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{{Coexpression_clusters
{
|full_id=C525_tubular_vagina_cervix_rectum_Placental_colon_Hair
|

Latest revision as of 11:24, 17 September 2013


Full id: C525_tubular_vagina_cervix_rectum_Placental_colon_Hair



Phase1 CAGE Peaks

Hg19::chr10:4007246..4007251,+p@chr10:4007246..4007251
+
Hg19::chr11:65144695..65144697,-p@chr11:65144695..65144697
-
Hg19::chr14:102027518..102027524,-p@chr14:102027518..102027524
-
Hg19::chr14:102027537..102027598,-p@chr14:102027537..102027598
-
Hg19::chr14:102027607..102027620,-p@chr14:102027607..102027620
-
Hg19::chr14:102027691..102027715,-p@chr14:102027691..102027715
-
Hg19::chr16:1128952..1128957,+p4@SSTR5
Hg19::chr16:1129001..1129004,+p6@SSTR5
Hg19::chr20:42980646..42980651,+p@chr20:42980646..42980651
+
Hg19::chr21:36208874..36208890,+p@chr21:36208874..36208890
+
Hg19::chr21:36208893..36208906,+p@chr21:36208893..36208906
+
Hg19::chr2:109605543..109605554,-p4@EDAR
Hg19::chr2:109605568..109605573,-p6@EDAR
Hg19::chr2:109605588..109605606,-p2@EDAR
Hg19::chr4:93623257..93623261,+p@chr4:93623257..93623261
+
Hg19::chr6:137365402..137365416,-p8@IL20RA
Hg19::chr7:45928212..45928215,+p14@IGFBP1


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:0065008regulation of biological quality0.0119799206895422
GO:0007431salivary gland development0.0124043961038235
GO:0004994somatostatin receptor activity0.0124043961038235
GO:0042346positive regulation of NF-kappaB import into nucleus0.0124043961038235
GO:0035272exocrine system development0.0124043961038235
GO:0042993positive regulation of transcription factor import into nucleus0.0124043961038235
GO:0050796regulation of insulin secretion0.0124043961038235
GO:0042307positive regulation of protein import into nucleus0.0124043961038235
GO:0046824positive regulation of nucleocytoplasmic transport0.0124043961038235
GO:0051222positive regulation of protein transport0.0124043961038235
GO:0042345regulation of NF-kappaB import into nucleus0.0124043961038235
GO:0042348NF-kappaB import into nucleus0.0124043961038235
GO:0065007biological regulation0.0124043961038235
GO:0030073insulin secretion0.0124043961038235
GO:0042593glucose homeostasis0.0124043961038235
GO:0033500carbohydrate homeostasis0.0124043961038235
GO:0022404molting cycle process0.0124043961038235
GO:0001942hair follicle development0.0124043961038235
GO:0022405hair cycle process0.0124043961038235
GO:0042633hair cycle0.0124043961038235
GO:0042303molting cycle0.0124043961038235
GO:0046883regulation of hormone secretion0.0124043961038235
GO:0002790peptide secretion0.0124043961038235
GO:0042475odontogenesis of dentine-containing teeth0.0124043961038235
GO:0030072peptide hormone secretion0.0124043961038235
GO:0042990regulation of transcription factor import into nucleus0.0124043961038235
GO:0042991transcription factor import into nucleus0.0124043961038235
GO:0042306regulation of protein import into nucleus0.0124043961038235
GO:0033157regulation of intracellular protein transport0.0124043961038235
GO:0004872receptor activity0.0127727213189944
GO:0042476odontogenesis0.0127727213189944
GO:0032386regulation of intracellular transport0.0127727213189944
GO:0051223regulation of protein transport0.0138701117521645
GO:0046822regulation of nucleocytoplasmic transport0.0139423432406483
GO:0046879hormone secretion0.0158756554137676
GO:0051050positive regulation of transport0.0166232626728935
GO:0005520insulin-like growth factor binding0.0166232626728935
GO:0015833peptide transport0.0166232626728935
GO:0004871signal transducer activity0.0166232626728935
GO:0060089molecular transducer activity0.0166232626728935
GO:0048732gland development0.0180796828083034
GO:0009653anatomical structure morphogenesis0.0180796828083034
GO:0008188neuropeptide receptor activity0.0181876457184049
GO:0042923neuropeptide binding0.0181876457184049
GO:0051046regulation of secretion0.0214033011731342
GO:0003001generation of a signal involved in cell-cell signaling0.0248296422928927
GO:0045177apical part of cell0.0298348531050072
GO:0019838growth factor binding0.0302283557850762
GO:0006606protein import into nucleus0.0316777496862145
GO:0051170nuclear import0.0316777496862145
GO:0007596blood coagulation0.0316777496862145
GO:0050817coagulation0.0316777496862145
GO:0007165signal transduction0.0316777496862145
GO:0007599hemostasis0.0316777496862145
GO:0051049regulation of transport0.0325756316374623
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0340193783461287
GO:0019935cyclic-nucleotide-mediated signaling0.0342424189330173
GO:0017038protein import0.0342424189330173
GO:0050878regulation of body fluid levels0.0344852227673087
GO:0042060wound healing0.0350398057358722
GO:0007154cell communication0.0350398057358722
GO:0008544epidermis development0.0353904821731165
GO:0030594neurotransmitter receptor activity0.0353904821731165
GO:0050794regulation of cellular process0.0353904821731165
GO:0042165neurotransmitter binding0.0353904821731165
GO:0007398ectoderm development0.0353904821731165
GO:0001653peptide receptor activity0.0353904821731165
GO:0008528peptide receptor activity, G-protein coupled0.0353904821731165
GO:0006913nucleocytoplasmic transport0.0362248593712815
GO:0051169nuclear transport0.0362248593712815
GO:0001558regulation of cell growth0.0370784581505363
GO:0048856anatomical structure development0.0372283652565221
GO:0004888transmembrane receptor activity0.0373534571022978
GO:0050789regulation of biological process0.038333343120518
GO:0016049cell growth0.0429041116610036
GO:0040008regulation of growth0.0429041116610036
GO:0008361regulation of cell size0.0432464846577091
GO:0042277peptide binding0.0432464846577091
GO:0006605protein targeting0.0447321235486876
GO:0016021integral to membrane0.0449080317908855
GO:0008285negative regulation of cell proliferation0.0449080317908855
GO:0031224intrinsic to membrane0.0449080317908855



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>

Cell Type
Ontology termp-valuen
epithelial cell of pancreas5.56e-264
Uber Anatomy
Ontology termp-valuen
pancreas2.73e-1110
viscus7.18e-0718
Disease
Ontology termp-valuen
tubular adenocarcinoma2.74e-502
pancreatic cancer5.56e-264
endocrine gland cancer7.67e-186


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)
MA0003.12.44612
MA0004.10.221943
MA0006.10.112549
MA0007.11.77009
MA0009.10.621697
MA0014.10.154351
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.11.19386
MA0038.10.302644
MA0040.10.548121
MA0041.11.2374
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.609862
MA0051.10.299199
MA0052.10.551663
MA0055.11.42965
MA0056.10
MA0057.10.0616251
MA0058.10.153757
MA0059.10.465036
MA0060.10.422819
MA0061.10.997605
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.746772
MA0072.10.593415
MA0073.10.360965
MA0074.12.24263
MA0076.10.493997
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.11.04103
MA0089.10
MA0090.10.174619
MA0091.10.223914
MA0092.10.570207
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.11.22726
MA0103.10.706501
MA0105.10.7537
MA0106.10.33677
MA0107.10.936151
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.537797
MA0115.10.850405
MA0116.10.949722
MA0117.10.656858
MA0119.11.39041
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.11.3388
MA0140.10.269307
MA0141.10.462123
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.10.838342
MA0146.11.81242
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.740647
MA0039.20.750837
MA0138.20.997372
MA0002.20.0459391
MA0137.20.398112
MA0104.20.188874
MA0047.20.326636
MA0112.20.08608
MA0065.20.211898
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.10.48172
MA0155.12.5589
MA0156.10.12788
MA0157.11.08073
MA0158.10
MA0159.10.571105
MA0160.10.252705
MA0161.10
MA0162.10.259032
MA0163.11.7822
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.21.05686
MA0102.21.14323
MA0258.10.0605489
MA0259.10.591641
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
FOXA1#316963.911089323312510.002778694543890080.0152218242575052
FOXA2#317057.244254044901540.000452266480154110.0042057037593104
MAFF#2376439.93800408646090.003157012861100890.0165719373844248
NR3C1#290854.403830391521480.004161988042321540.0198318217516206
RXRA#625644.723439326854890.008683952615939730.0330001574521024
SETDB1#986949.487064983061290.000694182090311990.00559497479009831
SMC3#912676.194972347913526.13164858570721e-050.00100531121921927
TBP#6908102.180453345350820.005649214921644630.0255145458052951
TCF7L2#693485.068318382652876.20084288736012e-050.00101585855735373



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

This analysis result is provided for C0 - C305 clusters.

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