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Coexpression cluster:C3854: Difference between revisions

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{{Coexpression_clusters
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79412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.0211771,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.0363723,0.150733,0.0254879,0.123917,0.184317,0.0183464,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.0232077,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.00339727,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.00206474,0.0271615,0.11528,0.194982,0.190993,0.0440463,0.283218,0.0032012,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.000758145,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,3.46304,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,1.40888,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,2.85005,0.63803,0.151453,0.726632,0.939121,0.808003,1.28131,1.55608,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,1.06461,3.7144,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,1.67826,1.26794,2.75834,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,4.35547,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.0471418,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.377374,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;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;1.15625,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;0.0185922,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;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,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;1.36919,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;2.29491,MA0114.1;1.35563,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;0.440097,MA0140.1;0.894983,MA0141.1;1.6959,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;1.31729,MA0145.1;0.752137,MA0146.1;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,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;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,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;2.02721,MA0156.1;2.7096,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;2.08754,MA0079.2;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3854_anaplastic_Cardiac_Mesothelial_mesothelioma_mesenchymal_Smooth_squamous
|id=C3854
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3854_anaplastic_Cardiac_Mesothelial_mesothelioma_mesenchymal_Smooth_squamous



Phase1 CAGE Peaks

Hg19::chr1:12679045..12679065,-p@chr1:12679045..12679065
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Hg19::chr1:12679075..12679086,-p@chr1:12679075..12679086
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Hg19::chr1:12679100..12679121,-p@chr1:12679100..12679121
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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
epithelial tube1.62e-16117
artery1.89e-1342
arterial blood vessel1.89e-1342
arterial system1.89e-1342
systemic artery6.72e-1233
systemic arterial system6.72e-1233
trunk7.77e-12199
trunk mesenchyme4.54e-11122
epithelial tube open at both ends9.25e-1159
blood vessel9.25e-1159
blood vasculature9.25e-1159
vascular cord9.25e-1159
splanchnic layer of lateral plate mesoderm1.10e-1083
organism subdivision2.30e-10264
circulatory system3.34e-10112
mesenchyme3.96e-10160
entire embryonic mesenchyme3.96e-10160
vessel6.43e-1068
vasculature1.64e-0978
vascular system1.64e-0978
cardiovascular system2.71e-09109
unilaminar epithelium4.97e-09148
muscle tissue9.24e-0964
musculature9.24e-0964
musculature of body9.24e-0964
skeletal muscle tissue2.46e-0862
striated muscle tissue2.46e-0862
myotome2.46e-0862
anatomical conduit6.54e-08240
pigment epithelium of eye6.64e-0811


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
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.12.29491
MA0114.11.35563
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
MA0139.10.440097
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.02721
MA0156.12.7096
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.22.08754
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284585953737729
CEBPB#105137.971147625824820.001974187055288560.0115230605190455
E2F6#187635.017155731697390.00791769806886330.0322271510430654
EGR1#195834.988179094810140.008056488137383440.0320696560041235
ELF1#199734.258097958807540.01295179875054610.0462404850684813
EP300#203336.77394172622320.003216880500103790.016746475054847
ESR1#2099330.76860329615453.43136389821584e-050.000676549394309541
FOS#235338.99795530889440.001372499272417130.00897629479065518
FOSL1#8061339.7135797163731.59554825631833e-050.00037113021011499
FOSL2#2355316.93020060456170.0002060162053171620.0024306514309895
FOXA1#3169311.08141974938550.000734755275698670.00581253645195374
FOXA2#3170324.63046375266526.68983856509345e-050.00107225299247973
GABPB1#255337.067683836182170.002832212825417420.0154155448860627
HDAC2#3066313.41562023662630.0004140761399857210.00391328368328375
HNF4A#3172323.13229036295378.07584663437677e-050.00122806253151962
HNF4G#3174328.75342252644684.20470658818262e-050.000756868926858333
JUN#3725312.51282919233630.0005103313992726250.00444228213107465
JUNB#3726330.61063265982113.4847716247536e-050.00068052741906814
JUND#372736.994663941871030.002921845042734990.0156803131605878
MAFK#7975327.10073313782995.02195559325033e-050.000857567070313067
MAX#414936.452555509007120.003721913834265510.0186540435232198
NR3C1#2908314.9730233311730.0002978331194675480.00309045138242139
REST#597839.650028716128020.001112636247114590.00767672702731061
RXRA#6256320.07461713913330.0001235730348432220.00165247684839838
SIN3A#2594235.408884726815140.006318961977991520.0276823015947759
SMC3#9126315.04493284493280.0002935825420371870.00309056215178124
SP1#666735.69838137814090.005403962701712170.0246563766100532
TCF7L2#6934310.77017656313730.0008003181298398380.00613914250182467
TRIM28#10155318.59052504526250.0001555969297255280.00197069945956881
ZBTB7A#5134137.35190930787590.002516255860282270.0140224772313121
ZNF263#1012738.221841637010680.001799043925565870.0109429440036211



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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