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

Latest revision as of 10:34, 17 September 2013


Full id: C113_thyroid_throat_lung_lymph_small_colon_trachea



Phase1 CAGE Peaks

Hg19::chr10:24527799..24527819,+p20@KIAA1217
Hg19::chr10:95995120..95995126,+p@chr10:95995120..95995126
+
Hg19::chr10:95995491..95995500,+p@chr10:95995491..95995500
+
Hg19::chr11:114043484..114043494,-p@chr11:114043484..114043494
-
Hg19::chr11:13517531..13517550,-p1@PTH
Hg19::chr11:13517565..13517580,-p2@PTH
Hg19::chr12:101603978..101603992,-p2@SLC5A8
Hg19::chr12:132850184..132850187,-p@chr12:132850184..132850187
-
Hg19::chr14:104516015..104516028,+p7@TDRD9
Hg19::chr14:104516061..104516124,+p@chr14:104516061..104516124
+
Hg19::chr14:36575014..36575016,+p@chr14:36575014..36575016
+
Hg19::chr14:36988752..36988767,-p1@ENST00000521945
Hg19::chr14:36990386..36990397,-p16@NKX2-1
Hg19::chr14:36990398..36990415,-p10@NKX2-1
Hg19::chr14:36990416..36990438,-p4@NKX2-1
Hg19::chr14:36993892..36993912,+p@chr14:36993892..36993912
+
Hg19::chr14:81421242..81421243,+p13@TSHR
Hg19::chr14:81421428..81421431,+p11@TSHR
Hg19::chr14:81421522..81421524,+p12@TSHR
Hg19::chr14:81421861..81421875,+p5@TSHR
Hg19::chr14:81421921..81421989,+p1@TSHR
Hg19::chr15:40675222..40675233,+p4@C15orf23
Hg19::chr15:55806824..55806840,-p@chr15:55806824..55806840
-
Hg19::chr15:55806847..55806854,-p@chr15:55806847..55806854
-
Hg19::chr15:63908106..63908107,-p@chr15:63908106..63908107
-
Hg19::chr15:63908112..63908124,-p@chr15:63908112..63908124
-
Hg19::chr15:64235138..64235147,-p@chr15:64235138..64235147
-
Hg19::chr15:64235172..64235180,-p@chr15:64235172..64235180
-
Hg19::chr15:64235185..64235196,-p@chr15:64235185..64235196
-
Hg19::chr15:64235201..64235208,-p@chr15:64235201..64235208
-
Hg19::chr15:64421903..64421920,+p@chr15:64421903..64421920
+
Hg19::chr15:72448259..72448278,+p@chr15:72448259..72448278
+
Hg19::chr16:16103486..16103493,+p19@ABCC1
Hg19::chr16:56781652..56781694,+p4@AB385278
Hg19::chr16:56781737..56781741,+p8@AB385278
Hg19::chr16:56781814..56781829,+p3@AB385278
Hg19::chr16:64451926..64451964,+p@chr16:64451926..64451964
+
Hg19::chr16:66420782..66420796,+p@chr16:66420782..66420796
+
Hg19::chr16:66420861..66420868,+p@chr16:66420861..66420868
+
Hg19::chr17:41243516..41243529,-p@chr17:41243516..41243529
-
Hg19::chr17:41243533..41243543,-p@chr17:41243533..41243543
-
Hg19::chr18:45354061..45354074,+p@chr18:45354061..45354074
+
Hg19::chr18:45563449..45563457,+p@chr18:45563449..45563457
+
Hg19::chr18:45869268..45869275,+p@chr18:45869268..45869275
+
Hg19::chr18:45869281..45869293,+p@chr18:45869281..45869293
+
Hg19::chr18:47087250..47087279,+p2@LIPG
Hg19::chr18:47087304..47087313,+p8@LIPG
Hg19::chr18:47087321..47087336,+p5@LIPG
Hg19::chr18:47087361..47087374,+p3@LIPG
Hg19::chr18:53858147..53858168,-p1@ENST00000382897
Hg19::chr18:77941319..77941321,-p@chr18:77941319..77941321
-
Hg19::chr19:16495444..16495471,-p@chr19:16495444..16495471
-
Hg19::chr19:20068797..20068802,+p@chr19:20068797..20068802
+
Hg19::chr19:20069252..20069265,+p@chr19:20069252..20069265
+
Hg19::chr19:20358361..20358398,+p@chr19:20358361..20358398
+
Hg19::chr19:20382476..20382481,-p@chr19:20382476..20382481
-
Hg19::chr19:20382633..20382642,-p@chr19:20382633..20382642
-
Hg19::chr19:20386982..20386989,+p@chr19:20386982..20386989
+
Hg19::chr19:20386998..20387003,+p@chr19:20386998..20387003
+
Hg19::chr19:20387031..20387036,+p@chr19:20387031..20387036
+
Hg19::chr19:20387078..20387085,+p@chr19:20387078..20387085
+
Hg19::chr19:20468965..20468977,+p@chr19:20468965..20468977
+
Hg19::chr19:20473354..20473358,+p@chr19:20473354..20473358
+
Hg19::chr19:20473375..20473380,+p@chr19:20473375..20473380
+
Hg19::chr19:20473389..20473398,+p@chr19:20473389..20473398
+
Hg19::chr19:20473404..20473414,+p@chr19:20473404..20473414
+
Hg19::chr19:20473429..20473445,+p@chr19:20473429..20473445
+
Hg19::chr19:20473448..20473452,+p@chr19:20473448..20473452
+
Hg19::chr19:20473506..20473536,+p@chr19:20473506..20473536
+
Hg19::chr1:109720258..109720279,-p@chr1:109720258..109720279
-
Hg19::chr1:12678746..12678753,-p@chr1:12678746..12678753
-
Hg19::chr1:186316121..186316146,-p@chr1:186316121..186316146
-
Hg19::chr1:220961678..220961683,+p@chr1:220961678..220961683
+
Hg19::chr1:28261645..28261657,+p4@SMPDL3B
Hg19::chr1:36771641..36771644,+p11@SH3D21
Hg19::chr20:17953210..17953230,+p@chr20:17953210..17953230
+
Hg19::chr20:57452679..57452686,+p@chr20:57452679..57452686
+
Hg19::chr21:43770677..43770683,+p@chr21:43770677..43770683
+
Hg19::chr21:44440926..44440935,+p8@PKNOX1
Hg19::chr21:44441244..44441257,+p6@PKNOX1
Hg19::chr21:44448694..44448703,+p@chr21:44448694..44448703
+
Hg19::chr22:31522733..31522740,+p@chr22:31522733..31522740
+
Hg19::chr22:31522774..31522780,+p@chr22:31522774..31522780
+
Hg19::chr2:134788828..134788834,-p@chr2:134788828..134788834
-
Hg19::chr2:134788843..134788848,-p@chr2:134788843..134788848
-
Hg19::chr2:134788853..134788858,-p@chr2:134788853..134788858
-
Hg19::chr2:1417228..1417247,+p1@TPO
Hg19::chr2:1417430..1417444,+p@chr2:1417430..1417444
+
Hg19::chr2:1426812..1426834,+p5@TPO
Hg19::chr2:1426850..1426859,+p10@TPO
Hg19::chr2:1488557..1488560,+p22@TPO
Hg19::chr2:172309636..172309643,+p11@DCAF17
Hg19::chr2:24551030..24551033,-p16@ITSN2
Hg19::chr2:29338034..29338054,+p20@CLIP4
Hg19::chr2:74517717..74517732,-p9@SLC4A5
Hg19::chr2:85935758..85935760,-p@chr2:85935758..85935760
-
Hg19::chr2:85938623..85938632,+p@chr2:85938623..85938632
+
Hg19::chr3:164169090..164169105,+p@chr3:164169090..164169105
+
Hg19::chr3:164169110..164169124,+p@chr3:164169110..164169124
+
Hg19::chr3:193201843..193201848,-p@chr3:193201843..193201848
-
Hg19::chr3:193201889..193201922,-p@chr3:193201889..193201922
-
Hg19::chr3:193201963..193201996,-p@chr3:193201963..193201996
-
Hg19::chr3:37725131..37725145,+p4@ITGA9
Hg19::chr3:9391106..9391117,-p@chr3:9391106..9391117
-
Hg19::chr3:97686432..97686471,-p10@MINA
Hg19::chr4:109015207..109015232,-p@chr4:109015207..109015232
-
Hg19::chr4:173916930..173916942,-p1@uc003isx.1
Hg19::chr4:41131475..41131507,-p@chr4:41131475..41131507
-
Hg19::chr4:42457338..42457350,-p@chr4:42457338..42457350
-
Hg19::chr4:89658763..89658771,-p42@FAM13A
Hg19::chr4:89658773..89658782,-p38@FAM13A
Hg19::chr4:89658785..89658794,-p41@FAM13A
Hg19::chr5:125798031..125798049,+p27@GRAMD3
Hg19::chr5:156399340..156399369,-p@chr5:156399340..156399369
-
Hg19::chr5:90151468..90151479,+p@chr5:90151468..90151479
+
Hg19::chr5:90151510..90151524,+p@chr5:90151510..90151524
+
Hg19::chr5:90151536..90151543,+p@chr5:90151536..90151543
+
Hg19::chr5:90151567..90151577,+p@chr5:90151567..90151577
+
Hg19::chr6:150690053..150690058,+p3@IYD
Hg19::chr6:150690140..150690175,+p1@IYD
Hg19::chr6:150719834..150719836,+p@chr6:150719834..150719836
+
Hg19::chr6:152746723..152746726,-p@chr6:152746723..152746726
-
Hg19::chr6:152746788..152746797,-p@chr6:152746788..152746797
-
Hg19::chr6:152749469..152749476,-p@chr6:152749469..152749476
-
Hg19::chr6:43837195..43837213,-p@chr6:43837195..43837213
-
Hg19::chr6:43837226..43837237,-p@chr6:43837226..43837237
-
Hg19::chr6:46996835..46996871,-p6@GPR110
Hg19::chr7:107301045..107301057,+p9@SLC26A4
Hg19::chr7:107301065..107301076,+p8@SLC26A4
Hg19::chr7:107301236..107301244,+p10@SLC26A4
Hg19::chr7:107301340..107301345,+p13@SLC26A4
Hg19::chr7:107301406..107301418,+p5@SLC26A4
Hg19::chr7:107301420..107301434,+p7@SLC26A4
Hg19::chr7:107301447..107301451,+p23@SLC26A4
Hg19::chr7:107301483..107301492,+p14@SLC26A4
Hg19::chr7:107301517..107301529,+p12@SLC26A4
Hg19::chr7:107302560..107302575,-p2@ENST00000449741
Hg19::chr7:107302587..107302611,-p1@ENST00000449741
Hg19::chr7:107303668..107303680,+p@chr7:107303668..107303680
+
Hg19::chr7:107678217..107678226,-p3@LAMB4
Hg19::chr7:116093470..116093490,-p@chr7:116093470..116093490
-
Hg19::chr7:48284041..48284057,+p@chr7:48284041..48284057
+
Hg19::chr7:48284075..48284080,+p@chr7:48284075..48284080
+
Hg19::chr7:48284886..48284925,+p@chr7:48284886..48284925
+
Hg19::chr7:88388567..88388605,+p5@ZNF804B
Hg19::chr7:88388628..88388669,+p6@ZNF804B
Hg19::chr7:88389004..88389019,+p1@ZNF804B
Hg19::chr7:90675197..90675213,+p@chr7:90675197..90675213
+
Hg19::chr8:110374683..110374759,+p1@PKHD1L1
Hg19::chr8:133899297..133899305,-p@chr8:133899297..133899305
-
Hg19::chr8:133900307..133900325,-p@chr8:133900307..133900325
-
Hg19::chr8:134147075..134147104,+p@chr8:134147075..134147104
+
Hg19::chr8:29177729..29177743,-p@chr8:29177729..29177743
-
Hg19::chr8:29177800..29177807,-p@chr8:29177800..29177807
-
Hg19::chr8:29177815..29177822,-p@chr8:29177815..29177822
-
Hg19::chr8:29177832..29177841,-p@chr8:29177832..29177841
-
Hg19::chr8:48610431..48610439,+p24@KIAA0146
Hg19::chr9:100614368..100614372,+p@chr9:100614368..100614372
+
Hg19::chr9:100615296..100615313,-p@chr9:100615296..100615313
-
Hg19::chr9:100615546..100615558,+p4@FOXE1
Hg19::chr9:100616714..100616732,+p@chr9:100616714..100616732
+
Hg19::chr9:130404639..130404649,+p@chr9:130404639..130404649
+
Hg19::chr9:130404725..130404737,+p@chr9:130404725..130404737
+
Hg19::chr9:3898653..3898681,+p1@GLIS3-AS1
Hg19::chrX:43587398..43587403,+p@chrX:43587398..43587403
+


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:0030878thyroid gland development0.00244326503363639
GO:0006590thyroid hormone generation0.00244326503363639
GO:0042403thyroid hormone metabolic process0.00298269866463447
GO:0015108chloride transmembrane transporter activity0.0141994706185855
GO:0035270endocrine system development0.0141994706185855
GO:0048732gland development0.0230772003905823
GO:0031856parathyroid hormone receptor binding0.027514158822059
GO:0060022hard palate development0.027514158822059
GO:0015103inorganic anion transmembrane transporter activity0.027514158822059
GO:0006576biogenic amine metabolic process0.027514158822059
GO:0004996thyroid-stimulating hormone receptor activity0.027514158822059
GO:0015111iodide transmembrane transporter activity0.027514158822059
GO:0060023soft palate development0.027514158822059
GO:0004447iodide peroxidase activity0.027514158822059
GO:0021798forebrain dorsal/ventral pattern formation0.027514158822059
GO:0008970phospholipase A1 activity0.027514158822059
GO:0042445hormone metabolic process0.029257394218803
GO:0006575amino acid derivative metabolic process0.029257394218803
GO:0035081induction of programmed cell death by hormones0.0314350345810171
GO:0008628induction of apoptosis by hormones0.0314350345810171
GO:0060021palate development0.0314350345810171
GO:0006357regulation of transcription from RNA polymerase II promoter0.0367889686043127
GO:0021871forebrain regionalization0.0367889686043127
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0367889686043127
GO:0019935cyclic-nucleotide-mediated signaling0.0383389715790313
GO:0048522positive regulation of cellular process0.0394759063720948
GO:0004465lipoprotein lipase activity0.0488536259329727



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
throat4.22e-982
thyroid gland1.81e-405
pharyngeal pouch1.81e-405
thyroid diverticulum1.81e-405
pharyngeal pouch 21.81e-405
thyroid primordium1.81e-405
neck1.04e-2010
entire pharyngeal arch endoderm4.28e-1911
early pharyngeal endoderm4.28e-1911
pharyngeal arch system4.07e-1218
endocrine gland9.98e-0735


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)
MA0003.11.35814e-10
MA0004.10.106217
MA0006.10.0050523
MA0007.12.42683
MA0009.10.129499
MA0014.11.08231e-05
MA0017.10.846137
MA0019.10.151702
MA0024.10.066695
MA0025.10.523159
MA0027.11.23018
MA0028.10.0171532
MA0029.10.076431
MA0030.10.600695
MA0031.11.68849
MA0038.10.85492
MA0040.10.0795419
MA0041.15.05366
MA0042.12.84633
MA0043.10.031882
MA0046.11.23244
MA0048.10.00375805
MA0050.10.0473926
MA0051.10.28795
MA0052.10.401003
MA0055.10.0275204
MA0056.10
MA0057.10.17001
MA0058.10.0821875
MA0059.10.0804928
MA0060.12.40561e-06
MA0061.10.798671
MA0063.10
MA0066.10.636897
MA0067.10.457967
MA0068.10.0820161
MA0069.13.24115
MA0070.10.111665
MA0071.11.6929
MA0072.10.493666
MA0073.10
MA0074.10.614345
MA0076.10.00184071
MA0077.10.768814
MA0078.10.0501194
MA0081.10.68
MA0083.10.0334619
MA0084.10.26253
MA0087.10.488438
MA0088.10.00163538
MA0089.10
MA0090.13.48347
MA0091.12.0308
MA0092.10.546226
MA0093.10.121251
MA0095.10
MA0098.10
MA0100.10.0199042
MA0101.11.76074
MA0103.11.54888
MA0105.10.383456
MA0106.10.257547
MA0107.11.18792
MA0108.21.29065
MA0109.10
MA0111.11.46296
MA0113.13.04417
MA0114.10.191558
MA0115.10.112623
MA0116.10.0754026
MA0117.10.0406109
MA0119.11.31785
MA0122.12.05986
MA0124.11.59458
MA0125.10.846219
MA0130.10
MA0131.10.137383
MA0132.10
MA0133.10
MA0135.10.0388105
MA0136.10.0493625
MA0139.10.01813
MA0140.10.12048
MA0141.10.043881
MA0142.10.838812
MA0143.11.48826
MA0144.10.100206
MA0145.10.00677704
MA0146.17.31214e-06
MA0147.10.00175666
MA0148.11.1043
MA0149.10.00763435
MA0062.20.000433003
MA0035.20.061254
MA0039.29.16111e-16
MA0138.20.381237
MA0002.20.732047
MA0137.20.240078
MA0104.20.000364167
MA0047.21.60821
MA0112.20.00251042
MA0065.20.223013
MA0150.10.519489
MA0151.10
MA0152.11.14741
MA0153.11.21974
MA0154.10.355461
MA0155.10.0284358
MA0156.10.00975136
MA0157.13.48607
MA0158.10
MA0159.10.0827717
MA0160.10.398486
MA0161.10
MA0162.16.89494e-14
MA0163.11.01492e-06
MA0164.11.57417
MA0080.20.0251925
MA0018.20.260351
MA0099.20.0292838
MA0079.20
MA0102.20.287916
MA0258.10.0190131
MA0259.10.000904668
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#2351292.733588049694340.006200522007882640.0273978811127625



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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