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Coexpression cluster:C154: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:44, 17 September 2013


Full id: C154_adenocarcinoma_Mesenchymal_Cardiac_small_sacrococcigeal_Smooth_Prostate



Phase1 CAGE Peaks

Hg19::chr10:118885954..118885990,-p16@KIAA1598
Hg19::chr10:14504151..14504156,-p41@FRMD4A
Hg19::chr10:20659504..20659530,+p@chr10:20659504..20659530
+
Hg19::chr10:78078088..78078092,+p6@C10orf11
Hg19::chr10:78078781..78078813,+p@chr10:78078781..78078813
+
Hg19::chr11:1853010..1853019,+p@chr11:1853010..1853019
+
Hg19::chr11:1853029..1853045,+p9@SYT8
Hg19::chr11:32418017..32418035,-p@chr11:32418017..32418035
-
Hg19::chr11:45274072..45274078,-p@chr11:45274072..45274078
-
Hg19::chr11:45274102..45274110,-p@chr11:45274102..45274110
-
Hg19::chr11:64068136..64068191,+p2@C11orf20
Hg19::chr11:64068193..64068201,+p4@C11orf20
Hg19::chr11:74203338..74203363,+p@chr11:74203338..74203363
+
Hg19::chr12:116356689..116356694,-p@chr12:116356689..116356694
-
Hg19::chr12:127841607..127841612,-p@chr12:127841607..127841612
-
Hg19::chr12:130554803..130554831,+p1@ENST00000535487
Hg19::chr12:4067801..4067810,-p@chr12:4067801..4067810
-
Hg19::chr12:51422113..51422122,-p13@SLC11A2
Hg19::chr13:23993097..23993108,+p1@SACS-AS1
Hg19::chr14:46185170..46185184,-p1@ENST00000555442
Hg19::chr15:66874502..66874507,+p1@ENST00000558797
p1@uc002aqe.2
Hg19::chr15:79550146..79550153,+p@chr15:79550146..79550153
+
Hg19::chr16:49601912..49601949,-p@chr16:49601912..49601949
-
Hg19::chr16:68415381..68415397,-p@chr16:68415381..68415397
-
Hg19::chr16:68415402..68415427,-p@chr16:68415402..68415427
-
Hg19::chr17:41319358..41319362,-p@chr17:41319358..41319362
-
Hg19::chr17:7945494..7945505,+p@chr17:7945494..7945505
+
Hg19::chr17:7945517..7945524,+p@chr17:7945517..7945524
+
Hg19::chr18:19664761..19664775,+p@chr18:19664761..19664775
+
Hg19::chr18:55562609..55562633,-p@chr18:55562609..55562633
-
Hg19::chr19:14911558..14911572,-p@chr19:14911558..14911572
-
Hg19::chr19:35298485..35298515,-p@chr19:35298485..35298515
-
Hg19::chr19:40729176..40729179,-p@chr19:40729176..40729179
-
Hg19::chr19:6573965..6573973,-p@chr19:6573965..6573973
-
Hg19::chr1:171183141..171183168,-p@chr1:171183141..171183168
-
Hg19::chr1:20509818..20509830,+p@chr1:20509818..20509830
+
Hg19::chr1:210730983..210730994,-p@chr1:210730983..210730994
-
Hg19::chr1:229972086..229972113,-p@chr1:229972086..229972113
-
Hg19::chr1:53925063..53925076,+p2@DMRTB1
Hg19::chr1:53925386..53925397,+p4@DMRTB1
Hg19::chr1:53926206..53926223,+p@chr1:53926206..53926223
+
Hg19::chr1:66713214..66713221,+p@chr1:66713214..66713221
+
Hg19::chr1:6784296..6784306,-p@chr1:6784296..6784306
-
Hg19::chr21:45232916..45232945,-p5@LOC284837
Hg19::chr22:32009392..32009402,+p14@SFI1
Hg19::chr22:32009407..32009413,+p17@SFI1
Hg19::chr22:40289822..40289826,+p@chr22:40289822..40289826
+
Hg19::chr22:48786318..48786324,-p@chr22:48786318..48786324
-
Hg19::chr2:101855021..101855022,+p@chr2:101855021..101855022
+
Hg19::chr2:108856421..108856429,+p@chr2:108856421..108856429
+
Hg19::chr2:108905228..108905241,+p5@SULT1C2
Hg19::chr2:108932073..108932081,-p@chr2:108932073..108932081
-
Hg19::chr2:11720189..11720191,-p@chr2:11720189..11720191
-
Hg19::chr2:145425540..145425556,+p1@ENST00000431734
p1@ENST00000445791
p1@ENST00000451027
p1@uc002twc.2
Hg19::chr2:160522..160528,-p@chr2:160522..160528
-
Hg19::chr2:178509557..178509590,+p@chr2:178509557..178509590
+
Hg19::chr2:33208767..33208789,+p@chr2:33208767..33208789
+
Hg19::chr3:106851639..106851650,-p@chr3:106851639..106851650
-
Hg19::chr3:20422728..20422736,+p@chr3:20422728..20422736
+
Hg19::chr4:17654780..17654789,-p@chr4:17654780..17654789
-
Hg19::chr4:185269961..185269964,-p@chr4:185269961..185269964
-
Hg19::chr4:2038237..2038246,+p@chr4:2038237..2038246
+
Hg19::chr4:27079602..27079607,+p@chr4:27079602..27079607
+
Hg19::chr4:56683266..56683270,+p@chr4:56683266..56683270
+
Hg19::chr4:87587967..87588007,+p@chr4:87587967..87588007
+
Hg19::chr5:108342105..108342113,+p@chr5:108342105..108342113
+
Hg19::chr5:127132..127168,+p@chr5:127132..127168
+
Hg19::chr5:133842199..133842211,+p2@ENST00000515627
Hg19::chr5:180455151..180455156,-p@chr5:180455151..180455156
-
Hg19::chr5:33297946..33297962,-p1@ENST00000510327
Hg19::chr5:92899690..92899725,-p@chr5:92899690..92899725
-
Hg19::chr6:30899924..30899954,-p1@SFTA2
Hg19::chr6:30899962..30899981,-p3@SFTA2
Hg19::chr6:32185040..32185049,-p@chr6:32185040..32185049
-
Hg19::chr6:32185064..32185097,+p@chr6:32185064..32185097
+
Hg19::chr6:32186154..32186158,-p@chr6:32186154..32186158
-
Hg19::chr6:39909704..39909749,+p@chr6:39909704..39909749
+
Hg19::chr7:128481478..128481523,+p7@FLNC
Hg19::chr7:138414274..138414282,-p@chr7:138414274..138414282
-
Hg19::chr7:138414322..138414330,-p@chr7:138414322..138414330
-
Hg19::chr7:1516517..1516531,-p@chr7:1516517..1516531
-
Hg19::chr7:155754053..155754062,+p@chr7:155754053..155754062
+
Hg19::chr7:34697812..34697844,+p1@NPSR1
Hg19::chr7:34697846..34697874,+p2@NPSR1
Hg19::chr7:34890932..34890934,+p@chr7:34890932..34890934
+
Hg19::chr7:44233871..44233878,+p@chr7:44233871..44233878
+
Hg19::chr7:81399329..81399345,-p3@HGF
Hg19::chr7:81399355..81399373,-p1@HGF
Hg19::chr7:81399905..81399916,-p13@HGF
Hg19::chr7:81500953..81500994,+p@chr7:81500953..81500994
+
Hg19::chr7:81631574..81631599,+p@chr7:81631574..81631599
+
Hg19::chr7:95115174..95115187,+p2@ASB4
Hg19::chr7:95115210..95115217,+p3@ASB4
Hg19::chr8:144822864..144822887,-p@chr8:144822864..144822887
-
Hg19::chr8:19930258..19930259,-p@chr8:19930258..19930259
-
Hg19::chr8:28102617..28102623,-p@chr8:28102617..28102623
-
Hg19::chr8:60149243..60149248,-p@chr8:60149243..60149248
-
Hg19::chr8:60441483..60441488,+p@chr8:60441483..60441488
+
Hg19::chr8:60441494..60441507,+p@chr8:60441494..60441507
+
Hg19::chr8:82351669..82351674,+p3@ENST00000524085
Hg19::chr9:139259676..139259683,-p@chr9:139259676..139259683
-
Hg19::chrX:31090138..31090151,-p2@FTHL17
Hg19::chrX:31090152..31090184,-p1@FTHL17
Hg19::chrX:41887620..41887656,+p@chrX:41887620..41887656
+
Hg19::chrX:43036245..43036248,+p1@ENST00000440955
p1@uc004dfw.1
Hg19::chrX:49460578..49460597,-p1@PAGE1
Hg19::chrX:49460603..49460612,-p2@PAGE1
Hg19::chrX:52572878..52572895,+p@chrX:52572878..52572895
+
Hg19::chrX:55101450..55101482,+p1@PAGE2B
Hg19::chrX:55101495..55101519,+p2@PAGE2B
Hg19::chrX:70886748..70886757,-p@chrX:70886748..70886757
-


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:0006826iron ion transport0.031978858554635



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><br>disease_data<br>

Disease
Ontology termp-valuen
adenocarcinoma2.15e-0925


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)
MA0003.12.99403e-11
MA0004.15.30578
MA0006.10.203572
MA0007.10.122597
MA0009.12.61289
MA0014.10.00154264
MA0017.10.81233
MA0019.10.671672
MA0024.10.0451994
MA0025.10.4335
MA0027.11.39806
MA0028.10.0220747
MA0029.10.421856
MA0030.10.0474082
MA0031.10.553633
MA0038.11.39432
MA0040.10.0524996
MA0041.10.0353191
MA0042.10.0063201
MA0043.10.0800788
MA0046.12.54908
MA0048.10.098091
MA0050.10.232473
MA0051.10.513948
MA0052.10.438484
MA0055.10.219417
MA0056.10
MA0057.10.0224537
MA0058.16.5488
MA0059.15.00082
MA0060.13.02841
MA0061.10.143737
MA0063.10
MA0066.10.0830069
MA0067.10.249504
MA0068.10.125262
MA0069.11.39732
MA0070.10.0702856
MA0071.10.41491
MA0072.10.242182
MA0073.13.09596e-05
MA0074.11.03693
MA0076.10.203104
MA0077.10.234399
MA0078.10.168469
MA0081.10.751833
MA0083.10.282188
MA0084.10.384661
MA0087.10.515034
MA0088.10.441062
MA0089.10
MA0090.10.0320285
MA0091.10.264343
MA0092.10.308568
MA0093.19.15842
MA0095.10
MA0098.10
MA0100.10.569667
MA0101.10.326014
MA0103.11.87101
MA0105.10.394282
MA0106.10.944017
MA0107.10.635499
MA0108.20.297264
MA0109.10
MA0111.10.787503
MA0113.10.269079
MA0114.11.13618
MA0115.10.582064
MA0116.10.0767083
MA0117.10.651275
MA0119.11.93346
MA0122.10.346133
MA0124.10.176386
MA0125.10.4104
MA0130.10
MA0131.10.0157595
MA0132.10
MA0133.10
MA0135.10.636736
MA0136.10.191493
MA0139.10.914985
MA0140.10.613061
MA0141.10.552571
MA0142.10.775437
MA0143.10.715083
MA0144.10.505805
MA0145.10.126365
MA0146.10.006325
MA0147.11.2669
MA0148.10.184353
MA0149.10.0508638
MA0062.20.254286
MA0035.20.405775
MA0039.20.0157951
MA0138.21.58222
MA0002.20.0164875
MA0137.20.265784
MA0104.21.21551
MA0047.20.394868
MA0112.20.0343346
MA0065.20.532904
MA0150.10.0674242
MA0151.10
MA0152.10.892079
MA0153.10.389095
MA0154.11.04281
MA0155.10.0765515
MA0156.10.272565
MA0157.10.42359
MA0158.10
MA0159.10.405304
MA0160.10.352539
MA0161.10
MA0162.15.38662e-08
MA0163.10.0707272
MA0164.10.757991
MA0080.20.442743
MA0018.20.427123
MA0099.20.259762
MA0079.24.24712e-11
MA0102.20.413769
MA0258.10.243343
MA0259.10.931138
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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