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{{Coexpression_clusters
{
|full_id=C150_merkel_carcinoid_nonsmall_gastrointestinal_argyrophil_pineal_small
 

Latest revision as of 10:43, 17 September 2013


Full id: C150_merkel_carcinoid_nonsmall_gastrointestinal_argyrophil_pineal_small



Phase1 CAGE Peaks

Hg19::chr11:31312303..31312307,-p@chr11:31312303..31312307
-
Hg19::chr11:31312513..31312524,-p@chr11:31312513..31312524
-
Hg19::chr12:54779280..54779298,-p10@ZNF385A
Hg19::chr12:54786411..54786421,-p@chr12:54786411..54786421
-
Hg19::chr12:65175253..65175283,-p@chr12:65175253..65175283
-
Hg19::chr12:660023..660044,+p@chr12:660023..660044
+
Hg19::chr12:70093235..70093242,-p6@BEST3
Hg19::chr13:79169067..79169071,-p@chr13:79169067..79169071
-
Hg19::chr13:79177629..79177636,-p4@POU4F1
Hg19::chr13:79177674..79177701,-p1@POU4F1
Hg19::chr14:106331164..106331201,-p2@IGHJ2P
Hg19::chr15:46610951..46610964,+p@chr15:46610951..46610964
+
Hg19::chr15:68114974..68114985,+p@chr15:68114974..68114985
+
Hg19::chr15:68117844..68117858,+p3@SKOR1
Hg19::chr15:68124190..68124195,-p@chr15:68124190..68124195
-
Hg19::chr16:3005195..3005202,-p@chr16:3005195..3005202
-
Hg19::chr16:53653257..53653264,-p@chr16:53653257..53653264
-
Hg19::chr16:67429759..67429769,-p@chr16:67429759..67429769
-
Hg19::chr16:70207349..70207353,-p1@ENST00000502126
p1@uc002eyi.1
Hg19::chr16:70207686..70207690,+p1@CLEC18C
Hg19::chr17:18012062..18012075,+p1@MYO15A
Hg19::chr17:48049323..48049330,+p6@DLX4
Hg19::chr17:61554829..61554849,+p@chr17:61554829..61554849
+
Hg19::chr17:61573742..61573786,+p@chr17:61573742..61573786
+
Hg19::chr17:61600483..61600515,+p2@KCNH6
Hg19::chr17:61600682..61600740,+p1@KCNH6
Hg19::chr17:61603769..61603773,+p@chr17:61603769..61603773
+
Hg19::chr18:5197501..5197504,-p3@C18orf42
Hg19::chr18:77543021..77543032,-p@chr18:77543021..77543032
-
Hg19::chr18:77543062..77543072,-p@chr18:77543062..77543072
-
Hg19::chr19:39401676..39401683,-p@chr19:39401676..39401683
-
Hg19::chr19:39402817..39402833,-p1@LOC643669
Hg19::chr19:47138167..47138185,-p1@GNG8
Hg19::chr19:47139424..47139443,-p@chr19:47139424..47139443
-
Hg19::chr19:49928618..49928665,+p@chr19:49928618..49928665
+
Hg19::chr19:49928666..49928692,+p@chr19:49928666..49928692
+
Hg19::chr19:57599766..57599777,+p@chr19:57599766..57599777
+
Hg19::chr1:155048200..155048207,+p@chr1:155048200..155048207
+
Hg19::chr1:160342039..160342041,+p@chr1:160342039..160342041
+
Hg19::chr1:17026663..17026700,-p@chr1:17026663..17026700
-
Hg19::chr1:216196797..216196801,-p@chr1:216196797..216196801
-
Hg19::chr1:216595350..216595395,-p@chr1:216595350..216595395
-
Hg19::chr1:242843433..242843446,-p@chr1:242843433..242843446
-
Hg19::chr1:40769918..40769923,-p@chr1:40769918..40769923
-
Hg19::chr1:40770344..40770353,-p29@COL9A2
Hg19::chr1:92949195..92949210,-p7@GFI1
Hg19::chr1:92949213..92949223,-p9@GFI1
Hg19::chr20:31116333..31116338,-p@chr20:31116333..31116338
-
Hg19::chr20:49727833..49727839,-p@chr20:49727833..49727839
-
Hg19::chr20:49727891..49727898,-p@chr20:49727891..49727898
-
Hg19::chr20:49727900..49727904,-p@chr20:49727900..49727904
-
Hg19::chr20:7391944..7391948,+p@chr20:7391944..7391948
+
Hg19::chr2:194367490..194367523,+p@chr2:194367490..194367523
+
Hg19::chr2:197078770..197078778,+p@chr2:197078770..197078778
+
Hg19::chr2:197080808..197080817,-p@chr2:197080808..197080817
-
Hg19::chr2:197081754..197081790,-p@chr2:197081754..197081790
-
Hg19::chr2:200325452..200325462,-p33@SATB2
Hg19::chr2:219846948..219846958,-p@chr2:219846948..219846958
-
Hg19::chr2:239149300..239149321,-p2@HES6
Hg19::chr2:96782288..96782301,-p2@ADRA2B
Hg19::chr2:96782304..96782315,-p1@ADRA2B
Hg19::chr3:181980650..181980653,-p@chr3:181980650..181980653
-
Hg19::chr3:182129789..182129798,-p@chr3:182129789..182129798
-
Hg19::chr3:182129807..182129809,-p@chr3:182129807..182129809
-
Hg19::chr3:182129895..182129901,-p@chr3:182129895..182129901
-
Hg19::chr3:182129918..182129932,-p@chr3:182129918..182129932
-
Hg19::chr3:182262882..182262922,-p@chr3:182262882..182262922
-
Hg19::chr3:192232532..192232549,-p@chr3:192232532..192232549
-
Hg19::chr3:85827683..85827691,+p@chr3:85827683..85827691
+
Hg19::chr3:85829954..85829989,-p@chr3:85829954..85829989
-
Hg19::chr4:132456095..132456124,-p@chr4:132456095..132456124
-
Hg19::chr4:173606828..173606840,-p@chr4:173606828..173606840
-
Hg19::chr4:17783004..17783015,-p3@FAM184B
Hg19::chr4:17783228..17783250,-p1@FAM184B
Hg19::chr4:6356121..6356152,-p@chr4:6356121..6356152
-
Hg19::chr4:77155662..77155702,-p@chr4:77155662..77155702
-
Hg19::chr4:94749897..94749909,+p1@ATOH1
Hg19::chr4:94750014..94750025,+p2@ATOH1
Hg19::chr4:94751839..94751843,+p@chr4:94751839..94751843
+
Hg19::chr4:94997408..94997423,-p@chr4:94997408..94997423
-
Hg19::chr5:145718398..145718410,+p1@POU4F3
Hg19::chr5:145718596..145718607,+p2@POU4F3
Hg19::chr5:145722450..145722456,+p@chr5:145722450..145722456
+
Hg19::chr5:145724630..145724641,+p@chr5:145724630..145724641
+
Hg19::chr5:145724642..145724652,+p@chr5:145724642..145724652
+
Hg19::chr5:145808948..145808956,+p@chr5:145808948..145808956
+
Hg19::chr5:168853885..168853910,-p@chr5:168853885..168853910
-
Hg19::chr5:50674304..50674338,-p@chr5:50674304..50674338
-
Hg19::chr5:63986233..63986261,+p2@FAM159B
Hg19::chr5:63986324..63986342,+p1@FAM159B
Hg19::chr5:64369050..64369067,+p@chr5:64369050..64369067
+
Hg19::chr5:64369069..64369083,+p@chr5:64369069..64369083
+
Hg19::chr5:64369097..64369105,+p@chr5:64369097..64369105
+
Hg19::chr6:112466463..112466468,+p@chr6:112466463..112466468
+
Hg19::chr6:129930311..129930322,-p@chr6:129930311..129930322
-
Hg19::chr6:129930348..129930359,-p@chr6:129930348..129930359
-
Hg19::chr6:133414003..133414011,-p@chr6:133414003..133414011
-
Hg19::chr6:152793691..152793718,-p8@SYNE1
Hg19::chr6:168502185..168502196,-p@chr6:168502185..168502196
-
Hg19::chr6:32862645..32862655,+p4@ENST00000499196
p4@uc003oci.1
Hg19::chr6:34507199..34507208,-p@chr6:34507199..34507208
-
Hg19::chr6:35773169..35773180,+p3@LHFPL5
Hg19::chr6:50807829..50807852,+p@chr6:50807829..50807852
+
Hg19::chr6:91865192..91865202,-p@chr6:91865192..91865202
-
Hg19::chr7:119914647..119914684,+p1@AB384090
Hg19::chr7:126173903..126173915,-p@chr7:126173903..126173915
-
Hg19::chr8:137528469..137528506,+p@chr8:137528469..137528506
+
Hg19::chr9:104302091..104302134,+p@chr9:104302091..104302134
+
Hg19::chr9:107573173..107573188,-p@chr9:107573173..107573188
-
Hg19::chr9:139089234..139089236,-p@chr9:139089234..139089236
-
Hg19::chr9:139096224..139096231,-p@chr9:139096224..139096231
-
Hg19::chr9:14346413..14346451,+p@chr9:14346413..14346451
+
Hg19::chr9:20236750..20236767,+p@chr9:20236750..20236767
+
Hg19::chrX:130021517..130021528,-p@chrX:130021517..130021528
-


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:0042491auditory receptor cell differentiation3.448801044842e-09
GO:0042490mechanoreceptor differentiation3.448801044842e-09
GO:0060113inner ear receptor cell differentiation3.448801044842e-09
GO:0042472inner ear morphogenesis3.31530321747534e-08
GO:0042471ear morphogenesis4.75021866280329e-08
GO:0048839inner ear development9.26960517688193e-08
GO:0043583ear development1.20355517019841e-07
GO:0007423sensory organ development1.97531279678092e-06
GO:0048598embryonic morphogenesis2.40976491361931e-06
GO:0006357regulation of transcription from RNA polymerase II promoter2.44749855030467e-05
GO:0032990cell part morphogenesis3.8893567802266e-05
GO:0048858cell projection morphogenesis3.8893567802266e-05
GO:0030030cell projection organization and biogenesis3.8893567802266e-05
GO:0007275multicellular organismal development4.0111506662543e-05
GO:0048731system development4.80974703124171e-05
GO:0032502developmental process4.80974703124171e-05
GO:0009790embryonic development5.21588078337726e-05
GO:0048869cellular developmental process8.44270344712617e-05
GO:0030154cell differentiation8.44270344712617e-05
GO:0048513organ development8.44270344712617e-05
GO:0006366transcription from RNA polymerase II promoter8.8279020785022e-05
GO:0032501multicellular organismal process0.000106438416945446
GO:0048856anatomical structure development0.000140090819149837
GO:0009887organ morphogenesis0.000200968586353601
GO:0007409axonogenesis0.000200968586353601
GO:0048667neuron morphogenesis during differentiation0.000210154693008892
GO:0048812neurite morphogenesis0.000210154693008892
GO:0001708cell fate specification0.000210154693008892
GO:0000904cellular morphogenesis during differentiation0.000233770238907642
GO:0050954sensory perception of mechanical stimulus0.000250333507452838
GO:0007605sensory perception of sound0.000250333507452838
GO:0003700transcription factor activity0.000250333507452838
GO:0031175neurite development0.00025199268930492
GO:0050885neuromuscular process controlling balance0.00025199268930492
GO:0006355regulation of transcription, DNA-dependent0.000270991047338285
GO:0006351transcription, DNA-dependent0.000308548976568433
GO:0032774RNA biosynthetic process0.000308548976568433
GO:0048666neuron development0.000324737421023006
GO:0050905neuromuscular process0.000352076630921378
GO:0032989cellular structure morphogenesis0.000352076630921378
GO:0000902cell morphogenesis0.000352076630921378
GO:0045449regulation of transcription0.000418666594506109
GO:0009653anatomical structure morphogenesis0.000448975509715475
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000448975509715475
GO:0006350transcription0.000522258809055618
GO:0010468regulation of gene expression0.000540803525951619
GO:0031323regulation of cellular metabolic process0.000637519357924391
GO:0030182neuron differentiation0.00064564947869513
GO:0016477cell migration0.000859842311100581
GO:0019222regulation of metabolic process0.000871800303826359
GO:0016070RNA metabolic process0.000871800303826359
GO:0048699generation of neurons0.000906070976962741
GO:0022008neurogenesis0.00111274255393528
GO:0045597positive regulation of cell differentiation0.00111274255393528
GO:0007399nervous system development0.00124687473016944
GO:0007411axon guidance0.00152510102005092
GO:0003677DNA binding0.00193362723345703
GO:0051094positive regulation of developmental process0.00193362723345703
GO:0045633positive regulation of mechanoreceptor differentiation0.00193362723345703
GO:0045609positive regulation of auditory receptor cell differentiation0.00193362723345703
GO:0019230proprioception0.00193362723345703
GO:0051355proprioception during equilibrioception0.00193362723345703
GO:0048934peripheral nervous system neuron differentiation0.00193362723345703
GO:0042660positive regulation of cell fate specification0.00193362723345703
GO:0042667auditory receptor cell fate specification0.00193362723345703
GO:0042659regulation of cell fate specification0.00193362723345703
GO:0010453regulation of cell fate commitment0.00193362723345703
GO:0009996negative regulation of cell fate specification0.00193362723345703
GO:0021535cell migration in hindbrain0.00193362723345703
GO:0010454negative regulation of cell fate commitment0.00193362723345703
GO:0045165cell fate commitment0.00193362723345703
GO:0043565sequence-specific DNA binding0.00201455786858099
GO:0006928cell motility0.00244243515136125
GO:0051674localization of cell0.00244243515136125
GO:0007600sensory perception0.00267080380076567
GO:0060088auditory receptor cell stereocilium organization and biogenesis0.00332701889408755
GO:0045606positive regulation of epidermal cell differentiation0.00332701889408755
GO:0045684positive regulation of epidermis development0.00332701889408755
GO:0000083G1/S-specific transcription in mitotic cell cycle0.00332701889408755
GO:0002093auditory receptor cell morphogenesis0.00332701889408755
GO:0060117auditory receptor cell development0.00332701889408755
GO:0031290retinal ganglion cell axon guidance0.00332701889408755
GO:0010467gene expression0.00361483690152535
GO:0050794regulation of cellular process0.00444716309051365
GO:0060122inner ear receptor stereocilium organization and biogenesis0.00444716309051365
GO:0005594collagen type IX0.00444716309051365
GO:0042668auditory receptor cell fate determination0.00444716309051365
GO:0001967suckling behavior0.00444716309051365
GO:0045607regulation of auditory receptor cell differentiation0.00444716309051365
GO:0031490chromatin DNA binding0.00444716309051365
GO:0060119inner ear receptor cell development0.00444716309051365
GO:0045631regulation of mechanoreceptor differentiation0.00444716309051365
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0051878503418388
GO:0007420brain development0.00545406274925008
GO:0048468cell development0.00545406274925008
GO:0048676axon extension involved in development0.00545406274925008
GO:0050884neuromuscular process controlling posture0.00545406274925008
GO:0004938alpha2-adrenergic receptor activity0.00545406274925008
GO:0060120inner ear receptor cell fate commitment0.00545406274925008
GO:0009912auditory receptor cell fate commitment0.00545406274925008
GO:0045595regulation of cell differentiation0.00552803704992555
GO:0050877neurological system process0.00575868598239465
GO:0005634nucleus0.00594071659596121
GO:0050789regulation of biological process0.00643815187902022
GO:0005521lamin binding0.00764273223252338
GO:0007638mechanosensory behavior0.00764273223252338
GO:0005593FACIT collagen0.00764273223252338
GO:0045604regulation of epidermal cell differentiation0.00875111188274745
GO:0021953central nervous system neuron differentiation0.00875111188274745
GO:0045682regulation of epidermis development0.0098190445325147
GO:0050957equilibrioception0.0098190445325147
GO:0003008system process0.0105738530424472
GO:0030934anchoring collagen0.0106938622956472
GO:0004936alpha-adrenergic receptor activity0.0106938622956472
GO:0065007biological regulation0.0106938622956472
GO:0007417central nervous system development0.0125548743887259
GO:0050793regulation of developmental process0.0125548743887259
GO:0051705behavioral interaction between organisms0.0138434269449018
GO:0006915apoptosis0.0149692882000764
GO:0012501programmed cell death0.0151842628104173
GO:0007030Golgi organization and biogenesis0.0157437484703259
GO:0004935adrenoceptor activity0.0167265920036523
GO:0016265death0.0169687109973151
GO:0008219cell death0.0169687109973151
GO:0007610behavior0.0179851279240935
GO:0048675axon extension0.0182029746793254
GO:0009612response to mechanical stimulus0.0182029746793254
GO:0048522positive regulation of cellular process0.0188364740872973
GO:0044464cell part0.0201172655834711
GO:0051179localization0.0215191334275471
GO:0030902hindbrain development0.0238460910724352
GO:0048518positive regulation of biological process0.0244914321799594
GO:0007422peripheral nervous system development0.0245036542724781
GO:0016043cellular component organization and biogenesis0.0251413212706414
GO:0007416synaptogenesis0.0251413212706414
GO:0045664regulation of neuron differentiation0.025771456854288
GO:0043283biopolymer metabolic process0.025771456854288
GO:0001709cell fate determination0.0284373899751289
GO:0003676nucleic acid binding0.0284373899751289
GO:0051402neuron apoptosis0.0290621776284089
GO:0000082G1/S transition of mitotic cell cycle0.0326766313474467
GO:0003779actin binding0.0339140597736452
GO:0001764neuron migration0.034100852326719
GO:0005834heterotrimeric G-protein complex0.0345575661049139
GO:0007631feeding behavior0.0345575661049139
GO:0006997nuclear organization and biogenesis0.0352412111652633
GO:0050808synapse organization and biogenesis0.0359151778143829
GO:0042692muscle cell differentiation0.0420147355717764
GO:0006811ion transport0.0424420126752048
GO:0009913epidermal cell differentiation0.044130865967173
GO:0019897extrinsic to plasma membrane0.0447240781727989
GO:0005581collagen0.0479447883679032
GO:0048730epidermis morphogenesis0.0485035166176686



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>

Uber Anatomy
Ontology termp-valuen
skin epidermis1.04e-1815
outer epithelium1.04e-1815
enveloping layer of ectoderm1.04e-1815
skin of body1.42e-0741
integument7.30e-0746
integumental system7.30e-0746


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)
MA0003.10.784687
MA0004.11.02654
MA0006.10.533857
MA0007.10.202165
MA0009.10.0758463
MA0014.10.859739
MA0017.10.574754
MA0019.10.409113
MA0024.10.372418
MA0025.10.419231
MA0027.11.38672
MA0028.10.223506
MA0029.10.179899
MA0030.10.0444387
MA0031.10.0288982
MA0038.10.168717
MA0040.10.413736
MA0041.10.867664
MA0042.10.508724
MA0043.10.0759646
MA0046.10.251177
MA0048.11.1736
MA0050.10.05625
MA0051.10.0729745
MA0052.10.0504637
MA0055.13.96466
MA0056.10
MA0057.10.298596
MA0058.12.36974
MA0059.12.01578
MA0060.10.14729
MA0061.10.0161669
MA0063.10
MA0066.10.734338
MA0067.10.242109
MA0068.10.276933
MA0069.10.247211
MA0070.10.871651
MA0071.10.0522896
MA0072.10.0649285
MA0073.10.584472
MA0074.10.482609
MA0076.10.0225237
MA0077.10.485872
MA0078.10.534908
MA0081.10.0853954
MA0083.10.0786875
MA0084.10.375921
MA0087.10.228951
MA0088.10.309769
MA0089.10
MA0090.10.0280859
MA0091.14.15847
MA0092.10.28481
MA0093.10.913286
MA0095.10
MA0098.10
MA0100.10.028481
MA0101.10.0703895
MA0103.12.36819
MA0105.10.511942
MA0106.11.99456
MA0107.10.16132
MA0108.20.522622
MA0109.10
MA0111.10.37702
MA0113.10.680075
MA0114.10.309559
MA0115.10.194186
MA0116.10.764941
MA0117.10.303506
MA0119.11.83616
MA0122.10.333238
MA0124.10.170074
MA0125.10.791103
MA0130.10
MA0131.10.177204
MA0132.10
MA0133.10
MA0135.10.295413
MA0136.10.0806983
MA0139.10.834629
MA0140.10.050875
MA0141.10.149207
MA0142.10.243199
MA0143.10.043147
MA0144.10.174622
MA0145.11.22765
MA0146.10.454375
MA0147.11.40519
MA0148.10.0340316
MA0149.10.0459406
MA0062.20.0255022
MA0035.20.119066
MA0039.20.394639
MA0138.24.62579
MA0002.20.239375
MA0137.20.241189
MA0104.21.76928
MA0047.20.0972012
MA0112.20.291985
MA0065.20.462962
MA0150.10.202225
MA0151.10
MA0152.10.126942
MA0153.10.375488
MA0154.11.56205
MA0155.10.949041
MA0156.10.158189
MA0157.10.208639
MA0158.10
MA0159.10.633915
MA0160.10.0985826
MA0161.10
MA0162.10.00894112
MA0163.12.36945
MA0164.10.722609
MA0080.20.0146229
MA0018.20.108252
MA0099.20.0546122
MA0079.21.51011
MA0102.20.404812
MA0258.10.0583546
MA0259.10.688975
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
SUZ12#23512125.275345359059253.30230218822868e-060.000110399852188353



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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