
MA0108.20.144705
MA0109.10
MA0111.11.32154
MA0113.10.959234
MA0114.10.453617
MA0115.10.42937
MA0116.12.30531
MA0117.10.273271
MA0119.10.996978
MA0122.10.291885
MA0124.10.395861
MA0125.10.330489
MA0130.10
MA0131.10.684278
MA0132.10
MA0133.10
MA0135.10.268144
MA0136.10.0586412
MA0139.10.583451
MA0140.10.16556
MA0141.10.756874
MA0142.10.129252
MA0143.10.0779387
MA0144.10.0698001
MA0145.15.09337
MA0146.13.48773
MA0147.12.34686
MA0148.10.314662
MA0149.10.0402234
MA0062.20.196268
MA0035.20.0428087
MA0039.23.12449
MA0138.25.07114
MA0002.24.81045
MA0137.20.00650365
MA0104.21.36674
MA0047.20.0666578
MA0112.25.22272
MA0065.20.269935
MA0150.10.0141424
MA0151.10
MA0152.10.0449747
MA0153.10.317813
MA0154.113.1065
MA0155.10.192339
MA0156.10.00670135
MA0157.11.2199
MA0158.10
MA0159.10.72134
MA0160.10.340065
MA0161.10
MA0162.10.319829
MA0163.11.80066
MA0164.10.0830315
MA0080.20.533766
MA0018.20.25124
MA0099.20.0450826
MA0079.20.148297
MA0102.20.690195
MA0258.11.92676
MA0259.12.04356
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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C251&oldid=2568762"