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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:48, 17 September 2013


Full id: C170_epitheloid_cervical_Hep2_keratoacanthoma_adult_neuroblastoma_signet



Phase1 CAGE Peaks

Hg19::chr10:1999815..1999826,+p@chr10:1999815..1999826
+
Hg19::chr10:2000003..2000019,+p@chr10:2000003..2000019
+
Hg19::chr10:63590622..63590636,-p@chr10:63590622..63590636
-
Hg19::chr10:63590639..63590661,-p@chr10:63590639..63590661
-
Hg19::chr10:89577636..89577647,-p9@ATAD1
Hg19::chr10:89577654..89577665,-p6@ATAD1
Hg19::chr11:66475681..66475728,-p@chr11:66475681..66475728
-
Hg19::chr11:66475737..66475745,-p@chr11:66475737..66475745
-
Hg19::chr11:66475770..66475777,-p@chr11:66475770..66475777
-
Hg19::chr11:72300830..72300878,-p@chr11:72300830..72300878
-
Hg19::chr11:72301355..72301374,-p4@PDE2A
Hg19::chr11:72301384..72301401,-p7@PDE2A
Hg19::chr11:72301425..72301432,-p15@PDE2A
Hg19::chr11:72301477..72301479,-p27@PDE2A
Hg19::chr12:10541596..10541616,-p2@KLRK1
Hg19::chr12:85316556..85316560,-p@chr12:85316556..85316560
-
Hg19::chr13:70514222..70514227,-p@chr13:70514222..70514227
-
Hg19::chr13:70514320..70514334,-p@chr13:70514320..70514334
-
Hg19::chr13:70514340..70514354,-p@chr13:70514340..70514354
-
Hg19::chr13:70514370..70514381,-p@chr13:70514370..70514381
-
Hg19::chr13:70514386..70514397,-p@chr13:70514386..70514397
-
Hg19::chr13:70554567..70554578,-p@chr13:70554567..70554578
-
Hg19::chr13:70554586..70554595,-p@chr13:70554586..70554595
-
Hg19::chr14:105155318..105155331,+p@chr14:105155318..105155331
+
Hg19::chr14:84327175..84327181,-p@chr14:84327175..84327181
-
Hg19::chr15:59576402..59576407,+p@chr15:59576402..59576407
+
Hg19::chr16:55813534..55813565,+p@chr16:55813534..55813565
+
Hg19::chr16:80966884..80966898,-p@chr16:80966884..80966898
-
Hg19::chr17:54872813..54872818,-p@chr17:54872813..54872818
-
Hg19::chr17:79106695..79106706,-p@chr17:79106695..79106706
-
Hg19::chr17:79106720..79106733,-p@chr17:79106720..79106733
-
Hg19::chr17:9739620..9739632,+p10@GLP2R
Hg19::chr17:9739653..9739669,+p9@GLP2R
Hg19::chr18:7038300..7038315,-p@chr18:7038300..7038315
-
Hg19::chr18:7038601..7038616,-p@chr18:7038601..7038616
-
Hg19::chr19:3562547..3562565,+p@chr19:3562547..3562565
+
Hg19::chr1:566871..566878,+p7@uc001aaz.2
Hg19::chr20:30182835..30182854,-p@chr20:30182835..30182854
-
Hg19::chr22:44311788..44311792,+p@chr22:44311788..44311792
+
Hg19::chr2:101972682..101972687,-p@chr2:101972682..101972687
-
Hg19::chr2:196548512..196548526,+p@chr2:196548512..196548526
+
Hg19::chr2:196548540..196548552,+p@chr2:196548540..196548552
+
Hg19::chr2:196548561..196548568,+p@chr2:196548561..196548568
+
Hg19::chr2:236658628..236658665,+p@chr2:236658628..236658665
+
Hg19::chr2:35400133..35400142,+p@chr2:35400133..35400142
+
Hg19::chr3:163231215..163231229,+p@chr3:163231215..163231229
+
Hg19::chr3:194451183..194451188,-p@chr3:194451183..194451188
-
Hg19::chr4:134084347..134084372,+p@chr4:134084347..134084372
+
Hg19::chr4:134189435..134189459,-p@chr4:134189435..134189459
-
Hg19::chr4:139173379..139173390,-p@chr4:139173379..139173390
-
Hg19::chr4:24323024..24323033,+p@chr4:24323024..24323033
+
Hg19::chr4:24323043..24323048,+p@chr4:24323043..24323048
+
Hg19::chr4:24330893..24330900,+p@chr4:24330893..24330900
+
Hg19::chr4:40337318..40337324,+p3@CHRNA9
Hg19::chr4:40337340..40337361,+p1@CHRNA9
Hg19::chr4:40337622..40337640,+p@chr4:40337622..40337640
+
Hg19::chr4:40337654..40337672,+p@chr4:40337654..40337672
+
Hg19::chr4:40337763..40337778,+p@chr4:40337763..40337778
+
Hg19::chr5:24271923..24271937,-p@chr5:24271923..24271937
-
Hg19::chr5:24283569..24283574,+p@chr5:24283569..24283574
+
Hg19::chr5:24491789..24491800,-p@chr5:24491789..24491800
-
Hg19::chr5:24491801..24491822,-p@chr5:24491801..24491822
-
Hg19::chr5:24491824..24491833,-p@chr5:24491824..24491833
-
Hg19::chr5:93807303..93807310,-p@chr5:93807303..93807310
-
Hg19::chr5:93807316..93807323,-p@chr5:93807316..93807323
-
Hg19::chr5:93807324..93807335,-p@chr5:93807324..93807335
-
Hg19::chr5:93807345..93807355,-p@chr5:93807345..93807355
-
Hg19::chr5:93807360..93807369,-p@chr5:93807360..93807369
-
Hg19::chr5:93807403..93807440,-p@chr5:93807403..93807440
-
Hg19::chr5:93807668..93807674,+p@chr5:93807668..93807674
+
Hg19::chr5:93855989..93856033,-p@chr5:93855989..93856033
-
Hg19::chr5:93856207..93856217,-p@chr5:93856207..93856217
-
Hg19::chr5:93856477..93856488,-p@chr5:93856477..93856488
-
Hg19::chr5:93953956..93953975,+p5@ANKRD32
Hg19::chr5:93953985..93954006,+p6@ANKRD32
Hg19::chr5:93954039..93954052,+p8@ANKRD32
Hg19::chr6:116866825..116866854,-p1@BET3L
Hg19::chr6:1588346..1588354,-p@chr6:1588346..1588354
-
Hg19::chr7:23948330..23948341,+p@chr7:23948330..23948341
+
Hg19::chr7:35289253..35289269,-p@chr7:35289253..35289269
-
Hg19::chr7:35289275..35289284,-p@chr7:35289275..35289284
-
Hg19::chr8:113988208..113988215,-p@chr8:113988208..113988215
-
Hg19::chr8:113988241..113988248,-p@chr8:113988241..113988248
-
Hg19::chr8:128218609..128218622,-p@chr8:128218609..128218622
-
Hg19::chr8:128221170..128221174,-p@chr8:128221170..128221174
-
Hg19::chr8:128221586..128221596,-p@chr8:128221586..128221596
-
Hg19::chr8:128221667..128221675,-p@chr8:128221667..128221675
-
Hg19::chr8:128221810..128221842,-p@chr8:128221810..128221842
-
Hg19::chr8:128240943..128240952,-p8@uc003ysb.2
Hg19::chr8:27749619..27749626,+p@chr8:27749619..27749626
+
Hg19::chr9:130487143..130487164,-p3@PTRH1
Hg19::chr9:138026348..138026371,+p@chr9:138026348..138026371
+
Hg19::chr9:33442625..33442633,+p@chr9:33442625..33442633
+
Hg19::chr9:33442964..33442978,-p4@AQP3
Hg19::chr9:33442986..33443001,-p3@AQP3
Hg19::chr9:33443031..33443039,-p25@AQP3
Hg19::chr9:33443052..33443089,-p2@AQP3
Hg19::chr9:33443092..33443120,-p8@AQP3
Hg19::chr9:33443132..33443142,-p26@AQP3
Hg19::chrX:39813397..39813401,+p@chrX:39813397..39813401
+
Hg19::chrX:47360213..47360218,+p@chrX:47360213..47360218
+


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:0004118cGMP-stimulated cyclic-nucleotide phosphodiesterase activity0.0166902154715648
GO:0002223stimulatory C-type lectin receptor signaling pathway0.0166902154715648
GO:0032394MHC class Ib receptor activity0.0166902154715648
GO:0004045aminoacyl-tRNA hydrolase activity0.0200259002886925
GO:0002220innate immune response activating cell surface receptor signaling pathway0.0200259002886925
GO:0032729positive regulation of interferon-gamma production0.0272951869353158
GO:0002218activation of innate immune response0.0272951869353158
GO:0002758innate immune response-activating signal transduction0.0272951869353158
GO:0001912positive regulation of leukocyte mediated cytotoxicity0.0272951869353158
GO:0045954positive regulation of natural killer cell mediated cytotoxicity0.0272951869353158
GO:0032649regulation of interferon-gamma production0.0272951869353158
GO:0042269regulation of natural killer cell mediated cytotoxicity0.0275064492554069
GO:0045429positive regulation of nitric oxide biosynthetic process0.0275064492554069
GO:0045428regulation of nitric oxide biosynthetic process0.0275064492554069
GO:0001910regulation of leukocyte mediated cytotoxicity0.0275064492554069
GO:0031341regulation of cell killing0.0275064492554069
GO:0045089positive regulation of innate immune response0.0275064492554069
GO:0042267natural killer cell mediated cytotoxicity0.0275064492554069
GO:0045088regulation of innate immune response0.0275064492554069
GO:0002228natural killer cell mediated immunity0.0275064492554069
GO:0001909leukocyte mediated cytotoxicity0.0333293770332215
GO:0001906cell killing0.0374778972836357
GO:0030101natural killer cell activation0.0374778972836357
GO:0032609interferon-gamma production0.0374778972836357
GO:0046209nitric oxide metabolic process0.0410230695087342
GO:0006809nitric oxide biosynthetic process0.0410230695087342
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0410230695087342
GO:0001819positive regulation of cytokine production0.0410230695087342



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
larynx2.42e-339
upper respiratory tract2.80e-1619
respiratory primordium1.60e-0838
endoderm of foregut1.60e-0838
segment of respiratory tract5.10e-0747
Disease
Ontology termp-valuen
carcinoma1.24e-11106
cell type cancer1.02e-08143


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)
MA0003.11.07731e-08
MA0004.10.0980935
MA0006.10.0576384
MA0007.10.442432
MA0009.10.644758
MA0014.16.44188e-06
MA0017.10.578852
MA0019.11.10393
MA0024.10.0551442
MA0025.10.158938
MA0027.11.43407
MA0028.10.0139993
MA0029.11.25939
MA0030.10.799865
MA0031.10.352217
MA0038.10.400288
MA0040.11.28112
MA0041.11.74373
MA0042.12.2219
MA0043.10.645397
MA0046.10.0892796
MA0048.10.0222041
MA0050.10.172599
MA0051.10.0357274
MA0052.10.0647107
MA0055.10.00852463
MA0056.10
MA0057.10.00506479
MA0058.10.070833
MA0059.10.227361
MA0060.18.07473e-05
MA0061.10.30528
MA0063.10
MA0066.10.62744
MA0067.10.751674
MA0068.10.0980849
MA0069.10.0876974
MA0070.10.998604
MA0071.10.503238
MA0072.10.0814142
MA0073.10.879734
MA0074.10.219489
MA0076.10.00340202
MA0077.10.569385
MA0078.10.205674
MA0081.10.0698114
MA0083.10.320816
MA0084.10.412815
MA0087.12.00893
MA0088.10.0608508
MA0089.10
MA0090.12.07756
MA0091.11.61985
MA0092.10.246592
MA0093.10.112267
MA0095.10
MA0098.10
MA0100.10.0081543
MA0101.10.58914
MA0103.10.160539
MA0105.10.138348
MA0106.10.0108428
MA0107.10.368367
MA0108.20.977526
MA0109.10
MA0111.10.0210058
MA0113.10.325182
MA0114.10.243774
MA0115.10.222871
MA0116.10.0693696
MA0117.10.110456
MA0119.12.61927
MA0122.10.122713
MA0124.10.197118
MA0125.10.149246
MA0130.10
MA0131.10.0207703
MA0132.10
MA0133.10
MA0135.11.16608
MA0136.10.238167
MA0139.10.00096261
MA0140.11.00953
MA0141.10.346808
MA0142.10.303632
MA0143.10.163033
MA0144.10.197447
MA0145.10.131559
MA0146.11.05357
MA0147.10.0187174
MA0148.10.123864
MA0149.10.0220265
MA0062.29.77699e-05
MA0035.21.68639
MA0039.20.164608
MA0138.20.0180274
MA0002.20.0156582
MA0137.20.144565
MA0104.20.00398444
MA0047.20.472389
MA0112.20.00811577
MA0065.20.0760517
MA0150.11.08789
MA0151.10
MA0152.11.73876
MA0153.11.37908
MA0154.10.174016
MA0155.10.00985783
MA0156.10.0829182
MA0157.10.493975
MA0158.10
MA0159.10.0746886
MA0160.11.20488
MA0161.10
MA0162.17.14955e-08
MA0163.11.11425e-05
MA0164.10.582714
MA0080.20.1124
MA0018.20.297951
MA0099.21.74134
MA0079.21.23434e-14
MA0102.20.442579
MA0258.10.109278
MA0259.10.00925327
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#1051534.141870825183489.5031077718047e-222.60497394377825e-19
EP300#2033402.65644773577381.45540919802955e-091.29694096615195e-07
GTF2F1#2962253.122465901166092.43877899762061e-071.27735024941073e-05
JUN#3725323.925593472105528.23227682683412e-121.03837048250933e-09
JUND#3727332.262979510605333.03637267827997e-060.000102759470559586
PRDM1#6391012.92460350759426.92661926749954e-095.398576042376e-07
STAT1#6772122.436069117317550.003807463502124670.0188057545849325
STAT3#6774252.578300244400557.85083440093994e-060.00022238494548407
TBP#6908562.035089788994092.46495575483572e-092.09128768545319e-07
TFAP2A#7020172.753105728840830.0001323652443809010.00173953614670906
TFAP2C#7022252.649320737710844.87871434547009e-060.0001509712733412



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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