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Coexpression cluster:C2157: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,1.92131,0.395818,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,1.23824,0.0842336,0.491074,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,1.72726,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.66252,0.521611,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,1.4628,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498
|tfbs_overrepresentation_for_novel_motifs=0.590005,1.03954,0.581696,0.741427,0.534346,0.739643,1.92131,0.395818,0.392841,0.902371,0.706765,0.867962,0.905351,0.809319,0.532789,0.559384,1.05593,0.471262,0.938585,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,1.23824,0.0842336,0.491074,0.740899,0.463978,0.971732,0.493145,0.66492,0.183156,0.53106,0.314427,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,1.94963,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,1.8276,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,1.27559,1.72726,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.66252,0.521611,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,1.4628,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.359498
|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,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;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.396851,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.946082,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;0.00636811,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;1.02755,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;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,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;1.63368,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;0.569905,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;1.813,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;1.13403,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.869502,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:27, 22 January 2013


Full id: C2157_Mallassezderived_Smooth_Alveolar_Bronchial_Keratocytes_Tracheal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr11:6704513..6704578,-p1@MRPL17
Hg19::chr12:120720030..120720046,+p1@NME2P1
Hg19::chr16:67880820..67880844,+p1@NUTF2
Hg19::chr17:49243792..49243828,+p2@NME1-NME2
p2@NME2


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

GO IDGO nameFDR corrected p-value
GO:0031967organelle envelope0.0286527553894789
GO:0031975envelope0.0286527553894789
GO:0006228UTP biosynthetic process0.0286527553894789
GO:0046051UTP metabolic process0.0286527553894789
GO:0004550nucleoside diphosphate kinase activity0.0286527553894789
GO:0046036CTP metabolic process0.0286527553894789
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0286527553894789
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0286527553894789
GO:0006241CTP biosynthetic process0.0286527553894789
GO:0006183GTP biosynthetic process0.0286527553894789
GO:0046039GTP metabolic process0.0286527553894789
GO:0009220pyrimidine ribonucleotide biosynthetic process0.0286527553894789
GO:0009218pyrimidine ribonucleotide metabolic process0.0286527553894789
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.032089061554363
GO:0006221pyrimidine nucleotide biosynthetic process0.032089061554363
GO:0031090organelle membrane0.0353004691211007
GO:0006220pyrimidine nucleotide metabolic process0.0353004691211007
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0353004691211007
GO:0005643nuclear pore0.0393385481596267
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0393385481596267
GO:0046930pore complex0.0393385481596267
GO:0044249cellular biosynthetic process0.0393385481596267
GO:0044453nuclear membrane part0.0393385481596267
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009145purine nucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009201ribonucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009142nucleoside triphosphate biosynthetic process0.0393385481596267
GO:0009205purine ribonucleoside triphosphate metabolic process0.0393385481596267
GO:0009144purine nucleoside triphosphate metabolic process0.0393385481596267
GO:0009199ribonucleoside triphosphate metabolic process0.0393385481596267
GO:0009152purine ribonucleotide biosynthetic process0.0393385481596267
GO:0009141nucleoside triphosphate metabolic process0.0393385481596267
GO:0031965nuclear membrane0.0393385481596267
GO:0009150purine ribonucleotide metabolic process0.0393385481596267
GO:0009260ribonucleotide biosynthetic process0.0393385481596267
GO:0006164purine nucleotide biosynthetic process0.0393385481596267
GO:0006163purine nucleotide metabolic process0.0393385481596267
GO:0009259ribonucleotide metabolic process0.0393385481596267
GO:0009058biosynthetic process0.0393385481596267
GO:0005635nuclear envelope0.0438641156314734



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><br>

Cell Type
Ontology termp-valuen
embryonic cell7.92e-39250
animal cell9.47e-31679
eukaryotic cell9.47e-31679
mesodermal cell1.83e-29121
epithelial cell2.84e-26253
contractile cell1.30e-1959
electrically responsive cell4.34e-1961
electrically active cell4.34e-1961
muscle precursor cell9.80e-1958
myoblast9.80e-1958
multi-potent skeletal muscle stem cell9.80e-1958
non-terminally differentiated cell1.80e-18106
muscle cell2.90e-1855
native cell2.79e-16722
smooth muscle cell9.74e-1643
smooth muscle myoblast9.74e-1643
somatic cell4.91e-14588
vascular associated smooth muscle cell9.59e-1432
lining cell2.23e-1058
barrier cell2.23e-1058
squamous epithelial cell1.85e-0963
meso-epithelial cell5.25e-0945
endothelial cell1.38e-0836
epithelial cell of nephron3.19e-0815
ectodermal cell1.39e-0772
kidney cortical cell3.52e-0712
renal cortical epithelial cell3.52e-0712
blood vessel endothelial cell3.97e-0718
embryonic blood vessel endothelial progenitor cell3.97e-0718
endothelial cell of vascular tree6.24e-0724
Uber Anatomy
Ontology termp-valuen
epithelial vesicle1.30e-2378
unilaminar epithelium2.31e-22148
multilaminar epithelium7.90e-2183
somite6.67e-2071
presomitic mesoderm6.67e-2071
presumptive segmental plate6.67e-2071
dermomyotome6.67e-2071
trunk paraxial mesoderm6.67e-2071
vasculature1.05e-1978
vascular system1.05e-1978
dense mesenchyme tissue2.43e-1973
paraxial mesoderm3.78e-1972
presumptive paraxial mesoderm3.78e-1972
mesenchyme4.08e-19160
entire embryonic mesenchyme4.08e-19160
epithelial tube5.74e-19117
trunk1.36e-18199
organism subdivision6.47e-18264
trunk mesenchyme3.93e-17122
skeletal muscle tissue6.52e-1762
striated muscle tissue6.52e-1762
myotome6.52e-1762
splanchnic layer of lateral plate mesoderm6.79e-1783
vessel1.29e-1668
epithelial tube open at both ends3.40e-1659
blood vessel3.40e-1659
blood vasculature3.40e-1659
vascular cord3.40e-1659
muscle tissue1.55e-1564
musculature1.55e-1564
musculature of body1.55e-1564
artery1.42e-1442
arterial blood vessel1.42e-1442
arterial system1.42e-1442
cell layer4.77e-13309
cardiovascular system2.05e-12109
epithelium2.47e-12306
circulatory system1.33e-11112
systemic artery3.10e-1033
systemic arterial system3.10e-1033
multi-tissue structure2.61e-09342
nephron epithelium3.19e-0815
renal tubule3.19e-0815
nephron tubule3.19e-0815
nephron3.19e-0815
uriniferous tubule3.19e-0815
nephrogenic mesenchyme3.19e-0815
parenchyma7.29e-0815
anatomical cluster1.22e-07373
excretory tube3.42e-0716
kidney epithelium3.42e-0716
cortex of kidney3.52e-0712
renal parenchyma3.52e-0712
blood vessel endothelium3.97e-0718
endothelium3.97e-0718
cardiovascular system endothelium3.97e-0718
simple squamous epithelium4.35e-0722
urinary system structure7.48e-0747
larynx8.48e-079


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
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
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.21.66396
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CCNT2#90534.752151182721970.01386206996689490.0487044819267463
GABPB1#255335.300762877136630.01012678824234270.0378414840331329
IRF1#365935.727872815172930.008097114790333330.0319887491143752
JUND#372735.245997956403270.01043432751748420.0386710692547386
NR2C2#7182216.30730545262040.005411825344648220.0245506744492101
RXRA#6256210.03730856956660.01391703805920110.048871306878212



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:C2157&oldid=2570668"