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Coexpression cluster:C1081: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,0.480078,0.554663,0.19223,0.190005,0.0394821,0.450635,0.597407,0.152895,0.543352,0.300614,0.863056,0.774423,0.250594,0.163559,0.264925,0.341703,0.047825,0.472508,0.29709,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,0.429397,0.810962,0.220667,0.154814,0.269459,0.0137136,0.266487,0.481208,1.96738,2.25462,0.268162,0.413601,0.0547276,0.299183,0.949078,0.371118,0.555735,0.440085,1.5855,0.304949,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.122557,0.513089,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.0911419,1.03748,0.149081,3.39864,0.799673,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,1.51085,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,2.81234,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,2.42894,0.459808,1.17281,2.07243,0.0278613,0.428232,0.710479,0.229841,1.02923,0.657218,2.08588,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,1.90503,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,2.1801,0.686615,1.88987,0.410382,0.637373,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,3.56519,0.796636,0.36101,0.71907,0.574616,0.213234,3.42981,0.00340764
|tfbs_overrepresentation_jaspar=MA0003.1;0.00101002,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;3.44775,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;2.19172,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;2.54821,MA0060.1;0.190336,MA0061.1;0.961853,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.133123,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;9.20286e-05,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;2.54896,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;4.71751,MA0101.1;2.28079,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;4.10963,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.944441,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;2.21238,MA0039.2;0.00133745,MA0138.2;0.653421,MA0002.2;5.67309,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.208783,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;1.26616,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;0.818924,MA0018.2;0.599912,MA0099.2;2.23733,MA0079.2;1.41562e-07,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0
}}
}}

Revision as of 19:41, 22 January 2013


Full id: C1081_papillotubular_Renal_Mast_giant_meningioma_mucinous_gall



Phase1 CAGE Peaks

Hg19::chr3:98699880..98699906,+p2@ENST00000473756
Hg19::chr3:98699909..98699935,+p3@ENST00000473756
Hg19::chr3:98700032..98700043,+p7@ENST00000473756
Hg19::chr3:98700102..98700111,+p8@ENST00000473756
Hg19::chr3:98700113..98700136,+p4@ENST00000473756
Hg19::chr3:98700139..98700150,+p6@ENST00000473756
Hg19::chr3:98700171..98700194,+p1@ENST00000473756
Hg19::chr3:98700196..98700204,+p9@ENST00000473756


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
multilaminar epithelium1.66e-1983
epithelial vesicle1.93e-1878
somite4.26e-1871
presomitic mesoderm4.26e-1871
presumptive segmental plate4.26e-1871
dermomyotome4.26e-1871
trunk paraxial mesoderm4.26e-1871
paraxial mesoderm1.24e-1772
presumptive paraxial mesoderm1.24e-1772
dense mesenchyme tissue3.51e-1773
skeletal muscle tissue1.33e-1662
striated muscle tissue1.33e-1662
myotome1.33e-1662
muscle tissue1.16e-1564
musculature1.16e-1564
musculature of body1.16e-1564
mesenchyme3.80e-14160
entire embryonic mesenchyme3.80e-14160
trunk mesenchyme4.85e-14122
organism subdivision1.32e-13264
cell layer5.60e-12309
epithelium5.76e-12306
nephron tubule epithelium6.85e-1210
unilaminar epithelium1.86e-11148
trunk3.69e-11199
artery1.86e-1042
arterial blood vessel1.86e-1042
arterial system1.86e-1042
pigment epithelium of eye8.48e-1011
epithelial tube9.93e-10117
blood vessel smooth muscle1.46e-0910
arterial system smooth muscle1.46e-0910
artery smooth muscle tissue1.46e-0910
aorta smooth muscle tissue1.46e-0910
systemic artery3.00e-0933
systemic arterial system3.00e-0933
smooth muscle tissue7.76e-0915
multi-tissue structure1.58e-08342
nephron epithelium2.48e-0815
renal tubule2.48e-0815
nephron tubule2.48e-0815
nephron2.48e-0815
uriniferous tubule2.48e-0815
nephrogenic mesenchyme2.48e-0815
female organism9.65e-0841
vasculature1.02e-0778
vascular system1.02e-0778
excretory tube1.37e-0716
kidney epithelium1.37e-0716
external ectoderm8.43e-078
Disease
Ontology termp-valuen
female reproductive organ cancer7.82e-1227
reproductive organ cancer1.48e-1029
ovarian cancer5.05e-1014


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)
MA0003.10.00101002
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.13.44775
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.12.19172
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.10.362328
MA0059.12.54821
MA0060.10.190336
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.12.54896
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.14.71751
MA0101.12.28079
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.14.10963
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.944441
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.22.21238
MA0039.20.00133745
MA0138.20.653421
MA0002.25.67309
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.11.26616
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.22.23733
MA0079.21.41562e-07
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
BATF#10538824.35780179230368.04188698177306e-121.0168119061615e-09
BCL11A#53335828.36945510360712.37350757777029e-123.22349490136218e-10
EBF1#187988.9064668465692.52252859723395e-081.75868066866833e-06
EP300#203386.77394172622322.25366016107097e-071.19054129267623e-05
FOS#235388.99795530889442.32446530602145e-081.63698470732012e-06
GATA2#2624812.7449317335541.43392692074517e-091.28107693477934e-07
JUND#372786.994663941871031.74369580801501e-079.5746501836635e-06
MEF2A#4205818.74323090964416.54751754202692e-117.25149718527836e-09
NFKB1#479085.488063424193841.21437192632393e-064.90819619246691e-05
POLR2A#543082.147453176558070.002210725788971910.012723795363961
SP1#666785.69838137814098.98832477855329e-073.86468362102646e-05
TCF12#6938810.63446490218646.10437051371448e-094.83346741532848e-07
USF1#739186.361499277207963.72538670743375e-071.83180631985722e-05



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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