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Coexpression cluster:C312: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.257041,0.171854,0.245434,1.31551,0.184223,1.30867,0.0986544,0.413163,0.129029,0.00944989,0.0548042,0.381903,0.0748266,0.31068,0.597213,0.215528,0.227456,1.65843,0.679055,0.0571902,0.463217,0.0163965,0.843538,0.349866,0.136856,0.412866,0.208277,0.0621526,0.368776,0.0906954,0.0474426,0.252701,0.183437,0.0305587,0.0509612,0.100228,0.00982223,0.235552,0.0382152,0.00197958,1.05123,0.163418,0.456284,0.88791,0.372946,0.29514,0.326545,0.743826,1.81301,0.188659,0.139988,0.341658,0.160553,0.308256,0.428303,0.64863,0.379014,0.0800554,0.423254,0.575431,0.281871,0.100296,0.129745,0.20909,0.109025,3.11765,0.502307,0.834098,1.27309,0.684258,0.151089,1.54174,0.00549875,0.426662,0.0074371,0.0217743,0.184138,0.198174,0.243236,0.131504,1.57308,1.13126,0.71495,0.42318,0.385048,2.30075e-05,1.15164,0.401189,1.46614,0.927861,0.583373,0.363684,0.730982,0.196104,0.0712326,0.389651,0.670782,1.45684,0.157427,0.0634941,0.921497,0.260534,0.291245,0.650718,0.179951,0.762483,1.1736,0.0917054,0.0339777,0.0127461,0.491796,0.289219,0.236911,0.463315,0.541356,0.72725,0.00821825,2.05166,0.54538,0.201231,0.419886,0.909353,0.231194,1.21488,0.639136,0.576709,0.653533,0.268089,0.45505,0.615082,0.364226,2.07722,0.467073,0.362733,0.594755,0.074833,0.173385,0.838668,0.557426,1.36861,0.977798,0.525027,0.657359,0.29275,0.181034,0.0764849,0.170865,1.21274,0.366412,0.190291,0.320589,9.57345e-06,0.955794,0.376944,0.328942,0.712168,0.145498,0.1656,0.0340611,0.506841,0.523979,0.923813,0.680507,1.19358,0.191069,0.35126,0.169514,1.10399,0.000231243
|tfbs_overrepresentation_jaspar=MA0003.1;4.20904e-06,MA0004.1;0.207099,MA0006.1;0.181728,MA0007.1;0.0501273,MA0009.1;0.332084,MA0014.1;0.000840624,MA0017.1;0.453168,MA0019.1;0.122811,MA0024.1;0.254518,MA0025.1;0.439186,MA0027.1;1.8466,MA0028.1;0.0801195,MA0029.1;0.739626,MA0030.1;0.260095,MA0031.1;1.15909,MA0038.1;1.11744,MA0040.1;0.272523,MA0041.1;0.227378,MA0042.1;0.0519308,MA0043.1;0.332327,MA0046.1;0.865123,MA0048.1;0.0969338,MA0050.1;0.753892,MA0051.1;0.664323,MA0052.1;0.755709,MA0055.1;0.0366635,MA0056.1;0,MA0057.1;0.0869805,MA0058.1;0.279956,MA0059.1;0.515441,MA0060.1;5.79051,MA0061.1;1.90872,MA0063.1;0,MA0066.1;0.32926,MA0067.1;0.597968,MA0068.1;0.000658324,MA0069.1;0.858527,MA0070.1;0.839437,MA0071.1;0.280207,MA0072.1;3.17376,MA0073.1;3.86678e-05,MA0074.1;0.0975962,MA0076.1;0.031919,MA0077.1;0.818719,MA0078.1;0.150427,MA0081.1;0.823617,MA0083.1;0.337888,MA0084.1;0.768496,MA0087.1;0.307032,MA0088.1;0.0232086,MA0089.1;0,MA0090.1;0.142663,MA0091.1;0.0575983,MA0092.1;0.386895,MA0093.1;0.364484,MA0095.1;0,MA0098.1;0,MA0100.1;0.106764,MA0101.1;1.68932,MA0103.1;0.169168,MA0105.1;0.203426,MA0106.1;0.383434,MA0107.1;0.866592,MA0108.2;1.80022,MA0109.1;0,MA0111.1;0.155179,MA0113.1;0.406016,MA0114.1;0.205078,MA0115.1;0.530757,MA0116.1;0.221217,MA0117.1;0.948959,MA0119.1;0.0239211,MA0122.1;0.382044,MA0124.1;0.494979,MA0125.1;0.42437,MA0130.1;0,MA0131.1;0.161082,MA0132.1;0,MA0133.1;0,MA0135.1;0.355725,MA0136.1;0.103403,MA0139.1;0.0307613,MA0140.1;0.982606,MA0141.1;0.0271979,MA0142.1;1.07776,MA0143.1;1.90179,MA0144.1;0.0268501,MA0145.1;0.114108,MA0146.1;0.000399001,MA0147.1;0.107681,MA0148.1;0.234511,MA0149.1;0.0768601,MA0062.2;0.0345451,MA0035.2;0.580816,MA0039.2;0.000217722,MA0138.2;0.151138,MA0002.2;0.217408,MA0137.2;0.0845704,MA0104.2;0.0551645,MA0047.2;0.367013,MA0112.2;0.0113131,MA0065.2;0.291904,MA0150.1;0.321767,MA0151.1;0,MA0152.1;0.0838926,MA0153.1;1.05663,MA0154.1;0.194783,MA0155.1;0.0223847,MA0156.1;0.0861658,MA0157.1;1.00872,MA0158.1;0,MA0159.1;1.59845,MA0160.1;0.0721072,MA0161.1;0,MA0162.1;0.00057372,MA0163.1;0.00107154,MA0164.1;0.423404,MA0080.2;0.364687,MA0018.2;0.385322,MA0099.2;0.285408,MA0079.2;3.61068e-11,MA0102.2;0.803155,MA0258.1;0.0728937,MA0259.1;0.427009,MA0442.1;0
}}
}}

Revision as of 19:03, 22 January 2013


Full id: C312_gall_squamous_small_chronic_thyroid_cholangiocellular_testicular



Phase1 CAGE Peaks

Hg19::chr12:127102703..127102711,-p@chr12:127102703..127102711
-
Hg19::chr13:102078188..102078192,+p@chr13:102078188..102078192
+
Hg19::chr13:87732242..87732246,-p@chr13:87732242..87732246
-
Hg19::chr13:91147974..91147980,+p@chr13:91147974..91147980
+
Hg19::chr14:38091563..38091607,+p@chr14:38091563..38091607
+
Hg19::chr17:47092049..47092091,+p@chr17:47092049..47092091
+
Hg19::chr17:67559529..67559532,+p@chr17:67559529..67559532
+
Hg19::chr18:2351165..2351175,+p@chr18:2351165..2351175
+
Hg19::chr18:2351233..2351242,+p@chr18:2351233..2351242
+
Hg19::chr18:35871337..35871346,+p@chr18:35871337..35871346
+
Hg19::chr18:61420275..61420297,+p7@SERPINB7
Hg19::chr18:61420303..61420306,+p17@SERPINB7
Hg19::chr18:61420311..61420320,+p13@SERPINB7
Hg19::chr18:61420321..61420328,+p14@SERPINB7
Hg19::chr19:28401158..28401162,-p@chr19:28401158..28401162
-
Hg19::chr21:28226981..28227000,+p@chr21:28226981..28227000
+
Hg19::chr3:145051912..145051917,+p@chr3:145051912..145051917
+
Hg19::chr3:145127555..145127558,+p@chr3:145127555..145127558
+
Hg19::chr4:117626532..117626537,+p@chr4:117626532..117626537
+
Hg19::chr4:159330456..159330459,+p@chr4:159330456..159330459
+
Hg19::chr4:189258158..189258183,-p@chr4:189258158..189258183
-
Hg19::chr4:190861941..190861951,+p3@FRG1
Hg19::chr5:18990592..18990594,-p@chr5:18990592..18990594
-
Hg19::chr5:19142450..19142468,-p1@ENST00000504827
Hg19::chr5:23443636..23443646,+p@chr5:23443636..23443646
+
Hg19::chr5:25649889..25649911,-p@chr5:25649889..25649911
-
Hg19::chr6:13191432..13191436,-p@chr6:13191432..13191436
-
Hg19::chr6:67772946..67772961,+p@chr6:67772946..67772961
+
Hg19::chr7:10125106..10125124,-p@chr7:10125106..10125124
-
Hg19::chr7:114026271..114026287,-p@chr7:114026271..114026287
-
Hg19::chr8:15939682..15939688,+p@chr8:15939682..15939688
+
Hg19::chr8:80289025..80289040,-p@chr8:80289025..80289040
-
Hg19::chr8:88823985..88824001,-p@chr8:88823985..88824001
-
Hg19::chrX:140336645..140336655,-p1@SPANXC
Hg19::chrX:140336680..140336697,-p2@SPANXC
Hg19::chrX:144329020..144329026,+p1@SPANXN1
Hg19::chrX:55115443..55115463,+p1@PAGE2
Hg19::chrX:55115467..55115475,+p2@PAGE2
Hg19::chrX:55115486..55115496,+p3@PAGE2


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
epithelial cell of gall bladder4.32e-262
Uber Anatomy
Ontology termp-valuen
testis1.11e-258
male reproductive organ5.14e-1911
gallbladder6.76e-183
gall bladder primordium6.76e-183
body cavity1.31e-1046
gonad1.69e-1021
indifferent external genitalia1.69e-1021
indifferent gonad1.69e-1021
gonad primordium1.69e-1021
external genitalia4.53e-1022
male organism4.53e-1022
male reproductive system4.53e-1022
body cavity or lining5.14e-1049
body cavity precursor3.61e-0954
anatomical cavity3.25e-0861
biliary system7.48e-079
biliary tree7.48e-079
biliary bud7.48e-079


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
MA0004.10.207099
MA0006.10.181728
MA0007.10.0501273
MA0009.10.332084
MA0014.10.000840624
MA0017.10.453168
MA0019.10.122811
MA0024.10.254518
MA0025.10.439186
MA0027.11.8466
MA0028.10.0801195
MA0029.10.739626
MA0030.10.260095
MA0031.11.15909
MA0038.11.11744
MA0040.10.272523
MA0041.10.227378
MA0042.10.0519308
MA0043.10.332327
MA0046.10.865123
MA0048.10.0969338
MA0050.10.753892
MA0051.10.664323
MA0052.10.755709
MA0055.10.0366635
MA0056.10
MA0057.10.0869805
MA0058.10.279956
MA0059.10.515441
MA0060.15.79051
MA0061.11.90872
MA0063.10
MA0066.10.32926
MA0067.10.597968
MA0068.10.000658324
MA0069.10.858527
MA0070.10.839437
MA0071.10.280207
MA0072.13.17376
MA0073.13.86678e-05
MA0074.10.0975962
MA0076.10.031919
MA0077.10.818719
MA0078.10.150427
MA0081.10.823617
MA0083.10.337888
MA0084.10.768496
MA0087.10.307032
MA0088.10.0232086
MA0089.10
MA0090.10.142663
MA0091.10.0575983
MA0092.10.386895
MA0093.10.364484
MA0095.10
MA0098.10
MA0100.10.106764
MA0101.11.68932
MA0103.10.169168
MA0105.10.203426
MA0106.10.383434
MA0107.10.866592
MA0108.21.80022
MA0109.10
MA0111.10.155179
MA0113.10.406016
MA0114.10.205078
MA0115.10.530757
MA0116.10.221217
MA0117.10.948959
MA0119.10.0239211
MA0122.10.382044
MA0124.10.494979
MA0125.10.42437
MA0130.10
MA0131.10.161082
MA0132.10
MA0133.10
MA0135.10.355725
MA0136.10.103403
MA0139.10.0307613
MA0140.10.982606
MA0141.10.0271979
MA0142.11.07776
MA0143.11.90179
MA0144.10.0268501
MA0145.10.114108
MA0146.10.000399001
MA0147.10.107681
MA0148.10.234511
MA0149.10.0768601
MA0062.20.0345451
MA0035.20.580816
MA0039.20.000217722
MA0138.20.151138
MA0002.20.217408
MA0137.20.0845704
MA0104.20.0551645
MA0047.20.367013
MA0112.20.0113131
MA0065.20.291904
MA0150.10.321767
MA0151.10
MA0152.10.0838926
MA0153.11.05663
MA0154.10.194783
MA0155.10.0223847
MA0156.10.0861658
MA0157.11.00872
MA0158.10
MA0159.11.59845
MA0160.10.0721072
MA0161.10
MA0162.10.00057372
MA0163.10.00107154
MA0164.10.423404
MA0080.20.364687
MA0018.20.385322
MA0099.20.285408
MA0079.23.61068e-11
MA0102.20.803155
MA0258.10.0728937
MA0259.10.427009
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.

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