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Coexpression cluster:C1021: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.600139,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.555925,0.0394821,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.163559,0.560708,0.341703,0.405031,0.472508,0.805193,0.385586,0.619829,0.135503,0.470396,0.304828,0.388322,0.429397,0.810962,0.220667,0.154814,0.742281,0.858275,0.266487,0.481208,0.685417,0.518171,0.268162,0.413601,0.444349,0.809926,0.198862,0.371118,0.555735,0.440085,0.416595,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.776738,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.304852,1.03748,0.455523,0.138565,0.401476,0.730167,0.797419,0.379656,0.96869,0.745864,0.575394,0.19474,0.986227,0.237806,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.162291,0.87,0.664183,0.345507,0.246049,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.116216,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.283443,0.0510299,0.960402,0.53901,0.557588,3.02211,0.643609,0.786331,0.385642,0.357927,1.15277,0.941964,0.796636,0.948033,0.71907,0.574616,0.213234,3.42981,0.0203307
|tfbs_overrepresentation_jaspar=MA0003.1;0.0264723,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.0484929,MA0017.1;0.337901,MA0019.1;2.49556,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;1.94446,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;2.0979,MA0048.1;0.0955945,MA0050.1;1.12793,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.118169,MA0056.1;0,MA0057.1;0.632427,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.0041831,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.199853,MA0089.1;0,MA0090.1;1.01596,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.792149,MA0105.1;0.0818021,MA0106.1;3.62859,MA0107.1;0.666147,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;1.82745,MA0145.1;0.830366,MA0146.1;0.239099,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.0817047,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.208783,MA0065.2;0.226158,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;2.32222,MA0154.1;0.274121,MA0155.1;0.43752,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.194027,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.00346431,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:38, 22 January 2013


Full id: C1021_Small_Bronchial_Tracheal_Mallassezderived_Gingival_Sebocyte_squamous



Phase1 CAGE Peaks

Hg19::chr12:56332022..56332030,+p17@DGKA
Hg19::chr1:153537328..153537329,-p5@S100A2
Hg19::chr1:183133608..183133625,-p@chr1:183133608..183133625
-
Hg19::chr1:209827500..209827512,-p@chr1:209827500..209827512
-
Hg19::chr1:209827520..209827532,-p@chr1:209827520..209827532
-
Hg19::chr8:29526932..29526947,-p@chr8:29526932..29526947
-
Hg19::chr8:49783129..49783154,+p@chr8:49783129..49783154
+
Hg19::chr9:21683189..21683195,+p@chr9:21683189..21683195
+


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:0043542endothelial cell migration0.0262720383888429
GO:0004143diacylglycerol kinase activity0.0262720383888429
GO:0005509calcium ion binding0.0262720383888429
GO:0007205protein kinase C activation0.0262720383888429
GO:0019992diacylglycerol binding0.0322487025371141
GO:0032147activation of protein kinase activity0.0322487025371141
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0347404066847027
GO:0048015phosphoinositide-mediated signaling0.0368975161749926
GO:0045860positive regulation of protein kinase activity0.0368975161749926
GO:0033674positive regulation of kinase activity0.0368975161749926
GO:0051347positive regulation of transferase activity0.0368975161749926
GO:0016477cell migration0.0434492764139489
GO:0045859regulation of protein kinase activity0.0434492764139489
GO:0043549regulation of kinase activity0.0434492764139489
GO:0051338regulation of transferase activity0.0434492764139489
GO:0043085positive regulation of catalytic activity0.0434492764139489
GO:0019932second-messenger-mediated signaling0.0434492764139489



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
endo-epithelial cell3.85e-3942
respiratory epithelial cell5.36e-3513
epithelial cell1.87e-30253
endodermal cell9.01e-2758
general ecto-epithelial cell3.28e-2614
epithelial cell of tracheobronchial tree2.98e-219
epithelial cell of lower respiratory tract2.98e-219
transitional epithelial cell7.39e-164
urothelial cell7.39e-164
squamous epithelial cell1.08e-1463
epithelial cell of alimentary canal1.15e-1320
bronchial epithelial cell3.97e-133
duct epithelial cell4.29e-133
branched duct epithelial cell4.29e-133
tracheal epithelial cell4.29e-133
tracheoblast4.29e-133
gingival epithelial cell5.23e-133
epithelial cell of Malassez7.17e-133
epidermal cell8.64e-119
stratified squamous epithelial cell1.17e-106
keratin accumulating cell1.17e-106
stratified epithelial cell1.17e-106
keratinizing barrier epithelial cell1.17e-106
epithelial fate stem cell1.17e-106
stratified epithelial stem cell1.17e-106
surface ectodermal cell1.17e-106
ecto-epithelial cell1.39e-0934
mammary gland epithelial cell4.49e-094
embryonic cell8.46e-09250
sebum secreting cell9.70e-092
epithelial cell of sweat gland9.70e-092
epithelial cell of skin gland9.70e-092
acinar cell of sebaceous gland9.70e-092
corneal epithelial cell1.93e-082
keratinocyte9.32e-085
Uber Anatomy
Ontology termp-valuen
urothelium6.93e-195
mouth mucosa2.69e-1713
mucosa1.40e-1620
transitional epithelium1.07e-156
mucosa of oral region2.03e-144
respiratory system mucosa2.03e-144
lower respiratory tract epithelium3.97e-133
epithelium of bronchus3.97e-133
gingival epithelium5.23e-133
endoderm-derived structure8.03e-13160
endoderm8.03e-13160
presumptive endoderm8.03e-13160
respiratory system1.26e-1274
tracheobronchial tree2.56e-1215
lower respiratory tract2.56e-1215
surface structure8.76e-1299
jaw skeleton9.37e-104
splanchnocranium9.37e-104
mammary gland4.49e-094
mammary bud4.49e-094
mammary ridge4.49e-094
mammary placode4.49e-094
skin gland9.70e-092
epidermis gland9.70e-092
gland of integumental system9.70e-092
sebaceous gland9.70e-092
skin sebaceous gland9.70e-092
sweat gland9.70e-092
sweat gland placode9.70e-092
sebaceous gland placode9.70e-092
head1.27e-0856
orifice1.86e-0836
endo-epithelium3.14e-0882
epithelium of mucosa4.99e-088
bronchus5.01e-085
respiratory tract6.78e-0854
primary subdivision of cranial skeletal system7.08e-085
epithelial fold1.29e-0747
anterior region of body1.59e-0762
craniocervical region1.59e-0762
oral opening1.75e-0722
mouth4.94e-0729
stomodeum4.94e-0729
epithelial bud7.62e-0737
Disease
Ontology termp-valuen
squamous cell carcinoma6.45e-2414


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)
MA0003.10.0264723
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.0484929
MA0017.10.337901
MA0019.12.49556
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.11.94446
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.12.0979
MA0048.10.0955945
MA0050.11.12793
MA0051.10.553205
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.10.632427
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0041831
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.0818021
MA0106.13.62859
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.82745
MA0145.10.830366
MA0146.10.239099
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.12.32222
MA0154.10.274121
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.194027
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.00346431
MA0102.21.46209
MA0258.10.603127
MA0259.10.25092
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
CEBPB#105154.981967266140510.001250523778793020.00840542237954462
STAT3#677456.57466562322140.0003394465772418640.00345059967690899
TCF7L2#693445.385088281568670.003825814635011350.0188785379005882



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1021&oldid=2569532"