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Coexpression cluster:C4173: Difference between revisions

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{{Coexpression_clusters
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935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.035048,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,1.23181,0.221898,3.18659,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,1.53533,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,0.439574,0.599922,0.427404,0.596053,0.855276,1.39264,0.469078,1.45745,1.82956,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,1.10051,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.507157,0.82001,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,2.83477,1.1798,1.09802,1.90788,2.61709,0.921547,0.743661,2.55998,1.67826,1.26794,0.684398,3.21962,1.58942,0.594137,0.553386,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,2.36206,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,1.33389,1.54007,0.250511,1.37083,3.10872,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,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;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;2.13518,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;0.0185922,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;1.70054,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;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;0.0526989,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;0.312019,MA0155.1;1.31345,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;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.181755,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4173_Smooth_mesenchymal_amniotic_tenocyte_ductus_seminal_Synoviocyte
|id=C4173
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4173_Smooth_mesenchymal_amniotic_tenocyte_ductus_seminal_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr2:20251339..20251367,-p3@LAPTM4A
Hg19::chr2:20251371..20251400,-p1@LAPTM4A
Hg19::chr2:20251406..20251451,-p2@LAPTM4A


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
fibroblast4.72e-1376
somatic cell2.93e-12588
multi fate stem cell5.16e-11427
somatic stem cell3.20e-10433
stem cell3.78e-10441
extraembryonic cell4.46e-0919
contractile cell7.46e-0959
muscle precursor cell2.13e-0858
myoblast2.13e-0858
multi-potent skeletal muscle stem cell2.13e-0858
mesodermal cell3.49e-08121
fat cell4.75e-0815
muscle cell1.19e-0755
stromal cell1.26e-0728
non-terminally differentiated cell2.77e-07106
animal cell6.68e-07679
eukaryotic cell6.68e-07679
Uber Anatomy
Ontology termp-valuen
mesoderm5.00e-15315
mesoderm-derived structure5.00e-15315
presumptive mesoderm5.00e-15315
multi-cellular organism1.52e-14656
anatomical system1.48e-10624
anatomical group2.83e-10625
mesenchyme5.46e-09160
entire embryonic mesenchyme5.46e-09160
extraembryonic membrane9.92e-0914
membranous layer9.92e-0914
musculoskeletal system4.55e-08167
trunk mesenchyme5.89e-08122
muscle tissue1.10e-0764
musculature1.10e-0764
musculature of body1.10e-0764
skeletal muscle tissue1.30e-0762
striated muscle tissue1.30e-0762
myotome1.30e-0762
organ2.41e-07503
multilaminar epithelium2.44e-0783
epithelial vesicle4.26e-0778
dense mesenchyme tissue5.34e-0773
somite6.16e-0771
presomitic mesoderm6.16e-0771
presumptive segmental plate6.16e-0771
dermomyotome6.16e-0771
trunk paraxial mesoderm6.16e-0771
extraembryonic structure7.76e-0724
surface structure8.62e-0799


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)
MA0003.10.401049
MA0004.10.826076
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
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.12.13518
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
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
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
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
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
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-050.000285077587912498
CHD2#1106310.34402283411690.0009033701102746880.00661574019682899
E2F6#187635.017155731697390.00791769806886330.0323102593917874
EBF1#187938.9064668465690.00141523283560980.00916964465030413
EGR1#195834.988179094810140.008056488137383440.0321357966841152
ELF1#199734.258097958807540.01295179875054610.046346635705759
FOS#235338.99795530889440.001372499272417130.00899375401631149
GATA1#2623313.56030814380040.0004009615963782630.00388604567224846
HNF4A#3172215.42152690863580.005444210486686610.0246825793982923
IRF1#365937.63716375356390.002244692747297240.012837931429548
IRF3#3661346.98195221148969.63568551583244e-060.000253806143653978
JUND#372736.994663941871030.002921845042734990.0157101819613982
MAX#414936.452555509007120.003721913834265510.0186971120219748
MXI1#460139.96157162875930.001011470541259020.007213669206402
MYC#460935.22228187160940.007020843755740150.0295165405766744
NFYA#4800318.42558069983050.0001598135507814160.00199985231608679
NFYB#4801316.75979325353650.0002123649923296180.00246298583386041
NRF1#4899312.21027944771090.0005492172401020010.00472057438392008
PBX3#5090321.91451268674419.49854535978121e-050.00136943481340446
POU2F2#545239.106124057742520.001324165192682130.0088350149210074
PPARGC1A#108913350.0511363636362.31814761783079e-081.63584472336912e-06
RFX5#5993312.04791082719510.0005717246050312580.00485489438367831
SIN3A#2594235.408884726815140.006318961977991520.0277451471461976
SMARCB1#6598318.25271578115740.000164397760679890.0020345464779769
SP1#666735.69838137814090.005403962701712170.0247071076743036
SP2#6668326.15353049384465.58768218891694e-050.000941548790139232
SREBF1#6720347.00584944048839.62099323994382e-060.00025502713527576
STAT1#6772320.70658749719920.0001125992441046670.00155060027097143
STAT3#6774310.51946499715420.0008589184530415310.00643782003137681
THAP1#55145331.36914460285133.23800758564397e-050.000648091748250423
USF1#739136.361499277207960.00388404057290560.0190757260001734



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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