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Coexpression cluster:C4609: Difference between revisions

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{{Coexpression_clusters
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.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.00501043,0.00267717,0.00756988,0.115817,0.218052,0.223831,0.11528,0.00144649,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.0107847|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,1.60265,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,1.86765,1.21459,1.3235,0.439574,2.48753,1.96994,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,0.430728,0.414196,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,1.14422,1.27663,1.05794,3.495,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,1.7605,0.622396,0.703975,2.82894,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;3.20493,MA0006.1;0.639288,MA0007.1;0.804807,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;2.15619,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;2.8588,MA0059.1;1.70014,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;0.0834661,MA0074.1;2.15449,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;3.82193,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,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;2.29531,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;2.37462,MA0148.1;1.98824,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;2.13189,MA0047.2;3.66129,MA0112.2;2.07067,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;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;0.455568,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;2.40872,MA0442.1;0}}
|full_id=C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric
|id=C4609
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric



Phase1 CAGE Peaks

Hg19::chr6:47277594..47277605,-p4@TNFRSF21
Hg19::chr6:47277620..47277631,-p3@TNFRSF21
Hg19::chr6:47277634..47277651,-p1@TNFRSF21


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>

Cell Type
Ontology termp-valuen
epithelial cell1.45e-16253
endodermal cell7.99e-1158
endo-epithelial cell1.03e-1042
embryonic cell3.43e-09250
Uber Anatomy
Ontology termp-valuen
anatomical system6.59e-28624
anatomical group1.92e-27625
multi-cellular organism3.28e-27656
embryo2.30e-23592
anatomical conduit5.72e-23240
developing anatomical structure2.73e-22581
anatomical cluster1.28e-21373
embryonic structure1.45e-19564
organ3.88e-19503
tube1.59e-18192
germ layer2.58e-18560
germ layer / neural crest2.58e-18560
embryonic tissue2.58e-18560
presumptive structure2.58e-18560
germ layer / neural crest derived structure2.58e-18560
epiblast (generic)2.58e-18560
cell layer1.65e-17309
epithelium5.19e-17306
multi-tissue structure8.87e-15342
organism subdivision9.33e-13264
organ system subdivision1.06e-12223
trunk7.64e-12199
endoderm-derived structure1.11e-11160
endoderm1.11e-11160
presumptive endoderm1.11e-11160
organ part1.51e-11218
epithelial tube2.34e-11117
immaterial anatomical entity1.32e-09117
digestive system6.31e-09145
digestive tract6.31e-09145
primitive gut6.31e-09145
subdivision of trunk1.08e-08112
subdivision of digestive tract1.86e-08118
trunk region element7.43e-08101
endo-epithelium3.37e-0782
unilaminar epithelium3.69e-07148
anatomical space3.89e-0795
central nervous system9.19e-0781


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)
MA0003.10.0471418
MA0004.13.20493
MA0006.10.639288
MA0007.10.804807
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
MA0051.12.15619
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.12.8588
MA0059.11.70014
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
MA0073.10.0834661
MA0074.12.15449
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
MA0093.13.82193
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
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
MA0143.12.29531
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.12.37462
MA0148.11.98824
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.23.66129
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
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#90536.336201576962630.003930750035764890.0191038951549746
CEBPB#105137.971147625824820.001974187055288560.0115735123136279
CTCF#1066435.360256373075030.0064925092527670.0281135691301353
E2F1#186934.907389214879320.008460985347239390.032746223779149
E2F6#187635.017155731697390.00791769806886330.0324115732612399
EGR1#195834.988179094810140.008056488137383440.0322305816509687
ELF1#199734.258097958807540.01295179875054610.0464708296587977
FOSL2#2355316.93020060456170.0002060162053171620.00243947012098856
FOXA1#3169311.08141974938550.000734755275698670.00583862940262446
FOXA2#3170324.63046375266526.68983856509345e-050.00107671451672029
GATA2#2624312.7449317335540.0004829527704283790.00438829862456669
HDAC2#3066313.41562023662630.0004140761399857210.0039332149144128
HMGN3#932438.178547723350590.001827766942164210.010913621386581
IRF1#365937.63716375356390.002244692747297240.0128675265291716
JUN#3725312.51282919233630.0005103313992726250.00446199254990654
JUNB#3726330.61063265982113.4847716247536e-050.00068256951184854
JUND#372736.994663941871030.002921845042734990.0157596743489232
MAFF#23764356.31535648994525.59409009993116e-060.000169296197028893
MAFK#7975327.10073313782995.02195559325033e-050.000859534611936204
MAX#414936.452555509007120.003721913834265510.0187322518884321
MXI1#460139.96157162875930.001011470541259020.00723045666382964
MYC#460935.22228187160940.007020843755740150.0295868095470986
NFKB1#479035.488063424193840.006049381815655430.0270760001476488
RAD21#5885310.35503389545630.0009004912073565420.00668133000888817
RFX5#5993312.04791082719510.0005717246050312580.00486636886918171
RXRA#6256320.07461713913330.0001235730348432220.00165927541604414
SIN3A#2594235.408884726815140.006318961977991520.0278129665382441
SMC3#9126315.04493284493280.0002935825420371870.00310684639860388
SRF#6722313.79717826216780.0003806615025800190.00376262603331011
TAF7#6879311.43306940492390.0006690181981945830.00545403103592569
TCF12#6938310.63446490218640.0008313523990202070.00631826613311537
TCF7L2#6934310.77017656313730.0008003181298398380.00617041378726878
USF1#739136.361499277207960.00388404057290560.0191062744757048
USF2#7392312.99219738506960.0004558979393427810.00422855460808355
ZNF143#7702313.50087655222790.0004062804962997170.00390390364826995
ZNF263#1012738.221841637010680.001799043925565870.0110051161800606



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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