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Coexpression cluster:C4255: Difference between revisions

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{{Coexpression_clusters
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934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,1.55576,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.36391,0.596053,1.99037,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,2.54524,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.853445,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,1.3017,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;2.05336,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.24048,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;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;5.46492,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;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;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,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;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.752137,MA0146.1;2.3244,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.757898,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;0.760954,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;0.149099,MA0163.1;0.776149,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;2.26143,MA0099.2;0.902716,MA0079.2;0.181755,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;3.52796,MA0442.1;0}}
|full_id=C4255_Adipocyte_amniotic_Smooth_Chondrocyte_chorionic_Ewing_Preadipocyte
|id=C4255
}}

Latest revision as of 12:42, 17 September 2013


Full id: C4255_Adipocyte_amniotic_Smooth_Chondrocyte_chorionic_Ewing_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr3:100211412..100211501,+p1@TMEM45A
Hg19::chr3:100211526..100211584,+p2@TMEM45A
Hg19::chr3:100211600..100211628,+p4@TMEM45A


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
trunk mesenchyme3.25e-16122
multilaminar epithelium6.57e-1683
somite1.49e-1571
presomitic mesoderm1.49e-1571
presumptive segmental plate1.49e-1571
dermomyotome1.49e-1571
trunk paraxial mesoderm1.49e-1571
dense mesenchyme tissue2.91e-1573
paraxial mesoderm7.90e-1572
presumptive paraxial mesoderm7.90e-1572
skeletal muscle tissue2.43e-1462
striated muscle tissue2.43e-1462
myotome2.43e-1462
mesenchyme3.57e-14160
entire embryonic mesenchyme3.57e-14160
muscle tissue5.71e-1464
musculature5.71e-1464
musculature of body5.71e-1464
epithelial vesicle3.34e-1378
trunk1.38e-11199
multi-cellular organism7.46e-11656
organism subdivision8.10e-11264
multi-tissue structure2.73e-10342
unilaminar epithelium3.20e-10148
splanchnic layer of lateral plate mesoderm2.60e-0983
surface structure6.71e-0999
systemic artery2.77e-0833
systemic arterial system2.77e-0833
artery3.96e-0842
arterial blood vessel3.96e-0842
arterial system3.96e-0842
primordium4.60e-08160
extraembryonic membrane4.79e-0814
membranous layer4.79e-0814
endoderm-derived structure1.01e-07160
endoderm1.01e-07160
presumptive endoderm1.01e-07160
integument1.02e-0746
integumental system1.02e-0746
anatomical group1.46e-07625
anatomical system1.73e-07624
organ component layer2.56e-0766
epithelial tube4.99e-07117
extraembryonic structure5.02e-0724
Disease
Ontology termp-valuen
ovarian cancer1.15e-0714


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
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.15.46492
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
MA0074.10.935474
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.12.3244
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
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
MA0162.10.149099
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.13.52796
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#90536.336201576962630.003930750035764890.0190560090509794
CHD2#1106310.34402283411690.0009033701102746880.00661759633492166
CTCF#1066435.360256373075030.0064925092527670.0280333708388347
E2F1#186934.907389214879320.008460985347239390.0326434003945451
E2F6#187635.017155731697390.00791769806886330.0323279435714459
EBF1#187938.9064668465690.00141523283560980.0091736284830097
ELF1#199734.258097958807540.01295179875054610.0463656992427601
FOS#235338.99795530889440.001372499272417130.00899657638310253
GABPB1#255337.067683836182170.002832212825417420.0154509755157632
IRF1#365937.63716375356390.002244692747297240.0128421509632965
IRF3#3661346.98195221148969.63568551583244e-060.000253870171439966
NFYA#4800318.42558069983050.0001598135507814160.00200057142874989
NFYB#4801316.75979325353650.0002123649923296180.00246353298166311
NRF1#4899312.21027944771090.0005492172401020010.00472251764688069
PAX5#507936.669565531177830.003370290999677260.0173308627137023
PBX3#5090321.91451268674419.49854535978121e-050.00137019140722402
RAD21#5885310.35503389545630.0009004912073565420.00666003832625946
RFX5#5993312.04791082719510.0005717246050312580.00485647385318093
SP1#666735.69838137814090.005403962701712170.0247179284633696
SP2#6668326.15353049384465.58768218891694e-050.000941700726364847
SPI1#668838.204323508522730.001810593189410520.0109247525627619
TCF12#6938310.63446490218640.0008313523990202070.00630450284644724
TCF7L2#6934310.77017656313730.0008003181298398380.00615632504694283
TFAP2A#7020316.5186343730450.0002218033880766340.00248844387660711
TFAP2C#7022310.80922860986020.0007916746575753130.00617258003452841



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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