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Coexpression cluster:C3722: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,2.05816,0.598234,0.777097,2.04167,0.63803,1.44641,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,2.14035,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,2.58389,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.82001,8.20448,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,2.96894,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,3.97057,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,3.65045,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.84557,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,1.26332,0.845342,0.635379,1.7611,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,1.46099,0.137917,0.596053,0.855276,0.567465,2.05816,0.598234,0.777097,2.04167,0.63803,1.44641,0.726632,0.939121,0.808003,1.28131,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,2.14035,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,2.58389,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.22068,0.82001,8.20448,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,2.96894,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,3.97057,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,1.37952,1.37044,0.798812,1.50051,3.65045,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;1.93041,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,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;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;3.3282,MA0058.1;2.8588,MA0059.1;2.854,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;1.84332,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;3.33427,MA0074.1;2.15449,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;5.67475,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;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;1.80901,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;0.707589,MA0147.1;2.37462,MA0148.1;0.854239,MA0149.1;6.40038,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;2.15877,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;2.13189,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;1.39232,MA0150.1;1.76247,MA0151.1;0,MA0152.1;2.08673,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;0.149099,MA0163.1;2.48891,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;14.6003,MA0102.2;1.88331,MA0258.1;2.22591,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:34, 22 January 2013


Full id: C3722_Preadipocyte_mature_Adipocyte_Fibroblast_Hepatic_Smooth_Pericytes



Phase1 CAGE Peaks

Hg19::chr18:46065483..46065540,+p2@CTIF
Hg19::chr18:46065541..46065568,+p3@CTIF
Hg19::chr18:46065570..46065579,+p6@CTIF


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
cell layer4.11e-22309
epithelium4.59e-21306
anatomical cluster2.81e-20373
anatomical conduit2.58e-19240
multi-cellular organism6.59e-19656
tube4.80e-17192
multi-tissue structure8.14e-16342
splanchnic layer of lateral plate mesoderm2.01e-1583
anatomical system2.64e-15624
anatomical group5.71e-15625
vasculature7.73e-1578
vascular system7.73e-1578
epithelial tube7.32e-14117
trunk mesenchyme1.77e-12122
vessel5.15e-1268
structure with developmental contribution from neural crest5.25e-12132
epithelial vesicle6.63e-1278
epithelial tube open at both ends1.00e-1159
blood vessel1.00e-1159
blood vasculature1.00e-1159
vascular cord1.00e-1159
multilaminar epithelium1.97e-1183
organism subdivision2.10e-11264
dense mesenchyme tissue2.61e-1173
artery3.08e-1142
arterial blood vessel3.08e-1142
arterial system3.08e-1142
mesenchyme3.42e-11160
entire embryonic mesenchyme3.42e-11160
unilaminar epithelium4.69e-11148
paraxial mesoderm6.00e-1172
presumptive paraxial mesoderm6.00e-1172
somite1.22e-1071
presomitic mesoderm1.22e-1071
presumptive segmental plate1.22e-1071
dermomyotome1.22e-1071
trunk paraxial mesoderm1.22e-1071
ectoderm-derived structure1.27e-10171
ectoderm1.27e-10171
presumptive ectoderm1.27e-10171
skeletal muscle tissue1.36e-1062
striated muscle tissue1.36e-1062
myotome1.36e-1062
muscle tissue1.56e-1064
musculature1.56e-1064
musculature of body1.56e-1064
embryonic structure2.17e-10564
cardiovascular system2.38e-10109
germ layer3.57e-10560
germ layer / neural crest3.57e-10560
embryonic tissue3.57e-10560
presumptive structure3.57e-10560
germ layer / neural crest derived structure3.57e-10560
epiblast (generic)3.57e-10560
systemic artery6.06e-1033
systemic arterial system6.06e-1033
trunk6.92e-10199
circulatory system8.40e-10112
developing anatomical structure1.83e-09581
embryo9.74e-09592
organ part5.35e-08218
surface structure1.83e-0799
aorta2.82e-0721
aortic system2.82e-0721
ecto-epithelium9.83e-07104


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)
MA0003.10.178364
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.13.3282
MA0058.12.8588
MA0059.12.854
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.33427
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.15.67475
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.16.40038
MA0062.20.449458
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.11.76247
MA0151.10
MA0152.12.08673
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
MA0162.10.149099
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.214.6003
MA0102.21.88331
MA0258.12.22591
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
ATF3#467322.46317452600878.81932387510763e-050.00129583760015808
BHLHE40#8553344.87181354697741.10603738662898e-050.000284445798133819
E2F6#187635.017155731697390.00791769806886330.0321982894094702
ELF1#199734.258097958807540.01295179875054610.0461994231260727
ETS1#211339.728760922202340.001085840092584840.00761816830777024
IRF1#365937.63716375356390.002244692747297240.0127993811877581
MAX#414936.452555509007120.003721913834265510.0186388376378257
MXI1#460139.96157162875930.001011470541259020.00719990266211498
MYC#460935.22228187160940.007020843755740150.029431239504124
NFKB1#479035.488063424193840.006049381815655430.0269466598756819
SIN3A#2594235.408884726815140.006318961977991520.0276521440551184
SIX5#147912317.0867153554590.0002004060546325010.00239585713596197
SP1#666735.69838137814090.005403962701712170.0246316266138924
SRF#6722313.79717826216780.0003806615025800190.0037491424620855
TCF7L2#6934310.77017656313730.0008003181298398380.00613373634419482
TFAP2C#7022310.80922860986020.0007916746575753130.00615695208597127
USF1#739136.361499277207960.00388404057290560.0190158125536137
USF2#7392312.99219738506960.0004558979393427810.00421433217268727
YY1#752834.911170749853860.008441455341808260.0329170426928691
ZNF143#7702313.50087655222790.0004062804962997170.00388851986373223



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3722&oldid=2572233"