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{{Coexpression_clusters
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|full_id=C111_medulla_lung_trachea_testis_caudate_epididymis_throat
|id=C111
}}

Latest revision as of 10:34, 17 September 2013


Full id: C111_medulla_lung_trachea_testis_caudate_epididymis_throat



Phase1 CAGE Peaks

Hg19::chr10:104679225..104679235,+p8@CNNM2
Hg19::chr10:105992059..105992138,-p1@WDR96
Hg19::chr10:127585118..127585175,+p1@FANK1
Hg19::chr10:134756030..134756103,-p1@TTC40
Hg19::chr10:23216944..23217002,+p1@ARMC3
Hg19::chr10:49482711..49482753,-p1@FRMPD2
Hg19::chr10:82116531..82116550,+p1@DYDC2
Hg19::chr11:3026677..3026691,-p@chr11:3026677..3026691
-
Hg19::chr11:31391276..31391292,-p1@DCDC1
Hg19::chr11:71791849..71791904,+p1@LRTOMT
Hg19::chr11:86085923..86085934,+p3@CCDC81
Hg19::chr11:86085937..86085948,+p6@CCDC81
Hg19::chr11:94245596..94245613,+p2@LOC643037
Hg19::chr11:94245617..94245660,+p1@LOC643037
Hg19::chr12:113587513..113587556,+p1@CCDC42B
Hg19::chr12:113587558..113587572,+p2@CCDC42B
Hg19::chr12:113658826..113658870,-p2@IQCD
Hg19::chr12:119772487..119772496,+p3@CCDC60
Hg19::chr12:119772502..119772522,+p2@CCDC60
Hg19::chr12:119772527..119772541,+p1@CCDC60
Hg19::chr12:25801481..25801520,-p1@IFLTD1
Hg19::chr12:7014126..7014191,+p3@LRRC23
Hg19::chr12:75723814..75723850,-p4@CAPS2
Hg19::chr12:85430110..85430161,+p1@LRRIQ1
Hg19::chr12:96883347..96883400,+p1@C12orf63
Hg19::chr13:103046837..103046881,-p3@FGF14-IT1
Hg19::chr13:114944748..114944765,+p@chr13:114944748..114944765
+
Hg19::chr13:31506775..31506817,+p2@C13orf26
Hg19::chr13:43355683..43355705,+p3@C13orf30
Hg19::chr13:52703187..52703214,-p1@NEK5
Hg19::chr14:60386853..60386872,+p@chr14:60386853..60386872
+
Hg19::chr14:89816607..89816659,+p1@ENST00000555407
p1@ENST00000556942
Hg19::chr15:74610894..74610905,+p1@CCDC33
Hg19::chr15:81426596..81426639,+p2@C15orf26
Hg19::chr15:81426643..81426656,+p5@C15orf26
Hg19::chr15:82555125..82555168,+p1@FAM154B
Hg19::chr16:22103828..22103869,+p1@VWA3A
Hg19::chr16:53078146..53078165,-p@chr16:53078146..53078165
-
Hg19::chr16:71264580..71264638,-p1@HYDIN
Hg19::chr16:84178874..84178931,+p1@DNAAF1
Hg19::chr16:89752965..89753012,-p1@BC031657
p2@AK090745
Hg19::chr17:11501773..11501806,+p1@DNAH9
Hg19::chr17:11501822..11501834,+p2@DNAH9
Hg19::chr17:17876159..17876272,+p1@LRRC48
Hg19::chr17:40086852..40086934,+p1@TTC25
Hg19::chr17:45909077..45909086,+p3@LRRC46
Hg19::chr17:62075703..62075725,+p1@C17orf72
Hg19::chr17:6735012..6735030,-p2@TEKT1
Hg19::chr17:6735035..6735068,-p1@TEKT1
Hg19::chr17:74137321..74137337,-p1@FOXJ1
Hg19::chr17:7621045..7621069,+p1@DNAH2
Hg19::chr17:78010428..78010465,+p1@CCDC40
Hg19::chr17:9479949..9479965,+p1@WDR16
Hg19::chr17:9479971..9480003,+p2@WDR16
Hg19::chr18:47792851..47792911,-p1@CCDC11
Hg19::chr18:71814968..71814976,-p5@FBXO15
Hg19::chr18:71815013..71815043,-p2@FBXO15
Hg19::chr19:18539843..18539882,+p@chr19:18539843..18539882
+
Hg19::chr19:48824038..48824075,-p2@CCDC114
Hg19::chr19:50554309..50554324,-p@chr19:50554309..50554324
-
Hg19::chr1:109655355..109655374,-p1@C1orf194
Hg19::chr1:109655377..109655396,-p3@C1orf194
Hg19::chr1:109655404..109655415,-p5@C1orf194
Hg19::chr1:1109255..1109268,+p2@TTLL10
Hg19::chr1:1109272..1109282,+p4@TTLL10
Hg19::chr1:111889212..111889269,+p1@C1orf88
Hg19::chr1:118727781..118727859,-p1@SPAG17
Hg19::chr1:154178834..154178835,-p4@C1orf189
Hg19::chr1:156890418..156890458,+p1@LRRC71
Hg19::chr1:159116916..159116923,-p13@AIM2
Hg19::chr1:159869912..159869966,-p3@CCDC19
Hg19::chr1:161337662..161337675,-p1@C1orf192
Hg19::chr1:183622423..183622434,-p2@APOBEC4
Hg19::chr1:1935234..1935245,-p5@C1orf222
p5@KIAA1751
Hg19::chr1:211849095..211849113,+p1@ENST00000415202
Hg19::chr1:24120009..24120027,-p@chr1:24120009..24120027
-
Hg19::chr1:3585622..3585657,+p@chr1:3585622..3585657
+
Hg19::chr1:36549680..36549720,+p1@TEKT2
Hg19::chr1:38022513..38022571,+p1@DNALI1
Hg19::chr1:43613566..43613608,+p1@FAM183A
Hg19::chr1:43637996..43638036,+p1@WDR65
Hg19::chr1:43638039..43638053,+p2@WDR65
Hg19::chr1:60539405..60539418,-p2@C1orf87
Hg19::chr1:60539422..60539447,-p1@C1orf87
Hg19::chr1:67390474..67390548,-p1@WDR78
Hg19::chr1:67600640..67600658,-p1@C1orf141
Hg19::chr1:85528018..85528039,+p1@WDR63
Hg19::chr1:85528056..85528077,+p3@WDR63
Hg19::chr20:20033161..20033219,+p1@C20orf26
Hg19::chr20:271347..271422,-p2@C20orf96
Hg19::chr20:30467600..30467641,+p1@TTLL9
Hg19::chr20:3762087..3762100,-p1@SPEF1
Hg19::chr21:43916312..43916363,-p1@RSPH1
Hg19::chr21:43916365..43916386,-p2@RSPH1
Hg19::chr22:21400229..21400252,+p1@LOC400891
Hg19::chr22:39052300..39052336,-p3@LOC646851
Hg19::chr22:44208092..44208107,-p3@EFCAB6
Hg19::chr2:11273246..11273261,+p2@C2orf50
Hg19::chr2:134901352..134901396,+p@chr2:134901352..134901396
+
Hg19::chr2:135805008..135805028,-p1@YSK4
Hg19::chr2:135805029..135805039,-p2@YSK4
Hg19::chr2:170550877..170550936,-p1@C2orf77
Hg19::chr2:171627597..171627621,+p3@ENST00000426475
p3@ENST00000429172
Hg19::chr2:182706018..182706043,+p@chr2:182706018..182706043
+
Hg19::chr2:202222054..202222084,-p1@ALS2CR12
Hg19::chr2:202938048..202938058,+p5@LOC100652824
Hg19::chr2:207629997..207630030,-p1@MDH1B
Hg19::chr2:219221573..219221610,+p1@C2orf62
Hg19::chr2:219906220..219906250,-p1@CCDC108
Hg19::chr2:241845747..241845758,+p@chr2:241845747..241845758
+
Hg19::chr2:26624775..26624809,+p1@CCDC164
Hg19::chr2:29204161..29204178,+p5@FAM179A
Hg19::chr2:84743562..84743651,+p1@DNAH6
Hg19::chr2:98703623..98703635,+p2@VWA3B
Hg19::chr3:113160334..113160373,-p1@WDR52
Hg19::chr3:126113734..126113794,+p1@CCDC37
Hg19::chr3:129147432..129147488,-p1@C3orf25
Hg19::chr3:167098059..167098120,-p1@ZBBX
Hg19::chr3:169530299..169530319,-p8@LRRC34
Hg19::chr3:169530320..169530344,-p2@LRRC34
Hg19::chr3:180397256..180397301,-p2@CCDC39
Hg19::chr3:19975665..19975719,-p2@EFHB
Hg19::chr3:38080691..38080770,+p1@DLEC1
Hg19::chr3:52351872..52351896,+p1@DNAH1
Hg19::chr3:57530107..57530118,-p2@DNAH12
Hg19::chr4:81256871..81256921,+p1@C4orf22
Hg19::chr5:110062349..110062380,-p2@TMEM232
Hg19::chr5:121659052..121659068,-p1@ENST00000512105
Hg19::chr5:35618058..35618078,+p2@SPEF2
Hg19::chr5:35938674..35938730,-p1@CAPSL
Hg19::chr5:68530376..68530408,+p7@CDK7
Hg19::chr5:7851192..7851256,-p1@C5orf49
Hg19::chr5:94728500..94728543,+p1@FAM81B
Hg19::chr6:109761774..109761866,-p1@PPIL6
Hg19::chr6:110011718..110011750,-p3@AKD1
Hg19::chr6:146920097..146920113,+p2@C6orf103
Hg19::chr6:146920116..146920150,+p1@C6orf103
Hg19::chr6:151815143..151815212,+p1@C6orf97
Hg19::chr6:165723088..165723119,-p1@C6orf118
Hg19::chr6:43612793..43612833,+p1@RSPH9
Hg19::chr6:44265446..44265462,-p2@TCTE1
Hg19::chr6:46714658..46714677,+p1@LOC100287718
Hg19::chr6:46714680..46714685,+p2@LOC100287718
Hg19::chr6:83767586..83767600,-p3@UBE2CBP
Hg19::chr7:102389155..102389172,-p3@RASA4
Hg19::chr7:102715263..102715289,-p3@FBXL13
Hg19::chr7:105221898..105221948,-p1@EFCAB10
Hg19::chr7:123174610..123174654,-p1@IQUB
Hg19::chr7:12544061..12544073,+p1@ENST00000424453
Hg19::chr7:133812086..133812122,+p1@LRGUK
Hg19::chr7:76751926..76751960,+p1@CCDC146
Hg19::chr7:91687055..91687071,+p19@AKAP9
Hg19::chr8:101118185..101118205,-p2@RGS22
Hg19::chr8:101118210..101118287,-p1@RGS22
Hg19::chr8:133687814..133687844,-p3@LRRC6
Hg19::chr8:49647808..49647873,-p1@EFCAB1
Hg19::chr8:67940755..67940821,-p1@PPP1R42
Hg19::chr9:100069597..100069628,+p3@C9orf174
Hg19::chr9:100069645..100069665,+p5@C9orf174
Hg19::chr9:130469257..130469288,+p1@C9orf117
Hg19::chr9:130469295..130469308,+p2@C9orf117
Hg19::chr9:135285558..135285565,+p4@C9orf171
Hg19::chr9:135285579..135285613,+p1@C9orf171
Hg19::chr9:135754263..135754338,+p3@C9orf9
Hg19::chr9:34381482..34381503,-p4@C9orf24
Hg19::chr9:34381511..34381522,-p8@C9orf24
Hg19::chr9:34381538..34381602,-p1@C9orf24
Hg19::chr9:3525848..3525863,-p6@RFX3
Hg19::chr9:35812140..35812191,-p1@SPAG8
Hg19::chrX:119030118..119030179,+p1@AKAP14
Hg19::chrX:35937843..35937868,+p2@CXorf22
Hg19::chrX:53449816..53449827,+p3@RIBC1


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:0005858axonemal dynein complex6.56779292423636e-09
GO:0044447axoneme part6.56779292423636e-09
GO:0005930axoneme2.24507952120803e-08
GO:0030286dynein complex1.28207533327857e-06
GO:0044463cell projection part1.2841998354596e-06
GO:0001539ciliary or flagellar motility4.21304448100169e-05
GO:0015630microtubule cytoskeleton0.000158805532537098
GO:0003777microtubule motor activity0.000198807572737233
GO:0005875microtubule associated complex0.000576924799331525
GO:0042995cell projection0.000594200600940216
GO:0044430cytoskeletal part0.00584502357339293
GO:0006928cell motility0.0135935998424969
GO:0051674localization of cell0.0135935998424969
GO:0005856cytoskeleton0.0183506095553789
GO:0004835tubulin-tyrosine ligase activity0.0479675318110294



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><br>

Uber Anatomy
Ontology termp-valuen
neural tube4.50e-7156
neural rod4.50e-7156
future spinal cord4.50e-7156
neural keel4.50e-7156
regional part of nervous system1.30e-6453
regional part of brain1.30e-6453
adult organism9.04e-61114
regional part of forebrain4.05e-5641
forebrain4.05e-5641
anterior neural tube4.05e-5641
future forebrain4.05e-5641
central nervous system2.58e-5281
brain6.67e-5068
future brain6.67e-5068
neural plate3.28e-4782
presumptive neural plate3.28e-4782
nervous system6.30e-4689
brain grey matter1.69e-4434
gray matter1.69e-4434
neurectoderm1.82e-4486
telencephalon3.56e-4434
cerebral hemisphere5.26e-4032
regional part of telencephalon6.65e-4032
pre-chordal neural plate3.49e-3761
ecto-epithelium1.02e-34104
regional part of cerebral cortex3.02e-3322
structure with developmental contribution from neural crest1.27e-30132
cerebral cortex8.45e-2925
pallium8.45e-2925
neocortex8.94e-2920
ectoderm-derived structure2.05e-19171
ectoderm2.05e-19171
presumptive ectoderm2.05e-19171
tube8.60e-19192
organ system subdivision9.35e-19223
neural nucleus1.45e-179
nucleus of brain1.45e-179
basal ganglion8.71e-179
nuclear complex of neuraxis8.71e-179
aggregate regional part of brain8.71e-179
collection of basal ganglia8.71e-179
cerebral subcortex8.71e-179
brainstem2.63e-166
posterior neural tube1.39e-1515
chordal neural plate1.39e-1515
anatomical conduit4.07e-14240
diencephalon2.71e-137
future diencephalon2.71e-137
telencephalic nucleus8.56e-137
limbic system9.84e-135
temporal lobe6.34e-126
corpus striatum2.02e-114
striatum2.02e-114
ventral part of telencephalon2.02e-114
future corpus striatum2.02e-114
anatomical cluster4.11e-11373
epithelium8.95e-11306
cell layer1.52e-10309
segmental subdivision of hindbrain5.02e-1012
hindbrain5.02e-1012
presumptive hindbrain5.02e-1012
gyrus1.07e-096
medulla oblongata2.77e-093
myelencephalon2.77e-093
future myelencephalon2.77e-093
segmental subdivision of nervous system3.67e-0913
caudate-putamen4.35e-093
dorsal striatum4.35e-093
pons1.00e-083
multi-tissue structure2.64e-08342
spinal cord3.56e-083
dorsal region element3.56e-083
dorsum3.56e-083
parietal lobe5.97e-085
organ7.41e-08503
occipital lobe1.13e-075
organ part3.79e-07218
caudate nucleus8.91e-072
future caudate nucleus8.91e-072
open tracheal system trachea9.93e-072


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)
MA0003.12.07918
MA0004.10.237306
MA0006.10.914591
MA0007.10.289408
MA0009.10.282664
MA0014.11.22567
MA0017.10.742951
MA0019.10.551195
MA0024.10.536274
MA0025.10.0635465
MA0027.11.21268
MA0028.12.22366
MA0029.10.0144971
MA0030.10.556628
MA0031.10.625452
MA0038.11.01415
MA0040.10.184549
MA0041.10.186072
MA0042.10.0733618
MA0043.10.117981
MA0046.10.110526
MA0048.10.149303
MA0050.10.0742764
MA0051.10.0356931
MA0052.10.0157591
MA0055.10.477733
MA0056.10
MA0057.10.424944
MA0058.10.344955
MA0059.10.456446
MA0060.15.81452
MA0061.10.55942
MA0063.10
MA0066.10.574006
MA0067.10.141036
MA0068.10.146336
MA0069.10.262864
MA0070.10.248315
MA0071.10.290636
MA0072.10.0981886
MA0073.10.0122008
MA0074.11.53913
MA0076.11.52651
MA0077.10.0935545
MA0078.10.0426792
MA0081.10.166228
MA0083.10.539784
MA0084.10.250798
MA0087.10.0967042
MA0088.10.2813
MA0089.10
MA0090.10.168031
MA0091.10.357747
MA0092.10.158307
MA0093.10.499016
MA0095.10
MA0098.10
MA0100.15.62085
MA0101.10.302868
MA0103.10.241021
MA0105.10.484804
MA0106.10.060852
MA0107.10.167142
MA0108.20.0067563
MA0109.10
MA0111.10.292644
MA0113.10.1476
MA0114.10.974686
MA0115.11.68866
MA0116.10.768545
MA0117.10.336352
MA0119.10.98111
MA0122.10.670075
MA0124.10.295135
MA0125.10.210495
MA0130.10
MA0131.10.580728
MA0132.10
MA0133.10
MA0135.10.139344
MA0136.10.0410939
MA0139.12.66811
MA0140.10.0214281
MA0141.10.583143
MA0142.10.183221
MA0143.10.25949
MA0144.10.360203
MA0145.10.361619
MA0146.12.23117
MA0147.10.665629
MA0148.10.120122
MA0149.10.0449791
MA0062.21.79875
MA0035.20.0506419
MA0039.22.14616
MA0138.20.0432252
MA0002.20.149777
MA0137.20.134727
MA0104.20.859129
MA0047.20.113143
MA0112.20.609492
MA0065.21.11173
MA0150.10.15529
MA0151.10
MA0152.10.190618
MA0153.10.432811
MA0154.10.798591
MA0155.10.503258
MA0156.10.0304177
MA0157.10.453551
MA0158.10
MA0159.10.809575
MA0160.10.232554
MA0161.10
MA0162.10.381795
MA0163.10.0613062
MA0164.10.881882
MA0080.20.0184427
MA0018.20.128775
MA0099.20.000204149
MA0079.20.0268267
MA0102.20.275729
MA0258.10.845992
MA0259.10.386803
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
CTCF#10664531.651706905656848.4342581453866e-050.00126561133110062
CTCFL#140690171.951686419200950.006713863967173870.0285407537800257
E2F1#1869571.626285960744896.16331880240379e-050.00101002801255963
ELF1#1997701.732946843700744.0382457522831e-071.94534293414527e-05
ESR1#2099173.041082883922255.19823726916867e-050.000884487947466124
ETS1#2113331.866564595538820.0003275224246973660.00333783318822875
FOXA1#3169402.57707436032222.08656383039225e-081.48344887598595e-06
FOXA2#3170162.291205930480490.001843743404438230.0109098423465226
GABPB1#2553401.64364740376330.0009205518914094910.00669322744269812
HSF1#329798.59660465116281.34614153530798e-065.30326955134024e-05
MAX#4149622.32592117185143.44289653179216e-113.95569494921717e-09
MXI1#4601653.764547417845083.74901027033113e-221.05253463339546e-19
NFYA#4800242.571011260441472.20338060213753e-050.000483138498229355
NFYB#4801242.338575802819049.69844677762145e-050.00138015544761958
NRF1#4899251.774749919725420.003674460943488440.0185479471472687
PBX3#5090151.911149362216060.01272003274242470.0458851719945457
PPARGC1A#1089136.105543076109940.01353013194544870.0477793220710302
RFX5#5993342.381563768166471.80536333721812e-066.77507515543382e-05
SIN3A#259421013.176147426792611.3042318688605e-315.58248656360336e-29
SIX5#147912262.582875576987998.89168549069174e-060.000239710568136901
SMARCC1#6599112.792424142534570.002196153834005480.0126559681217071
SP1#6667521.722766463158883.27054741465856e-050.000650862617072265
SREBF1#6720359.565143781494716.2171250565965e-241.89856819820433e-21
USF1#7391391.442432975645990.01050549624903390.0388975616957796
USF2#7392221.661792688787970.01318322385851750.0466473342105878
ZNF143#7702231.805349771518850.004348573556670220.0206258537483574
ZNF263#10127381.816453384920960.0001830962928126720.00221760335440828



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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