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

Latest revision as of 10:28, 17 September 2013


Full id: C88_Melanocyte_melanoma_Macrophage_Mesenchymal_migratory_Dendritic_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:106240041..106240047,-p1@ENST00000447860
Hg19::chr10:29811685..29811692,-p36@SVIL
Hg19::chr10:4046629..4046639,+p@chr10:4046629..4046639
+
Hg19::chr10:93335091..93335099,-p6@BC044257
Hg19::chr11:109962897..109962926,+p@chr11:109962897..109962926
+
Hg19::chr11:12398061..12398074,+p@chr11:12398061..12398074
+
Hg19::chr11:126225529..126225660,+p1@ST3GAL4
Hg19::chr11:14586167..14586191,+p@chr11:14586167..14586191
+
Hg19::chr11:2920725..2920736,-p5@SLC22A18AS
Hg19::chr11:2920738..2920749,-p7@SLC22A18AS
Hg19::chr11:2920857..2920864,+p13@SLC22A18
Hg19::chr11:61112944..61112955,+p9@DAK
Hg19::chr11:88909137..88909155,-p@chr11:88909137..88909155
-
Hg19::chr12:124850619..124850624,-p@chr12:124850619..124850624
-
Hg19::chr12:132312931..132312971,+p1@MMP17
Hg19::chr12:28947878..28947885,-p@chr12:28947878..28947885
-
Hg19::chr12:56351171..56351183,-p8@PMEL
Hg19::chr12:56364848..56364864,+p12@CDK2
Hg19::chr12:63025600..63025629,+p@chr12:63025600..63025629
+
Hg19::chr12:89817974..89818019,+p@chr12:89817974..89818019
+
Hg19::chr13:49155067..49155077,-p@chr13:49155067..49155077
-
Hg19::chr13:49155365..49155378,+p@chr13:49155365..49155378
+
Hg19::chr13:52459545..52459551,-p@chr13:52459545..52459551
-
Hg19::chr14:93559337..93559385,-p@chr14:93559337..93559385
-
Hg19::chr15:28341225..28341238,-p@chr15:28341225..28341238
-
Hg19::chr15:28344444..28344469,-p1@OCA2
Hg19::chr15:28360857..28360860,-p@chr15:28360857..28360860
-
Hg19::chr15:28413731..28413765,-p@chr15:28413731..28413765
-
Hg19::chr15:42694546..42694554,+p18@CAPN3
Hg19::chr15:42694558..42694570,+p10@CAPN3
Hg19::chr15:42694573..42694641,+p7@CAPN3
Hg19::chr15:42694649..42694650,+p24@CAPN3
Hg19::chr15:42694665..42694671,+p16@CAPN3
Hg19::chr15:42697065..42697078,+p8@CAPN3
Hg19::chr15:56649336..56649342,+p@chr15:56649336..56649342
+
Hg19::chr15:77861183..77861202,+p2@ENST00000560590
p2@ENST00000561123
Hg19::chr15:81474930..81474948,+p9@IL16
Hg19::chr15:93221398..93221407,-p@chr15:93221398..93221407
-
Hg19::chr15:93221436..93221457,-p@chr15:93221436..93221457
-
Hg19::chr16:1521954..1521959,-p@chr16:1521954..1521959
-
Hg19::chr16:27730289..27730294,+p@chr16:27730289..27730294
+
Hg19::chr16:27730402..27730415,+p@chr16:27730402..27730415
+
Hg19::chr16:27771451..27771455,+p@chr16:27771451..27771455
+
Hg19::chr16:68678809..68678833,+p5@CDH3
Hg19::chr16:68678836..68678860,+p4@CDH3
Hg19::chr16:68678879..68678886,+p10@CDH3
Hg19::chr16:68678892..68678897,+p12@CDH3
Hg19::chr16:68678900..68678907,+p11@CDH3
Hg19::chr16:68678922..68678943,+p6@CDH3
Hg19::chr16:68678959..68679004,+p7@CDH3
Hg19::chr16:68680075..68680109,-p@chr16:68680075..68680109
-
Hg19::chr16:84074735..84074743,+p@chr16:84074735..84074743
+
Hg19::chr16:89985263..89985286,+p1@ENST00000540694
Hg19::chr16:89986242..89986250,+p@chr16:89986242..89986250
+
Hg19::chr16:89986251..89986268,+p@chr16:89986251..89986268
+
Hg19::chr17:30850461..30850471,-p@chr17:30850461..30850471
-
Hg19::chr17:505227..505267,-p@chr17:505227..505267
-
Hg19::chr17:75316266..75316279,+p33@SEPT9
Hg19::chr17:75316336..75316406,+p5@SEPT9
Hg19::chr17:77923564..77923575,-p@chr17:77923564..77923575
-
Hg19::chr17:77923585..77923600,-p@chr17:77923585..77923600
-
Hg19::chr17:77924634..77924661,-p2@TBC1D16
Hg19::chr17:77924675..77924686,-p3@TBC1D16
Hg19::chr17:77924692..77924709,-p4@TBC1D16
Hg19::chr17:77925754..77925770,-p@chr17:77925754..77925770
-
Hg19::chr17:77925806..77925817,-p@chr17:77925806..77925817
-
Hg19::chr17:77925869..77925876,-p@chr17:77925869..77925876
-
Hg19::chr18:20715441..20715457,+p1@CABLES1
Hg19::chr18:67872552..67872584,-p@chr18:67872552..67872584
-
Hg19::chr18:67872703..67872710,-p@chr18:67872703..67872710
-
Hg19::chr18:74845949..74845955,-p47@MBP
Hg19::chr19:1168968..1168981,-p@chr19:1168968..1168981
-
Hg19::chr19:15235947..15235958,-p5@ILVBL
Hg19::chr19:15235970..15236010,-p3@ILVBL
Hg19::chr19:19569270..19569277,+p32@GATAD2A
Hg19::chr19:29374467..29374501,+p@chr19:29374467..29374501
+
Hg19::chr19:3544396..3544409,-p@chr19:3544396..3544409
-
Hg19::chr19:3544594..3544603,-p@chr19:3544594..3544603
-
Hg19::chr19:3544629..3544640,-p@chr19:3544629..3544640
-
Hg19::chr19:3546150..3546160,-p@chr19:3546150..3546160
-
Hg19::chr19:3546308..3546322,-p@chr19:3546308..3546322
-
Hg19::chr19:3547305..3547318,-p@chr19:3547305..3547318
-
Hg19::chr19:3547534..3547553,-p@chr19:3547534..3547553
-
Hg19::chr19:3547903..3547940,-p@chr19:3547903..3547940
-
Hg19::chr19:3547999..3548008,-p@chr19:3547999..3548008
-
Hg19::chr19:3551058..3551077,-p@chr19:3551058..3551077
-
Hg19::chr19:3551104..3551146,-p@chr19:3551104..3551146
-
Hg19::chr19:3551160..3551196,-p@chr19:3551160..3551196
-
Hg19::chr19:3553724..3553727,-p@chr19:3553724..3553727
-
Hg19::chr19:3554540..3554542,-p@chr19:3554540..3554542
-
Hg19::chr19:3557499..3557510,-p3@MFSD12
Hg19::chr19:3557570..3557590,-p1@MFSD12
Hg19::chr19:3557606..3557617,-p2@MFSD12
Hg19::chr19:3557773..3557778,-p13@MFSD12
Hg19::chr19:3557800..3557811,-p9@MFSD12
Hg19::chr19:3557823..3557843,-p5@MFSD12
Hg19::chr19:3557867..3557877,-p7@MFSD12
Hg19::chr19:3557918..3557927,-p8@MFSD12
Hg19::chr19:3557930..3557939,-p12@MFSD12
Hg19::chr19:3557974..3557985,-p11@MFSD12
Hg19::chr19:3557989..3557998,-p10@MFSD12
Hg19::chr19:3558028..3558043,-p6@MFSD12
Hg19::chr19:3558051..3558082,-p4@MFSD12
Hg19::chr19:3558086..3558102,-p@chr19:3558086..3558102
-
Hg19::chr19:3572689..3572697,+p22@HMG20B
Hg19::chr19:3572758..3572795,+p7@HMG20B
Hg19::chr19:3572925..3573014,+p1@HMG20B
Hg19::chr19:3573783..3573829,-p@chr19:3573783..3573829
-
Hg19::chr19:3574157..3574180,+p4@HMG20B
Hg19::chr19:3574330..3574393,+p2@HMG20B
Hg19::chr19:3574400..3574430,+p6@HMG20B
Hg19::chr19:3574468..3574478,+p19@HMG20B
Hg19::chr1:1497446..1497455,-p4@AK129493
Hg19::chr1:1497497..1497523,-p1@AK129493
Hg19::chr1:1497528..1497559,-p2@AK129493
Hg19::chr1:1497566..1497576,-p3@AK129493
Hg19::chr1:1535369..1535429,-p2@LOC643988
Hg19::chr1:1535455..1535568,-p1@LOC643988
Hg19::chr1:154401791..154401807,+p11@IL6R
Hg19::chr1:16007955..16007970,+p@chr1:16007955..16007970
+
Hg19::chr1:16007974..16007985,+p@chr1:16007974..16007985
+
Hg19::chr1:16007995..16008026,+p@chr1:16007995..16008026
+
Hg19::chr1:161676969..161676980,+p5@FCRLA
Hg19::chr1:161676983..161676994,+p3@FCRLA
Hg19::chr1:207083151..207083160,-p14@FAIM3
Hg19::chr1:207083172..207083189,-p8@FAIM3
Hg19::chr1:207083199..207083262,-p3@FAIM3
Hg19::chr1:207083310..207083326,-p6@FAIM3
Hg19::chr1:207083343..207083348,-p19@FAIM3
Hg19::chr1:207083660..207083669,-p20@FAIM3
Hg19::chr1:216221933..216221937,-p@chr1:216221933..216221937
-
Hg19::chr1:236035593..236035595,-p@chr1:236035593..236035595
-
Hg19::chr1:236046760..236046770,-p13@LYST
Hg19::chr1:2488970..2488979,+p21@TNFRSF14
Hg19::chr1:2488990..2488993,+p29@TNFRSF14
Hg19::chr1:2489069..2489079,+p20@TNFRSF14
Hg19::chr1:32705788..32705829,-p2@MTMR9LP
Hg19::chr1:64104373..64104382,+p@chr1:64104373..64104382
+
Hg19::chr1:64104401..64104429,+p@chr1:64104401..64104429
+
Hg19::chr20:55091919..55091934,+p1@FAM209A
Hg19::chr20:55091968..55091976,+p6@FAM209A
Hg19::chr21:38568192..38568213,+p@chr21:38568192..38568213
+
Hg19::chr21:38568227..38568233,+p@chr21:38568227..38568233
+
Hg19::chr22:19939035..19939049,+p21@COMT
Hg19::chr22:19939060..19939090,+p10@COMT
Hg19::chr22:20877924..20877934,+p39@MED15
Hg19::chr22:20877995..20878006,+p40@MED15
Hg19::chr22:20878024..20878053,+p16@MED15
Hg19::chr22:20878077..20878083,+p47@MED15
Hg19::chr22:20878094..20878105,+p41@MED15
Hg19::chr22:26899907..26899914,-p@chr22:26899907..26899914
-
Hg19::chr22:47377231..47377232,-p@chr22:47377231..47377232
-
Hg19::chr2:10559858..10559877,+p3@HPCAL1
Hg19::chr2:11752379..11752396,+p5@GREB1
Hg19::chr2:128400745..128400763,-p23@LIMS2
Hg19::chr2:128400774..128400781,-p51@LIMS2
Hg19::chr2:128400788..128400798,-p44@LIMS2
Hg19::chr2:128400821..128400830,-p39@LIMS2
Hg19::chr2:163099546..163099567,-p4@FAP
Hg19::chr2:202285267..202285291,-p3@TRAK2
Hg19::chr2:232086654..232086692,+p@chr2:232086654..232086692
+
Hg19::chr2:238395042..238395061,+p2@MLPH
Hg19::chr2:240116933..240116969,-p1@MGC16025
Hg19::chr2:242350325..242350332,+p8@FARP2
Hg19::chr2:242350337..242350369,+p3@FARP2
Hg19::chr2:65216118..65216131,+p7@SLC1A4
Hg19::chr2:65216141..65216162,+p9@SLC1A4
Hg19::chr2:65216462..65216567,+p1@SLC1A4
Hg19::chr3:132136879..132136891,+p@chr3:132136879..132136891
+
Hg19::chr3:48601207..48601222,-p1@UCN2
Hg19::chr3:69951861..69951868,+p@chr3:69951861..69951868
+
Hg19::chr3:69987438..69987455,+p@chr3:69987438..69987455
+
Hg19::chr5:159894757..159894771,+p4@uc003lyl.3
Hg19::chr5:159894797..159894808,+p9@uc003lyl.3
Hg19::chr5:159894810..159894819,+p12@uc003lyl.3
Hg19::chr5:159894828..159894839,+p6@uc003lyl.3
Hg19::chr5:159894844..159894853,+p10@uc003lyl.3
Hg19::chr5:159894864..159894881,+p5@uc003lyl.3
Hg19::chr5:159894905..159894938,+p2@uc003lyl.3
Hg19::chr5:159894950..159894958,+p8@uc003lyl.3
Hg19::chr5:159895000..159895003,+p7@uc003lyl.3
Hg19::chr5:159895082..159895093,+p11@uc003lyl.3
Hg19::chr5:159896855..159896863,+p@chr5:159896855..159896863
+
Hg19::chr5:159904569..159904581,-p@chr5:159904569..159904581
-
Hg19::chr5:39462314..39462332,-p15@DAB2
Hg19::chr5:79421543..79421571,-p@chr5:79421543..79421571
-
Hg19::chr6:10435032..10435061,-p1@LINC00518
Hg19::chr6:132834443..132834454,-p6@STX7
Hg19::chr6:16238880..16238915,+p2@GMPR
Hg19::chr6:9251842..9251865,+p@chr6:9251842..9251865
+
Hg19::chr7:150775279..150775302,-p@chr7:150775279..150775302
-
Hg19::chr7:20685431..20685438,+p@chr7:20685431..20685438
+
Hg19::chr7:2692208..2692218,+p51@TTYH3
Hg19::chr7:2692417..2692437,+p3@TTYH3
Hg19::chr7:2692544..2692555,+p17@TTYH3
Hg19::chr7:2701678..2701748,+p7@TTYH3
Hg19::chr7:2701975..2702006,+p18@TTYH3
Hg19::chr7:2702100..2702127,+p20@TTYH3
Hg19::chr7:4008614..4008625,-p@chr7:4008614..4008625
-
Hg19::chr7:43832250..43832263,+p@chr7:43832250..43832263
+
Hg19::chr7:47443023..47443044,-p16@TNS3
Hg19::chr8:12668962..12668969,-p2@ENST00000534827
Hg19::chr8:12669036..12669054,-p1@ENST00000534827
Hg19::chr8:20111065..20111086,-p@chr8:20111065..20111086
-
Hg19::chr8:20111535..20111554,-p@chr8:20111535..20111554
-
Hg19::chr8:29605604..29605613,-p4@C8orf75
Hg19::chr8:29605633..29605652,-p2@C8orf75
Hg19::chr8:41467069..41467095,+p@chr8:41467069..41467095
+
Hg19::chr8:72870195..72870205,+p@chr8:72870195..72870205
+
Hg19::chr9:12694022..12694033,+p15@TYRP1
Hg19::chr9:12709145..12709150,+p@chr9:12709145..12709150
+
Hg19::chr9:134406030..134406042,-p@chr9:134406030..134406042
-
Hg19::chr9:82185685..82185693,+p@chr9:82185685..82185693
+
Hg19::chrX:54522195..54522218,-p5@FGD1


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:0005886plasma membrane0.0034475627203576
GO:0045009chitosome0.00438051250148185
GO:0033162melanosome membrane0.00438051250148185
GO:0005737cytoplasm0.0147934230677054
GO:0048770pigment granule0.0147934230677054
GO:0042470melanosome0.0147934230677054
GO:0044459plasma membrane part0.0314164411585982
GO:0046148pigment biosynthetic process0.0389661244552435
GO:0044425membrane part0.0389661244552435
GO:0005515protein binding0.0389661244552435
GO:0030027lamellipodium0.0389661244552435
GO:0035173histone kinase activity0.0389661244552435
GO:0005395eye pigment precursor transporter activity0.0389661244552435
GO:0015173aromatic amino acid transmembrane transporter activity0.0389661244552435
GO:0005302L-tyrosine transmembrane transporter activity0.0389661244552435
GO:0005896interleukin-6 receptor complex0.0389661244552435
GO:0016206catechol O-methyltransferase activity0.0389661244552435
GO:0042440pigment metabolic process0.0389661244552435
GO:0016020membrane0.0389661244552435
GO:0031410cytoplasmic vesicle0.0441059691015092
GO:0031982vesicle0.0441059691015092
GO:0019748secondary metabolic process0.0441059691015092
GO:0008509anion transmembrane transporter activity0.0441059691015092
GO:0019981interleukin-6 binding0.0441059691015092
GO:0015746citrate transport0.0441059691015092
GO:0051302regulation of cell division0.0441059691015092
GO:0006842tricarboxylic acid transport0.0441059691015092
GO:0015137citrate transmembrane transporter activity0.0441059691015092
GO:0043209myelin sheath0.0441059691015092
GO:0004915interleukin-6 receptor activity0.0441059691015092
GO:0015105arsenite transmembrane transporter activity0.0441059691015092
GO:0004371glycerone kinase activity0.0441059691015092
GO:0015142tricarboxylic acid transmembrane transporter activity0.0441059691015092
GO:0015171amino acid transmembrane transporter activity0.0481266501877381



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><br>disease_data<br>

Disease
Ontology termp-valuen
melanoma6.70e-402


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)
MA0003.11.8255
MA0004.12.7257
MA0006.10.306979
MA0007.11.61965
MA0009.10.0141931
MA0014.10.222365
MA0017.10.172006
MA0019.10.298646
MA0024.10.336672
MA0025.10.345486
MA0027.11.12111
MA0028.10.0157447
MA0029.10.0337865
MA0030.10.352695
MA0031.10.585124
MA0038.10.0300311
MA0040.10.389323
MA0041.10.0172017
MA0042.10.375121
MA0043.10.581261
MA0046.10.164411
MA0048.10.11512
MA0050.10.0749161
MA0051.10.112202
MA0052.10.106309
MA0055.10.11613
MA0056.10
MA0057.10.00929636
MA0058.13.59271
MA0059.18.30672
MA0060.10.236992
MA0061.12.23585
MA0063.10
MA0066.10.0302192
MA0067.10.324454
MA0068.10.0258875
MA0069.10.160543
MA0070.10.302327
MA0071.10.42848
MA0072.10.294897
MA0073.10.00324474
MA0074.11.19334
MA0076.10.00168559
MA0077.10.282379
MA0078.10.841015
MA0081.10.849853
MA0083.10.0151335
MA0084.10.56305
MA0087.10.497145
MA0088.10.6891
MA0089.10
MA0090.11.34168
MA0091.15.43969
MA0092.10.206773
MA0093.14.36936
MA0095.10
MA0098.10
MA0100.10.0759573
MA0101.11.11967
MA0103.10.142901
MA0105.15.82841
MA0106.10.00721184
MA0107.11.67859
MA0108.20.0504007
MA0109.10
MA0111.10.439595
MA0113.10.48234
MA0114.10.680945
MA0115.10.893203
MA0116.11.74287
MA0117.10.0862207
MA0119.10.195312
MA0122.10.249119
MA0124.10.20458
MA0125.12.28151
MA0130.10
MA0131.10.933454
MA0132.10
MA0133.10
MA0135.10.662415
MA0136.10.319717
MA0139.10.0379085
MA0140.10.418316
MA0141.11.00187
MA0142.10.313743
MA0143.10.21279
MA0144.10.0447399
MA0145.10.0687409
MA0146.11.81547
MA0147.17.40791
MA0148.10.546429
MA0149.10.000220774
MA0062.20.00313487
MA0035.20.121999
MA0039.20.579109
MA0138.20.628792
MA0002.20.944608
MA0137.20.0187309
MA0104.24.86689
MA0047.20.161386
MA0112.20.804965
MA0065.21.26587
MA0150.10.588213
MA0151.10
MA0152.10.0392703
MA0153.10.0302312
MA0154.12.66056
MA0155.10.103129
MA0156.10.0904949
MA0157.10.146302
MA0158.10
MA0159.10.383984
MA0160.10.799908
MA0161.10
MA0162.10.0713266
MA0163.10.0250122
MA0164.10.140485
MA0080.21.65203
MA0018.20.0533185
MA0099.20.212996
MA0079.24.88332e-11
MA0102.20.215292
MA0258.11.03412
MA0259.12.18758
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
BCL11A#53335151.988513208196760.009409567929911350.0355018194802215
BHLHE40#8553112.306495088863330.009109750074354190.0344714923194013
BRF2#55290315.06414366442080.001104269212249570.00767579183082412
GATA2#2624271.608005405635320.01001663553595090.0375575284964162
PRDM1#639127.392390043595931.19925028668985e-076.91216891234003e-06
STAT1#6772222.12871460251580.000754559132250010.00593414165760985



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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