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Coexpression cluster:C1541: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=2.93784,0.333388,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.0880431,0.576478,1.00694,0.483957,0.730467,1.10781,0.574247,1.81189,1.04549,0.530785,0.92701,0.302275,0.640661,0.35719,0.134746,0.93226,0.585658,2.39592,0.248856,0.355745,1.2792,0.0979105,1.01199,1.89526,2.05586,1.59472,1.33909,0.630853,0.396429,1.76328,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,2.73856,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,2.7278,0.86037,0.684313,0.272514,1.10535,0.406668,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,4.76723,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,1.90697,0.548668,0.877269,1.56033,2.10687,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,2.79981,1.07915,2.04075,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,2.40891,0.912368,1.1583,0.83286,0.683502,0.29379,3.90135,0.307168
|tfbs_overrepresentation_for_novel_motifs=2.93784,0.333388,1.11302,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.236034,0.800617,0.436569,0.0880431,0.576478,1.00694,0.483957,0.730467,1.10781,0.574247,1.81189,1.04549,0.530785,0.92701,0.302275,0.640661,0.35719,0.134746,0.93226,0.585658,2.39592,0.248856,0.355745,1.2792,0.0979105,1.01199,1.89526,2.05586,1.59472,1.33909,0.630853,0.396429,1.76328,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,2.73856,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,2.7278,0.86037,0.684313,0.272514,1.10535,0.406668,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,4.76723,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,1.90697,0.548668,0.877269,1.56033,2.10687,0.376529,0.44815,0.978783,1.10061,0.563054,1.29401,0.352243,0.210279,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.826087,0.136746,2.79981,1.07915,2.04075,0.665754,1.48627,0.755083,0.986797,0.484017,1.15112,1.27379,2.40891,0.912368,1.1583,0.83286,0.683502,0.29379,3.90135,0.307168
|tfbs_overrepresentation_jaspar=MA0003.1;0.321379,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;1.56589,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;1.05129,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;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.450439,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;3.80179,MA0061.1;0.671725,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;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,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;0.993014,MA0105.1;6.79287,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;1.84113,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;0.641617,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.101413,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;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.113377,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;5.9246e-06,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 20:00, 22 January 2013


Full id: C1541_amniotic_Amniotic_MCF7_Placental_chorionic_oral_acantholytic



Phase1 CAGE Peaks

Hg19::chr8:102504507..102504532,-p@chr8:102504507..102504532
-
Hg19::chr8:102504651..102504683,+p1@GRHL2
Hg19::chr8:102504690..102504704,+p3@GRHL2
Hg19::chr8:102504932..102504952,+p4@GRHL2
Hg19::chr8:102504979..102505010,+p2@GRHL2
Hg19::chr8:102681493..102681497,+p@chr8:102681493..102681497
+


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
endoderm-derived structure3.87e-24160
endoderm3.87e-24160
presumptive endoderm3.87e-24160
digestive system2.60e-17145
digestive tract2.60e-17145
primitive gut2.60e-17145
subdivision of digestive tract2.26e-14118
extraembryonic membrane1.13e-1314
membranous layer1.13e-1314
respiratory system2.57e-1374
anatomical space5.09e-1295
epithelial bud1.40e-1037
endo-epithelium1.81e-1082
reproductive structure2.76e-1059
reproductive system2.76e-1059
chorion3.21e-107
respiratory tract4.50e-1054
thoracic cavity element5.06e-1034
thoracic cavity5.06e-1034
orifice1.08e-0936
thoracic segment organ1.47e-0935
immaterial anatomical entity1.75e-09117
reproductive organ3.31e-0948
renal system4.74e-0948
epithelial fold8.83e-0947
thoracic segment of trunk9.35e-0952
urinary system structure1.55e-0847
internal genitalia2.57e-0825
mucosa6.70e-0820
male organism9.91e-0822
male reproductive system9.91e-0822
male reproductive organ1.00e-0711
extraembryonic structure1.53e-0724
lung1.60e-0722
respiratory tube1.60e-0722
respiration organ1.60e-0722
pair of lungs1.60e-0722
lung primordium1.60e-0722
lung bud1.60e-0722
foregut1.71e-0787
oral opening4.95e-0722
neck7.12e-0710
organ7.83e-07503
trunk region element9.82e-07101
Disease
Ontology termp-valuen
carcinoma2.36e-17106
squamous cell carcinoma7.24e-1714
cell type cancer3.18e-11143
adenocarcinoma2.25e-1025


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.11.56589
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.11.05129
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
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.450439
MA0058.10.458909
MA0059.10.457555
MA0060.13.80179
MA0061.10.671725
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
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.993014
MA0105.16.79287
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
MA0131.11.84113
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
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
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.113377
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.25.9246e-06
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
E2F1#186954.089491012399440.001749817597761990.010761347314372
FOXA1#316959.234516457821213.31890114386024e-050.000660108010976233
GATA3#2625418.15767757147072.56597141799789e-050.000554954418977597
MYC#460954.35190155967450.001297956345724110.00869737346279229
NR3C1#290837.486511665586520.00510866965984070.0237584873582448
ZEB1#6935411.25895467836260.0001672700379805450.00204896968058294



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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