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

Latest revision as of 11:00, 17 September 2013


Full id: C226_Corneal_Keratinocyte_Esophageal_Urothelial_Mammary_Bronchial_Tracheal



Phase1 CAGE Peaks

Hg19::chr11:120008848..120008862,-p4@TRIM29
Hg19::chr11:66673490..66673527,-p@chr11:66673490..66673527
-
Hg19::chr11:66673538..66673570,-p@chr11:66673538..66673570
-
Hg19::chr11:72432950..72432974,-p9@ARAP1
Hg19::chr12:120105914..120105973,+p2@PRKAB1
Hg19::chr12:52887143..52887158,-p8@KRT6A
Hg19::chr12:52887160..52887186,-p3@KRT6A
Hg19::chr16:68679173..68679184,+p2@CDH3
Hg19::chr16:68679193..68679253,+p1@CDH3
Hg19::chr16:68679261..68679268,+p3@CDH3
Hg19::chr16:68716248..68716260,-p@chr16:68716248..68716260
-
Hg19::chr17:39925803..39925824,-p@chr17:39925803..39925824
-
Hg19::chr17:39942208..39942219,-p7@JUP
Hg19::chr17:39942220..39942242,-p2@JUP
Hg19::chr17:39942245..39942256,-p9@JUP
Hg19::chr17:39942268..39942282,-p6@JUP
Hg19::chr17:39942286..39942313,-p3@JUP
Hg19::chr17:39942940..39942970,-p1@JUP
Hg19::chr17:73717531..73717550,+p2@ITGB4
Hg19::chr17:73717551..73717609,+p1@ITGB4
Hg19::chr17:73717624..73717635,+p3@ITGB4
Hg19::chr17:7493405..7493419,-p1@SOX15
Hg19::chr17:8006982..8007017,-p@chr17:8006982..8007017
-
Hg19::chr1:153585571..153585629,-p2@S100A16
Hg19::chr1:153585634..153585651,-p7@S100A16
Hg19::chr1:153588789..153588808,-p1@S100A14
Hg19::chr1:200864020..200864063,+p1@C1orf106
Hg19::chr1:200864071..200864088,+p3@C1orf106
Hg19::chr1:201368430..201368460,-p1@LAD1
Hg19::chr1:201368476..201368498,-p4@LAD1
Hg19::chr1:207206059..207206084,-p3@C1orf116
Hg19::chr1:209825762..209825779,-p1@LAMB3
Hg19::chr1:209825932..209825936,-p10@LAMB3
Hg19::chr1:209826381..209826392,-p@chr1:209826381..209826392
-
Hg19::chr1:209979411..209979433,-p2@IRF6
Hg19::chr1:209979449..209979460,-p3@IRF6
Hg19::chr1:27189631..27189648,+p1@SFN
Hg19::chr1:27190343..27190365,-p4@uc010ofi.1
Hg19::chr1:27190373..27190427,-p1@uc010ofi.1
Hg19::chr1:27190643..27190678,-p2@uc010ofi.1
Hg19::chr1:31886034..31886099,+p1@SERINC2
Hg19::chr1:35220613..35220718,+p1@GJB5
Hg19::chr1:35220725..35220754,+p2@GJB5
Hg19::chr1:35247024..35247046,+p4@GJB3
Hg19::chr1:35247057..35247079,+p3@GJB3
Hg19::chr1:35247081..35247102,+p6@GJB3
Hg19::chr1:44399399..44399444,+p1@ARTN
Hg19::chr1:44399451..44399461,+p6@ARTN
Hg19::chr1:44399466..44399482,+p3@ARTN
Hg19::chr1:44401579..44401643,+p2@ARTN
Hg19::chr1:6479968..6479986,-p1@HES2
Hg19::chr20:60953877..60953897,-p@chr20:60953877..60953897
-
Hg19::chr22:38302285..38302361,+p1@MICALL1
Hg19::chr2:20424783..20424794,-p4@SDC1
Hg19::chr2:74669009..74669077,-p1@RTKN
Hg19::chr3:12800751..12800777,-p1@TMEM40
Hg19::chr6:30850697..30850739,+p2@DDR1
Hg19::chr6:35360450..35360509,+p@chr6:35360450..35360509
+
Hg19::chr7:150811705..150811763,+p4@AGAP3
Hg19::chr8:144815895..144815912,-p4@FAM83H
Hg19::chr8:144815914..144815961,-p1@FAM83H
Hg19::chr8:144815966..144815986,-p2@FAM83H
Hg19::chrX:54501038..54501075,-p@chrX:54501038..54501075
-


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

p.valueFDRnGenesnPathwayName
7.90940612888754e-050.0166888469319527385ECM-receptor interaction (KEGG):04512
6.12511642504549e-070.000387719869705379469Alpha6-Beta4 Integrin Signaling Pathway (Wikipathways):WP244
2.40906544721509e-060.000762469214043575497Cell junction organization (Reactome):REACT_20676
0.0001716388889811010.02716185418125924288{ACTB,297} (Static Module):NA



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:0009888tissue development0.000467859320844482
GO:0007398ectoderm development0.000467859320844482
GO:0014704intercalated disc0.000494265234320962
GO:0048731system development0.00501723215290283
GO:0007275multicellular organismal development0.00501723215290283
GO:0048513organ development0.00501723215290283
GO:0008544epidermis development0.0050388845571958
GO:0005922connexon complex0.00705063890640088
GO:0032502developmental process0.00733551717943004
GO:0005911intercellular junction0.00733551717943004
GO:0005921gap junction0.00749484253179777
GO:0048856anatomical structure development0.00749484253179777
GO:0022610biological adhesion0.00964929591541734
GO:0007155cell adhesion0.00964929591541734
GO:0032501multicellular organismal process0.0122266281545092
GO:0005604basement membrane0.0247177030320746
GO:0005610laminin-5 complex0.0273908549258614
GO:0008426protein kinase C inhibitor activity0.038791147396166
GO:0005515protein binding0.0448481256440162
GO:0043403skeletal muscle regeneration0.0465343065901034
GO:0030054cell junction0.0468426097393087
GO:0017049GTP-Rho binding0.0468426097393087
GO:0005916fascia adherens0.0468426097393087
GO:0005243gap junction channel activity0.0468426097393087
GO:0044459plasma membrane part0.0468426097393087
GO:0044420extracellular matrix part0.0468426097393087
GO:0022829wide pore channel activity0.0481077772224277
GO:0043588skin development0.0481077772224277
GO:0009898internal side of plasma membrane0.0481077772224277



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.98e-32160
endoderm4.98e-32160
presumptive endoderm4.98e-32160
respiratory system3.41e-2474
digestive system1.35e-23145
digestive tract1.35e-23145
primitive gut1.35e-23145
subdivision of digestive tract1.02e-20118
respiratory tract8.60e-1854
urinary system structure5.00e-1647
renal system1.77e-1548
foregut2.15e-1487
orifice4.42e-1436
respiratory primordium2.96e-1338
endoderm of foregut2.96e-1338
segment of respiratory tract7.71e-1347
anatomical space1.40e-1295
epithelial bud3.20e-1237
endo-epithelium3.43e-1182
oral opening7.38e-1122
organ part1.57e-10218
epithelial fold2.54e-1047
organ3.28e-10503
extraembryonic membrane5.31e-1014
membranous layer5.31e-1014
thoracic cavity element8.73e-1034
thoracic cavity8.73e-1034
immaterial anatomical entity1.11e-09117
nephron tubule epithelium1.30e-0910
organism subdivision1.89e-09264
thoracic segment organ2.51e-0935
trunk region element3.04e-09101
mouth2.73e-0829
stomodeum2.73e-0829
reproductive structure3.98e-0859
reproductive system3.98e-0859
mucosa5.48e-0820
surface structure7.03e-0899
multi-cellular organism1.05e-07656
chorion1.18e-077
excretory tube1.24e-0716
kidney epithelium1.24e-0716
urothelium1.58e-075
embryo2.08e-07592
anterior region of body2.64e-0762
craniocervical region2.64e-0762
tracheobronchial tree3.18e-0715
lower respiratory tract3.18e-0715
upper respiratory tract4.19e-0719
nephron epithelium4.83e-0715
renal tubule4.83e-0715
nephron tubule4.83e-0715
nephron4.83e-0715
uriniferous tubule4.83e-0715
nephrogenic mesenchyme4.83e-0715
thoracic segment of trunk6.16e-0752
male organism6.55e-0722
male reproductive system6.55e-0722
respiratory system epithelium7.76e-0728
Disease
Ontology termp-valuen
carcinoma5.95e-21106
squamous cell carcinoma2.76e-1314
cell type cancer9.42e-13143
adenocarcinoma1.01e-1025


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)
MA0003.16.92399
MA0004.10.0148246
MA0006.10.508799
MA0007.11.14479
MA0009.10.570861
MA0014.13.02673
MA0017.11.57736
MA0019.10.180053
MA0024.10.835639
MA0025.10.285416
MA0027.11.64023
MA0028.11.75024
MA0029.10.44873
MA0030.10.140185
MA0031.10.10769
MA0038.10.0351241
MA0040.10.149577
MA0041.10.0176845
MA0042.10.0620436
MA0043.10.196415
MA0046.10.189523
MA0048.14.17868
MA0050.10.0130821
MA0051.10.0340651
MA0052.10.151713
MA0055.13.01012
MA0056.10
MA0057.11.34293
MA0058.10.0277371
MA0059.10.18173
MA0060.10.907462
MA0061.15.50548
MA0063.10
MA0066.10.328394
MA0067.10.426099
MA0068.10.32078
MA0069.10.187175
MA0070.10.180428
MA0071.10.0261486
MA0072.10.177746
MA0073.19.65778
MA0074.10.319683
MA0076.11.15934
MA0077.10.99124
MA0078.10.85365
MA0081.10.329859
MA0083.10.200894
MA0084.10.58417
MA0087.10.176294
MA0088.11.04664
MA0089.10
MA0090.12.46989
MA0091.10.184212
MA0092.10.140498
MA0093.10.00192412
MA0095.10
MA0098.10
MA0100.10.038743
MA0101.10.533246
MA0103.14.5849
MA0105.16.27447
MA0106.11.53344
MA0107.11.33584
MA0108.20.106251
MA0109.10
MA0111.10.982123
MA0113.10.74825
MA0114.11.02124
MA0115.10.365583
MA0116.12.01536
MA0117.11.17644
MA0119.12.90501
MA0122.10.667475
MA0124.10.333911
MA0125.10.272745
MA0130.10
MA0131.10.248636
MA0132.10
MA0133.10
MA0135.10.215386
MA0136.10.0369375
MA0139.10.999742
MA0140.10.492673
MA0141.10.0812823
MA0142.10.0932211
MA0143.10.0516412
MA0144.10.225549
MA0145.18.68779
MA0146.16.73774
MA0147.10.300661
MA0148.10.0187432
MA0149.10.249619
MA0062.20.852077
MA0035.20.107918
MA0039.215.7093
MA0138.20.498427
MA0002.20.319182
MA0137.20.0538152
MA0104.20.514016
MA0047.20.042965
MA0112.25.7829
MA0065.20.102375
MA0150.10.393541
MA0151.10
MA0152.10.0269807
MA0153.10.260996
MA0154.12.28524
MA0155.14.41302
MA0156.10.0552371
MA0157.10.0816079
MA0158.10
MA0159.11.11902
MA0160.10.233502
MA0161.10
MA0162.12.00053
MA0163.14.76601
MA0164.10.055624
MA0080.20.0426084
MA0018.20.177725
MA0099.21.18243
MA0079.213.6984
MA0102.20.616902
MA0258.10.845592
MA0259.10.0193094
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#10664211.786752124358340.003956454479980330.0189928364329227
E2F1#1869231.791586538765470.002254273795155510.012804378141744
MYC#4609221.823653986911220.002340236975681950.0132673981925549
POLR2A#5430592.011106943125811.33117697459636e-152.46939239875433e-13
SMARCC1#659964.158415173298240.003206063014016610.0168167352278078
STAT3#6774152.504634523131960.0006787194324858910.00547457358737983
TFAP2A#7020102.622005456038880.004391873499157240.0208132714574137
TFAP2C#7022172.916775974089274.14543338165909e-050.00075229351337462
ZEB1#6935205.361406989696463.10677472077757e-103.12891461006065e-08



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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