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Coexpression cluster:C2890: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,2.11192,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.902371,0.706765,0.867962,2.45508,0.809319,0.532789,0.559384,2.39977,1.18793,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,3.41059,0.316693,0.728867,3.36111,0.297585,1.63433,1.09415,2.88708,0.344471,0.49475,0.0842336,0.491074,0.740899,2.0411,1.72725,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,1.0193,2.3411,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,3.25144,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,0.716653,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,2.58439,0.575476,0.717043,1.46636,0.489254,0.785429,2.74919,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,1.62065,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.175846,1.24902,1.76758,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,2.84244,0.820225,0.359498
|tfbs_overrepresentation_jaspar=MA0003.1;2.39007,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;2.45009,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;1.28887,MA0056.1;0,MA0057.1;3.6449,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;175.301,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,MA0113.1;0.886811,MA0114.1;1.13665,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;4.40632,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;1.25938,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;3.05702,MA0039.2;7.11691,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;2.43626,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;3.05999,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;5.0369,MA0163.1;3.83423,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;16.1395,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:59, 22 January 2013


Full id: C2890_Smooth_glioma_clear_Renal_endometrial_mesothelioma_gastric



Phase1 CAGE Peaks

Hg19::chr7:27153428..27153440,-p3@HOXA3
Hg19::chr7:27153443..27153450,-p8@HOXA3
Hg19::chr7:27153454..27153469,-p2@HOXA3
Hg19::chr7:27153613..27153630,-p6@HOXA3


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
trunk4.87e-22199
trunk region element1.27e-18101
epithelial tube8.12e-18117
mesenchyme2.72e-17160
entire embryonic mesenchyme2.72e-17160
organism subdivision1.72e-14264
subdivision of trunk2.59e-13112
trunk mesenchyme3.14e-12122
immaterial anatomical entity4.70e-12117
abdomen element1.62e-1154
abdominal segment element1.62e-1154
abdominal segment of trunk2.33e-1160
abdomen2.33e-1160
renal system3.07e-1148
cavitated compound organ3.41e-1131
unilaminar epithelium5.25e-11148
anatomical conduit6.09e-11240
urinary system structure6.32e-1147
epithelial tube open at both ends7.18e-1159
blood vessel7.18e-1159
blood vasculature7.18e-1159
vascular cord7.18e-1159
anatomical space8.58e-1195
tube2.66e-10192
excretory tube3.71e-1016
kidney epithelium3.71e-1016
kidney4.16e-1026
kidney mesenchyme4.16e-1026
upper urinary tract4.16e-1026
kidney rudiment4.16e-1026
kidney field4.16e-1026
nephron epithelium4.73e-1015
renal tubule4.73e-1015
nephron tubule4.73e-1015
nephron4.73e-1015
uriniferous tubule4.73e-1015
nephrogenic mesenchyme4.73e-1015
epithelium7.13e-10306
anatomical cluster1.22e-09373
vessel1.50e-0968
splanchnic layer of lateral plate mesoderm1.79e-0983
cell layer1.97e-09309
subdivision of digestive tract1.97e-09118
nephron tubule epithelium3.34e-0910
cortex8.30e-0915
compound organ1.01e-0868
multi-tissue structure1.23e-08342
body cavity precursor3.93e-0854
artery4.64e-0842
arterial blood vessel4.64e-0842
arterial system4.64e-0842
digestive system6.43e-08145
digestive tract6.43e-08145
primitive gut6.43e-08145
parenchyma1.14e-0715
cortex of kidney1.57e-0712
renal parenchyma1.57e-0712
endoderm-derived structure1.61e-07160
endoderm1.61e-07160
presumptive endoderm1.61e-07160
endo-epithelium3.43e-0782
epithelial vesicle3.84e-0778
muscle tissue4.27e-0764
musculature4.27e-0764
musculature of body4.27e-0764
vasculature4.42e-0778
vascular system4.42e-0778
skeletal muscle tissue8.79e-0762
striated muscle tissue8.79e-0762
myotome8.79e-0762
Disease
Ontology termp-valuen
cell type cancer2.16e-10143
carcinoma1.21e-09106
squamous cell carcinoma8.60e-0814
cancer3.04e-07235
disease of cellular proliferation7.98e-07239


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)
MA0003.12.39007
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.28887
MA0056.10
MA0057.13.6449
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.1175.301
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.14.40632
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.23.05702
MA0039.27.11691
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.15.0369
MA0163.13.83423
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.216.1395
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#1488347.03775025449611.60047699357395e-050.000370543597277477
RFX5#5993412.04791082719514.74457429336527e-050.00082876500188121



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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