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{{Coexpression_clusters
{
|full_id=C124_small_temporal_duodenum_colon_gall_signet_Hepatocyte
|

Latest revision as of 10:37, 17 September 2013


Full id: C124_small_temporal_duodenum_colon_gall_signet_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr10:102792271..102792279,-p@chr10:102792271..102792279
-
Hg19::chr10:126107767..126107781,-p6@OAT
Hg19::chr10:19489600..19489603,+p@chr10:19489600..19489603
+
Hg19::chr11:1096340..1096348,+p18@MUC2
Hg19::chr11:116691835..116691843,-p@chr11:116691835..116691843
-
Hg19::chr11:116693409..116693420,-p5@APOA4
Hg19::chr11:116693448..116693457,-p6@APOA4
Hg19::chr11:116693484..116693496,-p2@APOA4
Hg19::chr11:118897805..118897827,-p@chr11:118897805..118897827
-
Hg19::chr11:18512642..18512651,-p3@ENST00000540201
Hg19::chr11:3838626..3838635,+p@chr11:3838626..3838635
+
Hg19::chr11:3838641..3838642,+p@chr11:3838641..3838642
+
Hg19::chr11:618933..618946,+p@chr11:618933..618946
+
Hg19::chr11:65594646..65594649,-p@chr11:65594646..65594649
-
Hg19::chr11:65594666..65594676,-p@chr11:65594666..65594676
-
Hg19::chr12:45227522..45227535,-p@chr12:45227522..45227535
-
Hg19::chr13:22191218..22191245,+p@chr13:22191218..22191245
+
Hg19::chr13:28555129..28555135,+p@chr13:28555129..28555135
+
Hg19::chr13:53624170..53624209,+p@chr13:53624170..53624209
+
Hg19::chr13:53625392..53625401,+p@chr13:53625392..53625401
+
Hg19::chr13:99381229..99381232,-p@chr13:99381229..99381232
-
Hg19::chr14:56691968..56692018,+p@chr14:56691968..56692018
+
Hg19::chr15:42691624..42691627,+p@chr15:42691624..42691627
+
Hg19::chr15:78112553..78112567,-p@chr15:78112553..78112567
-
Hg19::chr16:3057189..3057196,-p@chr16:3057189..3057196
-
Hg19::chr16:70451307..70451340,+p@chr16:70451307..70451340
+
Hg19::chr17:72949277..72949292,-p@chr17:72949277..72949292
-
Hg19::chr17:77704836..77704841,+p5@ENPP7
Hg19::chr17:77704870..77704893,+p1@ENPP7
Hg19::chr17:77704898..77704905,+p4@ENPP7
Hg19::chr18:19749933..19749951,+p@chr18:19749933..19749951
+
Hg19::chr19:44012170..44012191,-p@chr19:44012170..44012191
-
Hg19::chr19:55833692..55833705,-p@chr19:55833692..55833705
-
Hg19::chr1:102312517..102312566,-p6@OLFM3
Hg19::chr1:102312620..102312642,-p7@OLFM3
Hg19::chr1:144925109..144925113,-p@chr1:144925109..144925113
-
Hg19::chr1:160855045..160855065,-p4@ITLN1
Hg19::chr1:171217677..171217703,+p4@FMO1
Hg19::chr1:228332714..228332751,+p16@GUK1
Hg19::chr1:26097919..26097931,+p@chr1:26097919..26097931
+
Hg19::chr1:26380747..26380757,-p@chr1:26380747..26380757
-
Hg19::chr1:26380767..26380772,-p@chr1:26380767..26380772
-
Hg19::chr1:26380790..26380808,-p@chr1:26380790..26380808
-
Hg19::chr1:27240046..27240053,-p8@NR0B2
Hg19::chr1:27240078..27240086,-p7@NR0B2
Hg19::chr1:3334836..3334840,+p@chr1:3334836..3334840
+
Hg19::chr1:57775515..57775519,-p@chr1:57775515..57775519
-
Hg19::chr1:6508571..6508581,+p13@ESPN
Hg19::chr1:6510384..6510394,+p23@ESPN
Hg19::chr1:86942133..86942142,+p@chr1:86942133..86942142
+
Hg19::chr1:86942166..86942175,+p@chr1:86942166..86942175
+
Hg19::chr1:86959078..86959081,+p@chr1:86959078..86959081
+
Hg19::chr1:86961281..86961288,+p@chr1:86961281..86961288
+
Hg19::chr20:47736667..47736692,-p14@STAU1
Hg19::chr22:45680822..45680843,+p1@UPK3A
Hg19::chr2:163978248..163978254,+p@chr2:163978248..163978254
+
Hg19::chr2:211409814..211409826,+p@chr2:211409814..211409826
+
Hg19::chr2:211409862..211409890,+p@chr2:211409862..211409890
+
Hg19::chr2:211409894..211409903,+p@chr2:211409894..211409903
+
Hg19::chr2:211409943..211409950,+p@chr2:211409943..211409950
+
Hg19::chr2:228228128..228228132,-p@chr2:228228128..228228132
-
Hg19::chr3:124624497..124624504,-p@chr3:124624497..124624504
-
Hg19::chr3:124625073..124625076,-p@chr3:124625073..124625076
-
Hg19::chr3:124632009..124632024,-p@chr3:124632009..124632024
-
Hg19::chr3:124646562..124646577,+p@chr3:124646562..124646577
+
Hg19::chr3:124646690..124646794,-p2@MUC13
Hg19::chr3:137851220..137851236,-p1@A4GNT
Hg19::chr3:141061589..141061593,+p@chr3:141061589..141061593
+
Hg19::chr3:151488200..151488222,+p1@ENST00000471766
Hg19::chr3:171489085..171489158,-p2@PLD1
Hg19::chr3:196731017..196731038,-p4@MFI2
Hg19::chr3:196731042..196731058,-p6@MFI2
Hg19::chr3:44248030..44248052,-p@chr3:44248030..44248052
-
Hg19::chr4:156787425..156787429,-p1@ACCN5
Hg19::chr4:18413418..18413449,+p@chr4:18413418..18413449
+
Hg19::chr4:3498096..3498102,+p@chr4:3498096..3498102
+
Hg19::chr4:82136518..82136527,-p5@PRKG2
Hg19::chr4:82136547..82136556,-p8@PRKG2
Hg19::chr5:111964224..111964247,+p1@ENST00000507565
Hg19::chr5:1252162..1252173,+p@chr5:1252162..1252173
+
Hg19::chr5:13580356..13580367,+p@chr5:13580356..13580367
+
Hg19::chr5:176005056..176005065,+p10@CDHR2
Hg19::chr5:180415839..180415851,+p2@BTNL3
Hg19::chr5:180415854..180415855,+p3@BTNL3
Hg19::chr6:24667649..24667660,-p12@TDP2
Hg19::chr6:30131318..30131342,+p1@TRIM15
Hg19::chr6:33771777..33771783,-p1@MLN
Hg19::chr6:41007060..41007069,-p5@UNC5CL
Hg19::chr6:46048051..46048065,-p7@CLIC5
Hg19::chr6:49735878..49735918,+p@chr6:49735878..49735918
+
Hg19::chr7:100547045..100547068,+p5@MUC3A
p5@MUC3B
Hg19::chr7:100547108..100547121,+p10@MUC3A
p10@MUC3B
Hg19::chr7:100547126..100547133,+p17@MUC3A
p17@MUC3B
Hg19::chr7:100549628..100549639,+p@chr7:100549628..100549639
+
Hg19::chr7:100549753..100549760,+p@chr7:100549753..100549760
+
Hg19::chr7:100549962..100549971,+p29@MUC3A
p29@MUC3B
Hg19::chr7:100550005..100550012,+p32@MUC3A
p32@MUC3B
Hg19::chr7:100550054..100550059,+p30@MUC3A
p30@MUC3B
Hg19::chr7:100550098..100550108,+p18@MUC3A
p18@MUC3B
Hg19::chr7:100550117..100550128,+p20@MUC3A
p20@MUC3B
Hg19::chr7:100550132..100550163,+p13@MUC3A
p13@MUC3B
Hg19::chr7:100550170..100550189,+p14@MUC3A
p14@MUC3B
Hg19::chr7:100550244..100550247,+p35@MUC3A
p35@MUC3B
Hg19::chr7:100550336..100550433,+p4@MUC3A
p4@MUC3B
Hg19::chr7:100550489..100550538,+p8@MUC3A
p8@MUC3B
Hg19::chr7:100550555..100550565,+p7@uc003uxk.1
p7@uc003uxl.1
Hg19::chr7:100550596..100550604,+p6@uc003uxk.1
p6@uc003uxl.1
Hg19::chr7:100550674..100550679,+p8@uc003uxk.1
p8@uc003uxl.1
Hg19::chr7:100550681..100550704,+p2@uc003uxk.1
p2@uc003uxl.1
Hg19::chr7:100550763..100550784,+p3@uc003uxk.1
p3@uc003uxl.1
Hg19::chr7:100551088..100551101,+p16@MUC3A
p16@MUC3B
Hg19::chr7:100551219..100551228,+p26@MUC3A
p26@MUC3B
Hg19::chr7:100551230..100551237,+p27@MUC3A
p27@MUC3B
Hg19::chr7:100551239..100551256,+p19@MUC3A
p19@MUC3B
Hg19::chr7:100551308..100551323,+p24@MUC3A
p24@MUC3B
Hg19::chr7:100551899..100551912,+p@chr7:100551899..100551912
+
Hg19::chr7:100552070..100552081,+p@chr7:100552070..100552081
+
Hg19::chr7:100552090..100552101,+p@chr7:100552090..100552101
+
Hg19::chr7:100686250..100686262,+p2@MUC17
Hg19::chr7:100686366..100686377,+p3@MUC17
Hg19::chr7:104566986..104566997,-p2@ENST00000453666
Hg19::chr7:2660988..2661037,-p@chr7:2660988..2661037
-
Hg19::chr8:145548806..145548817,-p@chr8:145548806..145548817
-
Hg19::chr8:145640490..145640504,-p7@SLC39A4
Hg19::chr8:145640522..145640534,-p12@SLC39A4
Hg19::chr8:22210333..22210344,+p4@PIWIL2
Hg19::chr8:24204448..24204463,+p8@ADAM28
Hg19::chr8:24204479..24204495,+p9@ADAM28
Hg19::chr8:97016684..97016693,+p@chr8:97016684..97016693
+
Hg19::chr9:104183943..104183950,-p4@BC005314
Hg19::chr9:139746767..139746770,+p11@MAMDC4
Hg19::chr9:139746792..139746818,+p1@MAMDC4
Hg19::chr9:139746832..139746855,+p2@MAMDC4
Hg19::chr9:140125826..140125846,+p2@SLC34A3
Hg19::chr9:140130843..140130851,-p@chr9:140130843..140130851
-
Hg19::chr9:140130858..140130892,-p@chr9:140130858..140130892
-
Hg19::chr9:79224043..79224051,+p@chr9:79224043..79224051
+
Hg19::chrX:117264792..117264799,-p@chrX:117264792..117264799
-
Hg19::chrX:117265007..117265018,-p@chrX:117265007..117265018
-
Hg19::chrX:117265048..117265054,-p@chrX:117265048..117265054
-
Hg19::chrX:128902672..128902685,+p7@XPNPEP2
Hg19::chrX:16668278..16668282,+p1@S100G
Hg19::chrX:99891213..99891231,-p9@TSPAN6


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:0005903brush border0.000687362843644439
GO:0042995cell projection0.0029084699085851
GO:0030197extracellular matrix constituent, lubricant activity0.00785812005792903
GO:0035091phosphoinositide binding0.0118441401365482
GO:0005902microvillus0.0130601985075169
GO:0008289lipid binding0.0168587629736622
GO:0048503GPI anchor binding0.0168587629736622
GO:0005543phospholipid binding0.017651127421833
GO:0016021integral to membrane0.0216586827033733
GO:0031224intrinsic to membrane0.0216586827033733
GO:0016020membrane0.0216586827033733
GO:0044425membrane part0.0305015895443306
GO:0004587ornithine-oxo-acid transaminase activity0.0305015895443306
GO:0005727extrachromosomal circular DNA0.0305015895443306
GO:0046821extrachromosomal DNA0.0305015895443306
GO:0000267cell fraction0.0481377214765729
GO:0033194response to hydroperoxide0.0481377214765729
GO:0006982response to lipid hydroperoxide0.0481377214765729
GO:0009624response to nematode0.0481377214765729
GO:0006629lipid metabolic process0.0484555892396601



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>

Cell Type
Ontology termp-valuen
intestinal epithelial cell2.61e-084
Uber Anatomy
Ontology termp-valuen
intestine2.71e-5617
small intestine1.37e-514
gastrointestinal system3.81e-3925
colon1.69e-139
large intestine3.14e-1111
duodenum7.42e-112
subdivision of digestive tract8.74e-09118
intestinal mucosa2.61e-084
wall of intestine2.61e-084
gastrointestinal system mucosa2.61e-084
gastrointestinal system epithelium2.61e-084
intestinal epithelium2.61e-084
digestive system3.50e-07145
digestive tract3.50e-07145
primitive gut3.50e-07145


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)
MA0003.15.56743e-11
MA0004.10.0544436
MA0006.10.0326903
MA0007.10.00544475
MA0009.10.0460346
MA0014.12.89677e-08
MA0017.14.90623
MA0019.10.0523398
MA0024.10.0226067
MA0025.10.30663
MA0027.11.29058
MA0028.10.000266262
MA0029.11.16311
MA0030.10.474237
MA0031.10.17518
MA0038.10.0809309
MA0040.10.114202
MA0041.10.132331
MA0042.10.2615
MA0043.10.0461215
MA0046.10.671928
MA0048.10.0229072
MA0050.10.0929601
MA0051.10.0775591
MA0052.10.02804
MA0055.10.27035
MA0056.10
MA0057.10.0063608
MA0058.10.0039526
MA0059.10.244755
MA0060.10.0102923
MA0061.10.60721
MA0063.10
MA0066.13.00089
MA0067.10.539614
MA0068.10.0012258
MA0069.10.162642
MA0070.10.353554
MA0071.10.205461
MA0072.10.150064
MA0073.12.23088e-10
MA0074.10.272002
MA0076.10.0015323
MA0077.10.14408
MA0078.11.39303
MA0081.10.0977496
MA0083.10.181399
MA0084.10.304581
MA0087.10.967796
MA0088.10.267137
MA0089.10
MA0090.11.54611
MA0091.10.19262
MA0092.10.621641
MA0093.10.00734654
MA0095.10
MA0098.10
MA0100.11.23381
MA0101.10.612031
MA0103.11.92048
MA0105.11.22981
MA0106.10.050346
MA0107.10.315233
MA0108.20.171889
MA0109.10
MA0111.10.542931
MA0113.10.256403
MA0114.13.99034
MA0115.11.38623
MA0116.10.842335
MA0117.10.795305
MA0119.10.54951
MA0122.10.503161
MA0124.10.770077
MA0125.10.0846128
MA0130.10
MA0131.10.580686
MA0132.10
MA0133.10
MA0135.10.77639
MA0136.10.17309
MA0139.10.0950975
MA0140.11.17734
MA0141.10.806194
MA0142.10.0522281
MA0143.10.0592133
MA0144.13.29997
MA0145.10.0603668
MA0146.10.00452278
MA0147.10.00724907
MA0148.10.950808
MA0149.10.0461021
MA0062.26.29661e-07
MA0035.22.93149
MA0039.23.98081e-10
MA0138.21.40026
MA0002.23.64175
MA0137.20.719198
MA0104.20.0100228
MA0047.20.759854
MA0112.20.104852
MA0065.20.883052
MA0150.10.138231
MA0151.10
MA0152.10.212648
MA0153.11.43551
MA0154.10.143926
MA0155.10.000658943
MA0156.10.052631
MA0157.10.246084
MA0158.10
MA0159.10.188783
MA0160.10.801529
MA0161.10
MA0162.11.02556e-12
MA0163.10.0155047
MA0164.10.676963
MA0080.20.106217
MA0018.20.579454
MA0099.20.0210554
MA0079.20
MA0102.20.331438
MA0258.10.83193
MA0259.10.394219
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
HNF4A#3172142.264699755813650.003764925949741760.0186009319866162



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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