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Coexpression cluster:C4551: Difference between revisions

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{{Coexpression_clusters
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,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,1.91835,0.985163,1.11328,2.13378,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,1.7611,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,1.36391,0.596053,0.855276,0.567465,2.05816,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,4.62073,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,2.94614,1.50815,0.703975,1.26794,0.684398,1.94007,1.58942,0.594137,1.66424,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,2.48899,0.883164,1.08214,2.31409,0.773313,0.539692,4.20421,0.698641,1.37083,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,3.92523|tfbs_overrepresentation_jaspar=MA0003.1;2.05336,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;8.34001,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;3.37768,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.67416,MA0056.1;0,MA0057.1;0.333427,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;1.04561,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,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;0.715722,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;2.626,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;1.5295,MA0106.1;0.986396,MA0107.1;0.556367,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;1.12079,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;1.37817,MA0146.1;3.00132,MA0147.1;1.38767,MA0148.1;0.854239,MA0149.1;3.38595,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;3.37171,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;1.34467,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;3.52399,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;1.22771,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;1.40979,MA0442.1;0}}
|full_id=C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth
|id=C4551
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4551_osteoclastoma_Mesothelial_Preadipocyte_Mallassezderived_hepatic_rectal_Smooth



Phase1 CAGE Peaks

Hg19::chr6:117803797..117803844,+p1@DCBLD1
Hg19::chr6:117803847..117803869,+p2@DCBLD1
Hg19::chr6:117803876..117803888,+p3@DCBLD1


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><br>

Uber Anatomy
Ontology termp-valuen
unilaminar epithelium2.61e-24148
trunk mesenchyme9.07e-21122
trunk6.28e-17199
multi-cellular organism3.00e-16656
organism subdivision5.20e-16264
mesenchyme6.78e-16160
entire embryonic mesenchyme6.78e-16160
epithelial vesicle9.84e-1678
anatomical group9.92e-16625
multilaminar epithelium1.68e-1583
anatomical system1.97e-15624
epithelial tube5.49e-15117
somite1.32e-1471
presomitic mesoderm1.32e-1471
presumptive segmental plate1.32e-1471
dermomyotome1.32e-1471
trunk paraxial mesoderm1.32e-1471
paraxial mesoderm5.50e-1472
presumptive paraxial mesoderm5.50e-1472
skeletal muscle tissue5.62e-1462
striated muscle tissue5.62e-1462
myotome5.62e-1462
cell layer5.67e-14309
muscle tissue8.79e-1464
musculature8.79e-1464
musculature of body8.79e-1464
dense mesenchyme tissue9.13e-1473
epithelium1.04e-13306
vasculature2.61e-1378
vascular system2.61e-1378
epithelial tube open at both ends3.48e-1359
blood vessel3.48e-1359
blood vasculature3.48e-1359
vascular cord3.48e-1359
vessel6.12e-1368
embryonic structure3.47e-12564
splanchnic layer of lateral plate mesoderm8.20e-1283
multi-tissue structure1.23e-11342
germ layer2.96e-11560
germ layer / neural crest2.96e-11560
embryonic tissue2.96e-11560
presumptive structure2.96e-11560
germ layer / neural crest derived structure2.96e-11560
epiblast (generic)2.96e-11560
artery6.89e-1142
arterial blood vessel6.89e-1142
arterial system6.89e-1142
developing anatomical structure1.12e-10581
anatomical cluster2.48e-10373
embryo1.14e-09592
anatomical conduit1.66e-09240
endoderm-derived structure1.95e-09160
endoderm1.95e-09160
presumptive endoderm1.95e-09160
systemic artery4.59e-0933
systemic arterial system4.59e-0933
surface structure1.43e-0799
digestive system2.19e-07145
digestive tract2.19e-07145
primitive gut2.19e-07145
simple squamous epithelium2.82e-0722
mesoderm3.78e-07315
mesoderm-derived structure3.78e-07315
presumptive mesoderm3.78e-07315
tube6.47e-07192


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)
MA0003.12.05336
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.18.34001
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.13.00132
MA0147.11.38767
MA0148.10.854239
MA0149.13.38595
MA0062.20.449458
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.11.2663
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
MA0102.21.88331
MA0258.11.29138
MA0259.11.40979
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#90536.336201576962630.003930750035764890.0190950092090446
CTCF#1066435.360256373075030.0064925092527670.0281007531641
CTCFL#140690319.74647435897440.0001298372005551160.0017223507416202
E2F1#186934.907389214879320.008460985347239390.0327328807482714
E2F6#187635.017155731697390.00791769806886330.0324001437432025
EBF1#187938.9064668465690.00141523283560980.00918560077796609
EGR1#195834.988179094810140.008056488137383440.0322170067228315
ELF1#199734.258097958807540.01295179875054610.0464580611934429
ESR1#2099330.76860329615453.43136389821584e-050.000678984869582728
ETS1#211339.728760922202340.001085840092584840.00764745117199189
GABPB1#255337.067683836182170.002832212825417420.0154719884545334
IRF1#365937.63716375356390.002244692747297240.0128639961498561
MYC#460935.22228187160940.007020843755740150.0295808415768011
PAX5#507936.669565531177830.003370290999677260.0173582119398014
SIN3A#2594235.408884726815140.006318961977991520.0278035924342541
SPI1#668838.204323508522730.001810593189410520.0109361252737751
THAP1#55145331.36914460285133.23800758564397e-050.000648713359365185
USF1#739136.361499277207960.00388404057290560.0191017759179548
YY1#752834.911170749853860.008441455341808260.0330974642205621
ZEB1#6935316.88843201754390.0002075486917327580.00243689463922175
ZNF263#1012738.221841637010680.001799043925565870.0109993179102081



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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