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Coexpression cluster:C1349: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.946942,1.94876,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,2.33626,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.29639,0.576478,1.00694,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.93226,0.585658,0.329602,0.248856,0.936389,0.513952,0.323162,0.390088,0.0393783,0.468392,1.59472,2.29967,0.630853,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,1.03549,0.62023,0.186533,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.206105,1.68655,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.126687,0.181871,0.771626,1.71797,1.34233,2.44471,0.94406,0.30974,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,1.58445,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,3.11809,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,2.8488,0.529546,0.824029,0.312699,1.14892,1.81315,1.42251,1.66144,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.986797,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,2.36361
|tfbs_overrepresentation_jaspar=MA0003.1;0.0799681,MA0004.1;0.558729,MA0006.1;1.01439,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.108006,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.906394,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;1.71708,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.199491,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,MA0074.1;1.58758,MA0076.1;0.475586,MA0077.1;2.28163,MA0078.1;0.763954,MA0081.1;1.15882,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;1.09824,MA0089.1;0,MA0090.1;1.22966,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;1.76074,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;0.323925,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;1.47313,MA0145.1;0.107156,MA0146.1;2.91645,MA0147.1;0.87383,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.0929059,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.735746,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;0.109623,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;1.57484,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.347838,MA0163.1;2.08316,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;1.52352,MA0079.2;0.0146751,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:52, 22 January 2013


Full id: C1349_Alveolar_bile_chorionic_clear_amniotic_papillotubular_serous



Phase1 CAGE Peaks

Hg19::chr11:65778943..65778967,+p2@CST6
Hg19::chr11:65778976..65778988,+p4@CST6
Hg19::chr11:65778994..65779015,+p3@CST6
Hg19::chr11:65779257..65779267,+p6@CST6
Hg19::chr11:65779283..65779289,+p10@CST6
Hg19::chr11:65779378..65779390,+p8@CST6


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>

Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.10e-2114
membranous layer1.10e-2114
endoderm-derived structure6.14e-17160
endoderm6.14e-17160
presumptive endoderm6.14e-17160
endo-epithelium8.99e-1682
urinary system structure2.74e-1547
renal system7.25e-1548
chorion4.88e-147
nephron tubule epithelium2.10e-1210
extraembryonic structure1.52e-1124
respiratory system8.09e-1174
organ component layer8.74e-1166
respiratory tract1.03e-1054
nephron epithelium2.02e-1015
renal tubule2.02e-1015
nephron tubule2.02e-1015
nephron2.02e-1015
uriniferous tubule2.02e-1015
nephrogenic mesenchyme2.02e-1015
acellular anatomical structure9.56e-103
egg chorion9.56e-103
excretory tube1.13e-0916
kidney epithelium1.13e-0916
amnion1.53e-097
digestive system1.72e-09145
digestive tract1.72e-09145
primitive gut1.72e-09145
organ part1.93e-09218
epithelial bud5.41e-0937
renal cortex tubule6.28e-093
region of nephron tubule6.28e-093
proximal tubule6.28e-093
trunk region element1.56e-08101
urothelium2.00e-085
somatic layer of lateral plate mesoderm2.70e-088
thoracic cavity element3.32e-0834
thoracic cavity3.32e-0834
gingival epithelium3.65e-083
lung3.90e-0822
respiratory tube3.90e-0822
respiration organ3.90e-0822
pair of lungs3.90e-0822
lung primordium3.90e-0822
lung bud3.90e-0822
cortex4.82e-0815
thoracic segment organ6.74e-0835
cortex of kidney8.49e-0812
renal parenchyma8.49e-0812
orifice1.71e-0736
biliary system2.63e-079
biliary tree2.63e-079
biliary bud2.63e-079
transitional epithelium5.13e-076
mucosa7.24e-0720
Disease
Ontology termp-valuen
carcinoma5.01e-09106
clear cell adenocarcinoma7.25e-072


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)
MA0003.10.0799681
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.10.108006
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.11.71708
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.11.58758
MA0076.10.475586
MA0077.12.28163
MA0078.10.763954
MA0081.11.15882
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.09824
MA0089.10
MA0090.11.22966
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.11.76074
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.11.47313
MA0145.10.107156
MA0146.12.91645
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.0929059
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.20.332548
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.11.57484
MA0160.10.600559
MA0161.10
MA0162.10.347838
MA0163.12.08316
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.21.52352
MA0079.20.0146751
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
ESR1#2099630.76860329615451.17571957705476e-091.07522746854661e-07
FOXA1#3169611.08141974938555.39600313513231e-072.50468076191148e-05
POLR2A#543062.147453176558070.01019570676818780.0379984091340244
STAT3#677458.766220830961874.28672496720299e-050.000766087044575141



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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