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Coexpression cluster:C127: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:37, 17 September 2013


Full id: C127_maxillary_small_hepatoblastoma_hepatocellular_alveolar_colon_argyrophil



Phase1 CAGE Peaks

Hg19::chr10:111171762..111171773,-p@chr10:111171762..111171773
-
Hg19::chr10:115327155..115327166,+p5@HABP2
Hg19::chr10:115939099..115939117,+p2@TDRD1
Hg19::chr10:115999510..115999521,+p5@VWA2
Hg19::chr10:1895618..1895626,+p@chr10:1895618..1895626
+
Hg19::chr10:72576444..72576454,+p12@SGPL1
Hg19::chr10:72576468..72576497,+p2@SGPL1
Hg19::chr10:72576503..72576516,+p11@SGPL1
Hg19::chr10:72576547..72576568,+p10@SGPL1
Hg19::chr11:36489757..36489777,+p@chr11:36489757..36489777
+
Hg19::chr11:69633471..69633482,+p@chr11:69633471..69633482
+
Hg19::chr11:69633974..69633997,-p1@FGF3
Hg19::chr11:69634335..69634346,-p6@FGF3
Hg19::chr11:69634506..69634517,-p5@FGF3
Hg19::chr11:71939032..71939040,+p23@INPPL1
Hg19::chr11:78177177..78177186,-p@chr11:78177177..78177186
-
Hg19::chr12:130617921..130617932,+p@chr12:130617921..130617932
+
Hg19::chr12:130617944..130617953,+p@chr12:130617944..130617953
+
Hg19::chr12:130822499..130822514,+p5@PIWIL1
Hg19::chr12:130822519..130822529,+p7@PIWIL1
Hg19::chr12:79406759..79406766,+p@chr12:79406759..79406766
+
Hg19::chr12:79611340..79611358,+p1@AB384875
Hg19::chr12:79611372..79611384,+p2@AB384875
Hg19::chr12:92247545..92247559,-p@chr12:92247545..92247559
-
Hg19::chr12:92247594..92247605,-p@chr12:92247594..92247605
-
Hg19::chr12:92247611..92247618,-p@chr12:92247611..92247618
-
Hg19::chr12:92247626..92247635,-p@chr12:92247626..92247635
-
Hg19::chr12:92247725..92247764,+p@chr12:92247725..92247764
+
Hg19::chr13:101081145..101081150,+p@chr13:101081145..101081150
+
Hg19::chr14:106922517..106922528,-p@chr14:106922517..106922528
-
Hg19::chr14:51338763..51338776,+p3@ABHD12B
Hg19::chr14:51338801..51338814,+p2@ABHD12B
Hg19::chr14:51338816..51338857,+p1@ABHD12B
Hg19::chr14:61952109..61952155,+p@chr14:61952109..61952155
+
Hg19::chr14:79331180..79331190,+p@chr14:79331180..79331190
+
Hg19::chr14:79331221..79331232,+p@chr14:79331221..79331232
+
Hg19::chr14:79331250..79331261,+p@chr14:79331250..79331261
+
Hg19::chr14:79331318..79331327,+p@chr14:79331318..79331327
+
Hg19::chr14:79502968..79502972,+p@chr14:79502968..79502972
+
Hg19::chr15:46241272..46241278,+p@chr15:46241272..46241278
+
Hg19::chr15:46282024..46282028,+p@chr15:46282024..46282028
+
Hg19::chr15:46316623..46316627,+p@chr15:46316623..46316627
+
Hg19::chr15:46351173..46351177,+p@chr15:46351173..46351177
+
Hg19::chr15:46499592..46499596,+p@chr15:46499592..46499596
+
Hg19::chr15:46595297..46595301,+p@chr15:46595297..46595301
+
Hg19::chr15:67649625..67649632,+p10@IQCH
Hg19::chr15:67649672..67649692,+p4@IQCH
Hg19::chr16:50539857..50539869,+p@chr16:50539857..50539869
+
Hg19::chr16:50539874..50539887,+p@chr16:50539874..50539887
+
Hg19::chr16:50581680..50581691,+p@chr16:50581680..50581691
+
Hg19::chr16:50581702..50581732,+p@chr16:50581702..50581732
+
Hg19::chr16:50582222..50582230,+p2@NKD1
Hg19::chr16:50582298..50582316,+p1@NKD1
Hg19::chr16:68420720..68420727,-p@chr16:68420720..68420727
-
Hg19::chr17:17529513..17529535,-p@chr17:17529513..17529535
-
Hg19::chr17:17529540..17529545,-p@chr17:17529540..17529545
-
Hg19::chr17:69077405..69077409,+p@chr17:69077405..69077409
+
Hg19::chr17:79974342..79974365,+p@chr17:79974342..79974365
+
Hg19::chr17:908734..908738,+p3@BC129815
Hg19::chr17:908765..908774,+p2@BC129815
Hg19::chr18:37322033..37322043,+p@chr18:37322033..37322043
+
Hg19::chr18:8625916..8625925,+p@chr18:8625916..8625925
+
Hg19::chr19:36222531..36222539,+p@chr19:36222531..36222539
+
Hg19::chr19:46518842..46518860,+p@chr19:46518842..46518860
+
Hg19::chr19:46519977..46519985,-p@chr19:46519977..46519985
-
Hg19::chr19:46580353..46580358,-p1@AK057802
Hg19::chr19:46580361..46580396,-p2@ENST00000366172
p2@uc002pdz.1
Hg19::chr19:46580415..46580420,-p10@ENST00000366172
p10@uc002pdz.1
Hg19::chr19:46580452..46580460,-p9@ENST00000366172
p9@uc002pdz.1
Hg19::chr19:46580826..46580845,-p3@ENST00000366172
p3@uc002pdz.1
Hg19::chr19:46580912..46580923,-p4@ENST00000366172
p4@uc002pdz.1
Hg19::chr1:11000123..11000131,-p@chr1:11000123..11000131
-
Hg19::chr1:172613350..172613353,+p@chr1:172613350..172613353
+
Hg19::chr1:213822723..213822727,-p@chr1:213822723..213822727
-
Hg19::chr1:213822756..213822765,-p@chr1:213822756..213822765
-
Hg19::chr20:33565400..33565413,+p7@MYH7B
Hg19::chr20:36470640..36470649,+p6@CTNNBL1
Hg19::chr20:36470708..36470717,+p10@CTNNBL1
Hg19::chr20:36470727..36470734,+p11@CTNNBL1
Hg19::chr20:5681874..5681885,+p@chr20:5681874..5681885
+
Hg19::chr21:46193671..46193689,-p9@UBE2G2
Hg19::chr21:46194934..46194979,-p17@UBE2G2
Hg19::chr2:175389279..175389282,+p@chr2:175389279..175389282
+
Hg19::chr2:223043326..223043344,-p@chr2:223043326..223043344
-
Hg19::chr2:99909329..99909333,-p@chr2:99909329..99909333
-
Hg19::chr3:11675723..11675735,-p@chr3:11675723..11675735
-
Hg19::chr3:11675748..11675759,-p@chr3:11675748..11675759
-
Hg19::chr3:11675763..11675778,-p@chr3:11675763..11675778
-
Hg19::chr3:129690202..129690210,-p@chr3:129690202..129690210
-
Hg19::chr3:137483141..137483162,+p1@SOX14
Hg19::chr3:193656555..193656579,-p@chr3:193656555..193656579
-
Hg19::chr3:193678383..193678395,+p@chr3:193678383..193678395
+
Hg19::chr3:195943343..195943360,+p3@OSTalpha
Hg19::chr3:52643526..52643537,-p8@PBRM1
Hg19::chr3:86926149..86926150,+p@chr3:86926149..86926150
+
Hg19::chr3:95928627..95928643,-p@chr3:95928627..95928643
-
Hg19::chr3:95928653..95928656,-p@chr3:95928653..95928656
-
Hg19::chr3:95928667..95928672,-p@chr3:95928667..95928672
-
Hg19::chr3:95928676..95928681,-p@chr3:95928676..95928681
-
Hg19::chr3:95928689..95928701,-p@chr3:95928689..95928701
-
Hg19::chr4:16460563..16460585,+p@chr4:16460563..16460585
+
Hg19::chr5:115481500..115481504,+p@chr5:115481500..115481504
+
Hg19::chr5:146939412..146939419,+p2@LOC153469
Hg19::chr5:146939429..146939436,+p3@LOC153469
Hg19::chr5:16737865..16737876,-p@chr5:16737865..16737876
-
Hg19::chr5:175298205..175298209,-p@chr5:175298205..175298209
-
Hg19::chr5:175298256..175298267,-p@chr5:175298256..175298267
-
Hg19::chr6:138428938..138428953,-p8@PERP
Hg19::chr6:138428975..138428985,-p13@PERP
Hg19::chr6:56507200..56507216,-p@chr6:56507200..56507216
-
Hg19::chr6:56507254..56507276,-p@chr6:56507254..56507276
-
Hg19::chr7:120778392..120778412,-p@chr7:120778392..120778412
-
Hg19::chr7:120789549..120789552,+p44@C7orf58
Hg19::chr7:120789556..120789585,+p11@C7orf58
Hg19::chr7:120789593..120789628,+p10@C7orf58
Hg19::chr7:123634848..123634862,+p1@uc010lkv.1
Hg19::chr7:47728559..47728598,+p@chr7:47728559..47728598
+
Hg19::chr7:80086544..80086546,-p@chr7:80086544..80086546
-
Hg19::chr7:80141328..80141339,-p2@GNAT3
Hg19::chr7:80141358..80141392,-p1@GNAT3
Hg19::chr7:80141406..80141411,-p3@GNAT3
Hg19::chr7:93169246..93169258,+p@chr7:93169246..93169258
+
Hg19::chr8:117816627..117816634,+p@chr8:117816627..117816634
+
Hg19::chr8:117816648..117816663,+p@chr8:117816648..117816663
+
Hg19::chr8:48079099..48079105,-p@chr8:48079099..48079105
-
Hg19::chr8:48079110..48079116,-p@chr8:48079110..48079116
-
Hg19::chr8:74985038..74985063,+p@chr8:74985038..74985063
+
Hg19::chr9:11935598..11935637,+p@chr9:11935598..11935637
+
Hg19::chr9:135932153..135932160,+p@chr9:135932153..135932160
+
Hg19::chr9:140335777..140335785,-p3@ENTPD8
Hg19::chr9:140335789..140335818,-p1@ENTPD8
Hg19::chr9:140348364..140348386,-p@chr9:140348364..140348386
-
Hg19::chr9:140348397..140348421,-p@chr9:140348397..140348421
-
Hg19::chr9:140348438..140348460,-p@chr9:140348438..140348460
-
Hg19::chrX:10645724..10645735,-p12@MID1
Hg19::chrX:11455274..11455297,-p@chrX:11455274..11455297
-
Hg19::chrX:11460430..11460434,-p@chrX:11460430..11460434
-
Hg19::chrX:11502792..11502801,-p@chrX:11502792..11502801
-
Hg19::chrX:11502822..11502831,-p@chrX:11502822..11502831
-
Hg19::chrX:11503012..11503022,-p@chrX:11503012..11503022
-
Hg19::chrX:151620193..151620201,-p4@GABRA3


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

Uber Anatomy
Ontology termp-valuen
maxillary sinus9.37e-991
paranasal sinus9.37e-991
Disease
Ontology termp-valuen
paranasal sinus cancer9.37e-991
maxillary sinus cancer9.37e-991
lung small cell carcinoma7.14e-264
respiratory system cancer7.63e-2616
bronchus cancer1.91e-157
bronchogenic carcinoma1.91e-157
lung carcinoma2.45e-129
lung cancer5.93e-0815


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)
MA0003.16.22053e-05
MA0004.10.454186
MA0006.10.00760704
MA0007.10.260564
MA0009.10.403855
MA0014.10.000163729
MA0017.10.532149
MA0019.10.606462
MA0024.10.101461
MA0025.11.07737
MA0027.11.29654
MA0028.10.00424248
MA0029.10.275146
MA0030.10.78158
MA0031.11.24161
MA0038.10.661073
MA0040.10.0283962
MA0041.10.942841
MA0042.10.568447
MA0043.10.0477117
MA0046.10.170565
MA0048.10.148332
MA0050.10.0986488
MA0051.10.0817223
MA0052.10.120708
MA0055.13.11752e-05
MA0056.10
MA0057.10.122252
MA0058.10.673715
MA0059.10.850294
MA0060.10.00583527
MA0061.10.1011
MA0063.10
MA0066.10.459039
MA0067.10.186693
MA0068.10.0309756
MA0069.10.380024
MA0070.10.362367
MA0071.10.119319
MA0072.10.154556
MA0073.10.000108236
MA0074.10.641227
MA0076.10.00171159
MA0077.10.969146
MA0078.10.791832
MA0081.10.851428
MA0083.10.049764
MA0084.10.308852
MA0087.10.15261
MA0088.10.663723
MA0089.10
MA0090.11.0827
MA0091.10.00860926
MA0092.10.844365
MA0093.10.963711
MA0095.10
MA0098.10
MA0100.10.0017642
MA0101.10.0202807
MA0103.13.89517
MA0105.10.0164424
MA0106.10.00260729
MA0107.10.121542
MA0108.20.586024
MA0109.10
MA0111.10.954994
MA0113.10.651066
MA0114.10.408217
MA0115.10.144573
MA0116.10.262976
MA0117.10.21381
MA0119.10.430946
MA0122.10.513571
MA0124.10.391442
MA0125.10.293279
MA0130.10
MA0131.10.0999496
MA0132.10
MA0133.10
MA0135.10.0566312
MA0136.10.309908
MA0139.10.0176407
MA0140.10.116203
MA0141.10.101711
MA0142.10.148052
MA0143.10.910473
MA0144.10.0508213
MA0145.12.58376
MA0146.10.00092196
MA0147.10.138564
MA0148.12.56995
MA0149.10.470569
MA0062.20.000609704
MA0035.20.702364
MA0039.20.704969
MA0138.20.190279
MA0002.20.959694
MA0137.20.0955066
MA0104.20.0212216
MA0047.22.08291
MA0112.20.237244
MA0065.20.0582188
MA0150.11.53494
MA0151.10
MA0152.10.222288
MA0153.10.0803324
MA0154.10.00526352
MA0155.10.188564
MA0156.10.0135511
MA0157.10.122472
MA0158.10
MA0159.10.76039
MA0160.10.285507
MA0161.10
MA0162.10.000551796
MA0163.10.0857695
MA0164.10.696687
MA0080.20.257089
MA0018.20.125708
MA0099.20.357676
MA0079.25.43013e-07
MA0102.20.335846
MA0258.10.147417
MA0259.10.160921
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

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