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Coexpression cluster:C436: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.610853,4.11427,0.283006,0.165202,1.79318,0.164151,0.21518,3.00484,0.0978594,0.153481,0.446032,0.246281,0.0638208,0.207164,0.0634553,0.928857,0.386278,1.03518,1.27483,0.222044,0.0832107,0.681145,0.480786,0.061867,0.346469,2.06241,3.2421,0.157865,0.232674,0.242092,0.132203,1.07066,0.30708,3.02832,0.417757,0.6851,0.0488212,0.16489,0.157401,0.082891,0.185583,0.388602,0.777426,0.488521,1.02551,0.66769,0.617815,0.429484,1.21614,0.232836,0.273745,0.637443,1.28087,0.482679,1.50023,0.209199,0.512266,0.186863,4.08,0.18619,0.451758,0.217609,0.742416,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.10522,0.0215101,0.616804,0.0126142,1.07288,0.984849,0.349828,0.405538,0.103348,0.0167689,0.362659,0.230109,0.251709,0.570388,0.0119898,0.0475979,0.911538,0.293613,1.14619,0.786844,0.546282,0.43117,2.29069,0.496807,0.348406,0.0155039,0.467605,0.297172,1.8323,0.0408868,1.09109,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.0887009,0.460417,0.0805233,0.460536,0.741849,0.181704,0.0189649,0.131498,0.887846,0.14017,0.60929,0.291743,0.162396,0.670128,0.846043,0.350442,0.210743,0.435409,0.648109,0.350382,1.34916,0.826452,0.66129,1.23665,0.798972,0.215,0.128702,0.929703,0.759101,1.59408,1.19737,0.724259,1.14509,1.17354,0.327989,0.181235,0.84518,3.16865,0.3837,0.314918,0.41217,0.000779656,0.547236,0.706679,0.217268,0.922839,0.281215,0.058186,0.346552,0.0916077,0.723128,1.31504,0.404879,0.64194,0.340824,0.229543,0.029532,0.214247,1.33302
|tfbs_overrepresentation_for_novel_motifs=0.610853,4.11427,0.283006,0.165202,1.79318,0.164151,0.21518,3.00484,0.0978594,0.153481,0.446032,0.246281,0.0638208,0.207164,0.0634553,0.928857,0.386278,1.03518,1.27483,0.222044,0.0832107,0.681145,0.480786,0.061867,0.346469,2.06241,3.2421,0.157865,0.232674,0.242092,0.132203,1.07066,0.30708,3.02832,0.417757,0.6851,0.0488212,0.16489,0.157401,0.082891,0.185583,0.388602,0.777426,0.488521,1.02551,0.66769,0.617815,0.429484,1.21614,0.232836,0.273745,0.637443,1.28087,0.482679,1.50023,0.209199,0.512266,0.186863,4.08,0.18619,0.451758,0.217609,0.742416,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.10522,0.0215101,0.616804,0.0126142,1.07288,0.984849,0.349828,0.405538,0.103348,0.0167689,0.362659,0.230109,0.251709,0.570388,0.0119898,0.0475979,0.911538,0.293613,1.14619,0.786844,0.546282,0.43117,2.29069,0.496807,0.348406,0.0155039,0.467605,0.297172,1.8323,0.0408868,1.09109,0.462798,0.389311,0.326595,0.142545,0.376249,0.204779,0.106511,0.057369,0.0887009,0.460417,0.0805233,0.460536,0.741849,0.181704,0.0189649,0.131498,0.887846,0.14017,0.60929,0.291743,0.162396,0.670128,0.846043,0.350442,0.210743,0.435409,0.648109,0.350382,1.34916,0.826452,0.66129,1.23665,0.798972,0.215,0.128702,0.929703,0.759101,1.59408,1.19737,0.724259,1.14509,1.17354,0.327989,0.181235,0.84518,3.16865,0.3837,0.314918,0.41217,0.000779656,0.547236,0.706679,0.217268,0.922839,0.281215,0.058186,0.346552,0.0916077,0.723128,1.31504,0.404879,0.64194,0.340824,0.229543,0.029532,0.214247,1.33302
|tfbs_overrepresentation_jaspar=MA0003.1;0.0316581,MA0004.1;0.454064,MA0006.1;0.226525,MA0007.1;1.3585,MA0009.1;0.510226,MA0014.1;0.0358715,MA0017.1;2.63311,MA0019.1;0.250001,MA0024.1;0.419164,MA0025.1;0.630648,MA0027.1;2.07466,MA0028.1;0.0703882,MA0029.1;0.435662,MA0030.1;0.425859,MA0031.1;0.371592,MA0038.1;0.21714,MA0040.1;0.440685,MA0041.1;0.160207,MA0042.1;0.140252,MA0043.1;0.510506,MA0046.1;0.500598,MA0048.1;0.997626,MA0050.1;0.14079,MA0051.1;0.214141,MA0052.1;0.444013,MA0055.1;1.49238,MA0056.1;0,MA0057.1;0.952301,MA0058.1;0.645288,MA0059.1;2.16453,MA0060.1;0.0226691,MA0061.1;0.0163713,MA0063.1;0,MA0066.1;1.16636,MA0067.1;0.802392,MA0068.1;0.0481509,MA0069.1;0.497197,MA0070.1;0.487346,MA0071.1;0.556315,MA0072.1;0.483399,MA0073.1;0.149666,MA0074.1;0.213609,MA0076.1;0.102323,MA0077.1;0.476645,MA0078.1;0.287843,MA0081.1;0.0933581,MA0083.1;0.516887,MA0084.1;0.981601,MA0087.1;0.481255,MA0088.1;3.17436,MA0089.1;0,MA0090.1;1.18649,MA0091.1;0.15013,MA0092.1;0.797436,MA0093.1;0.497967,MA0095.1;0,MA0098.1;0,MA0100.1;0.227084,MA0101.1;0.234552,MA0103.1;1.7266,MA0105.1;0.05512,MA0106.1;0.690773,MA0107.1;0.147785,MA0108.2;0.965791,MA0109.1;0,MA0111.1;0.755523,MA0113.1;0.719094,MA0114.1;5.55179,MA0115.1;0.730438,MA0116.1;0.982098,MA0117.1;0.543727,MA0119.1;2.06695,MA0122.1;0.567011,MA0124.1;0.691722,MA0125.1;0.614264,MA0130.1;0,MA0131.1;0.302006,MA0132.1;0,MA0133.1;0,MA0135.1;0.537249,MA0136.1;0.222179,MA0139.1;2.03732,MA0140.1;0.551956,MA0141.1;2.15395,MA0142.1;0.345512,MA0143.1;0.259501,MA0144.1;0.0312488,MA0145.1;1.13922,MA0146.1;4.07901,MA0147.1;1.42161,MA0148.1;0.164295,MA0149.1;0.18183,MA0062.2;0.0710269,MA0035.2;0.550801,MA0039.2;0.225951,MA0138.2;0.288795,MA0002.2;0.0879293,MA0137.2;0.073361,MA0104.2;1.08293,MA0047.2;0.238164,MA0112.2;8.20982,MA0065.2;5.00358,MA0150.1;0.347297,MA0151.1;0,MA0152.1;0.192836,MA0153.1;0.598889,MA0154.1;1.11603,MA0155.1;2.72219,MA0156.1;0.0744198,MA0157.1;0.323429,MA0158.1;0,MA0159.1;1.00105,MA0160.1;2.25313,MA0161.1;0,MA0162.1;0.000349302,MA0163.1;6.42452,MA0164.1;0.268764,MA0080.2;0.0646165,MA0018.2;0.248141,MA0099.2;0.193081,MA0079.2;0.00272793,MA0102.2;1.01759,MA0258.1;5.88135,MA0259.1;0.374822,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


Full id: C436_Sebocyte_Prostate_Keratinocyte_Urothelial_Small_Mammary_salivary



Phase1 CAGE Peaks

Hg19::chr16:68729719..68729736,+p@chr16:68729719..68729736
+
Hg19::chr17:38632848..38632877,-p@chr17:38632848..38632877
-
Hg19::chr17:38633713..38633724,-p@chr17:38633713..38633724
-
Hg19::chr17:38643526..38643552,-p@chr17:38643526..38643552
-
Hg19::chr17:38643557..38643572,-p@chr17:38643557..38643572
-
Hg19::chr17:38644869..38644880,-p6@TNS4
Hg19::chr17:38644941..38644954,-p3@TNS4
Hg19::chr17:38644978..38645006,-p2@TNS4
Hg19::chr17:38645025..38645036,-p5@TNS4
Hg19::chr17:38645088..38645099,-p20@TNS4
Hg19::chr17:38652289..38652317,-p4@TNS4
Hg19::chr17:38652332..38652344,-p18@TNS4
Hg19::chr17:38652393..38652403,-p16@TNS4
Hg19::chr17:38652451..38652464,-p8@TNS4
Hg19::chr17:73736444..73736457,+p@chr17:73736444..73736457
+
Hg19::chr17:73746889..73746902,+p@chr17:73746889..73746902
+
Hg19::chr17:73747066..73747079,+p@chr17:73747066..73747079
+
Hg19::chr17:73748563..73748616,+p@chr17:73748563..73748616
+
Hg19::chr17:73750773..73750793,+p@chr17:73750773..73750793
+
Hg19::chr17:73750800..73750821,+p@chr17:73750800..73750821
+
Hg19::chr17:73750858..73750868,+p@chr17:73750858..73750868
+
Hg19::chr17:73753525..73753536,+p@chr17:73753525..73753536
+
Hg19::chr5:93905715..93905716,+p2@uc003kkq.1


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

No GOStat results

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 cell1.48e-4042
epithelial cell1.47e-33253
endodermal cell1.04e-3058
epithelial cell of alimentary canal3.68e-2420
respiratory epithelial cell6.19e-2013
general ecto-epithelial cell9.30e-1314
acinar cell2.16e-125
epithelial cell of tracheobronchial tree5.90e-129
epithelial cell of lower respiratory tract5.90e-129
transitional epithelial cell1.66e-104
urothelial cell1.66e-104
protein secreting cell3.12e-106
extraembryonic cell5.18e-0819
bronchial epithelial cell6.99e-083
acinar cell of salivary gland7.32e-083
duct epithelial cell8.57e-083
branched duct epithelial cell8.57e-083
tracheal epithelial cell8.57e-083
tracheoblast8.57e-083
gingival epithelial cell1.60e-073
chorionic membrane mesenchymal stem cell1.71e-073
stratified squamous epithelial cell6.89e-076
keratin accumulating cell6.89e-076
stratified epithelial cell6.89e-076
keratinizing barrier epithelial cell6.89e-076
epithelial fate stem cell6.89e-076
stratified epithelial stem cell6.89e-076
surface ectodermal cell6.89e-076
epidermal cell8.47e-079
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.03e-28160
endoderm2.03e-28160
presumptive endoderm2.03e-28160
respiratory system2.55e-2174
orifice1.41e-1836
digestive system5.64e-18145
digestive tract5.64e-18145
primitive gut5.64e-18145
subdivision of digestive tract7.02e-15118
extraembryonic membrane4.47e-1414
membranous layer4.47e-1414
oral opening9.47e-1422
respiratory tract1.73e-1354
foregut2.03e-1387
surface structure4.07e-1399
urothelium3.25e-125
mouth1.61e-1129
stomodeum1.61e-1129
chorion9.24e-117
mucosa1.13e-1020
transitional epithelium4.36e-106
segment of respiratory tract5.55e-1047
mouth mucosa1.08e-0913
respiratory primordium4.49e-0938
endoderm of foregut4.49e-0938
organ component layer5.70e-0966
mucosa of oral region1.13e-084
respiratory system mucosa1.13e-084
tracheobronchial tree1.88e-0815
lower respiratory tract1.88e-0815
epithelial bud1.89e-0837
head2.72e-0856
epithelial fold2.84e-0847
endo-epithelium6.09e-0882
lower respiratory tract epithelium6.99e-083
epithelium of bronchus6.99e-083
subdivision of head1.20e-0749
gingival epithelium1.60e-073
acellular anatomical structure1.71e-073
egg chorion1.71e-073
extraembryonic structure2.73e-0724
anterior region of body4.53e-0762
craniocervical region4.53e-0762
urinary system structure6.92e-0747
Disease
Ontology termp-valuen
carcinoma1.58e-12106
squamous cell carcinoma3.46e-0814
cell type cancer3.23e-07143


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)
MA0003.10.0316581
MA0004.10.454064
MA0006.10.226525
MA0007.11.3585
MA0009.10.510226
MA0014.10.0358715
MA0017.12.63311
MA0019.10.250001
MA0024.10.419164
MA0025.10.630648
MA0027.12.07466
MA0028.10.0703882
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.160207
MA0042.10.140252
MA0043.10.510506
MA0046.10.500598
MA0048.10.997626
MA0050.10.14079
MA0051.10.214141
MA0052.10.444013
MA0055.11.49238
MA0056.10
MA0057.10.952301
MA0058.10.645288
MA0059.12.16453
MA0060.10.0226691
MA0061.10.0163713
MA0063.10
MA0066.11.16636
MA0067.10.802392
MA0068.10.0481509
MA0069.10.497197
MA0070.10.487346
MA0071.10.556315
MA0072.10.483399
MA0073.10.149666
MA0074.10.213609
MA0076.10.102323
MA0077.10.476645
MA0078.10.287843
MA0081.10.0933581
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.13.17436
MA0089.10
MA0090.11.18649
MA0091.10.15013
MA0092.10.797436
MA0093.10.497967
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.10.234552
MA0103.11.7266
MA0105.10.05512
MA0106.10.690773
MA0107.10.147785
MA0108.20.965791
MA0109.10
MA0111.10.755523
MA0113.10.719094
MA0114.15.55179
MA0115.10.730438
MA0116.10.982098
MA0117.10.543727
MA0119.12.06695
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.302006
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.222179
MA0139.12.03732
MA0140.10.551956
MA0141.12.15395
MA0142.10.345512
MA0143.10.259501
MA0144.10.0312488
MA0145.11.13922
MA0146.14.07901
MA0147.11.42161
MA0148.10.164295
MA0149.10.18183
MA0062.20.0710269
MA0035.20.550801
MA0039.20.225951
MA0138.20.288795
MA0002.20.0879293
MA0137.20.073361
MA0104.21.08293
MA0047.20.238164
MA0112.28.20982
MA0065.25.00358
MA0150.10.347297
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.11.11603
MA0155.12.72219
MA0156.10.0744198
MA0157.10.323429
MA0158.10
MA0159.11.00105
MA0160.12.25313
MA0161.10
MA0162.10.000349302
MA0163.16.42452
MA0164.10.268764
MA0080.20.0646165
MA0018.20.248141
MA0099.20.193081
MA0079.20.00272793
MA0102.21.01759
MA0258.15.88135
MA0259.10.374822
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
BHLHE40#855335.852845245257920.01403799033604320.0492678833492177



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:C436&oldid=2568947"