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Coexpression cluster:C3843: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,1.65103,0.855819,0.641468,0.853988,3.5527,0.494933,0.491742,0.63186,3.18659,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,4.25502,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,2.47502,0.855276,3.49216,3.05174,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,2.16194,0.808003,0.247669,0.645308,1.02504,2.18821,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,2.0644,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,4.33203,0.502203,0.333216,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,6.48145,2.26789,0.993996,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,0.684398,1.94007,1.58942,0.594137,5.80456,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,5.59159,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,2.56478
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,1.65103,0.855819,0.641468,0.853988,3.5527,0.494933,0.491742,0.63186,3.18659,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,4.25502,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,2.47502,0.855276,3.49216,3.05174,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,2.16194,0.808003,0.247669,0.645308,1.02504,2.18821,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,2.0644,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,4.33203,0.502203,0.333216,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,6.48145,2.26789,0.993996,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,3.17067,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,0.684398,1.94007,1.58942,0.594137,5.80456,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,1.96632,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,5.59159,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,1.3017,0.936473,2.56478
|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;1.88666,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;4.54482,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;3.70241,MA0107.1;1.36919,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.348055,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.432958,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;1.31345,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0107199,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0
}}
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Revision as of 21:39, 22 January 2013


Full id: C3843_merkel_pineal_small_heart_maxillary_skeletal_salivary



Phase1 CAGE Peaks

Hg19::chr1:10856639..10856662,-p2@CASZ1
Hg19::chr1:10856665..10856683,-p4@CASZ1
Hg19::chr1:10856694..10856715,-p3@CASZ1


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
epithelial cell6.62e-16253
endo-epithelial cell2.21e-1442
endodermal cell5.30e-1058
epithelial cell of alimentary canal2.77e-0920
epithelial cell of lung9.58e-0819
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.82e-17160
endoderm9.82e-17160
presumptive endoderm9.82e-17160
digestive system2.73e-14145
digestive tract2.73e-14145
primitive gut2.73e-14145
subdivision of digestive tract2.99e-14118
epithelial fold1.30e-1147
respiratory system1.66e-1174
epithelial bud1.90e-1137
thoracic segment organ7.84e-1135
multi-cellular organism1.21e-10656
adult organism1.87e-10114
thoracic cavity element4.18e-1034
thoracic cavity4.18e-1034
organ system subdivision4.38e-10223
multi-tissue structure9.79e-10342
anatomical space1.03e-0995
lung1.82e-0922
respiratory tube1.82e-0922
respiration organ1.82e-0922
pair of lungs1.82e-0922
lung primordium1.82e-0922
lung bud1.82e-0922
organ4.43e-09503
embryo5.37e-09592
trunk region element1.68e-08101
anatomical cluster1.86e-08373
foregut1.93e-0887
orifice2.88e-0836
thoracic segment of trunk4.37e-0852
endo-epithelium4.59e-0882
organism subdivision8.84e-08264
respiratory tract epithelium9.58e-0819
lung epithelium9.58e-0819
developing anatomical structure1.95e-07581
gastrointestinal system2.47e-0725
respiratory tract2.48e-0754
immaterial anatomical entity2.76e-07117
renal system6.69e-0748
Disease
Ontology termp-valuen
cell type cancer2.97e-14143
carcinoma3.45e-14106
respiratory system cancer1.07e-0716
gastrointestinal system cancer2.29e-0714
lung cancer7.02e-0715
adenocarcinoma7.10e-0725


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.14.54482
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.13.70241
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CTBP2#1488362.71700033932814.049570681927e-060.00012973408357355
EGR1#195834.988179094810140.008056488137383440.0320672115774301
EP300#203336.77394172622320.003216880500103790.0167456403603818
GABPB1#255337.067683836182170.002832212825417420.0154131350775765
GATA3#2625327.2365163572064.94721007899563e-050.00085106518438515
JUND#372736.994663941871030.002921845042734990.0156787018660124
NRF1#4899312.21027944771090.0005492172401020010.00471204299178616
RAD21#5885310.35503389545630.0009004912073565420.00664122598722617
RFX5#5993312.04791082719510.0005717246050312580.00484543909963966
SP1#666735.69838137814090.005403962701712170.0246531455293809
TCF7L2#6934310.77017656313730.0008003181298398380.00613824081386083
YY1#752834.911170749853860.008441455341808260.0329441035253956



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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