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{{Coexpression_clusters
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8,0.0455518,0.0398662,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.00213411,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,5.97373e-06,0.123917,0.184317,0.185335,0.0723291,0.258496,0.00371613,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0030448,0.173026,0.0215816,0.139785,0.00149718,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.0257454,0.00347819,0.202065,0.00591081,2.67472e-05,0.0537737,0.15113,8.4053e-05,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,6.87647e-05,0.0812887,0.0981146,0.064145,0.000332324,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,1.91331e-06,0.286691,0.347036,0.0005308,0.263159,0.255956,0.200105,0.00236454,0.29837,0.00335066,0.00107794,1.43917e-06,0.264413,0.131761,0.160658,0.00172878,1.38202e-07,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.0445413,2.51329e-08,0.164638,0.0272695,0.0935776,0.00776295,0.225752,0.207791,0.0958756,0.0859274,0.000648999,0.171683,0.158847,0.271275,0.071111,0.00414049,0.101021,2.84978e-07,0.00104522,0.157274,0.215705,0.252796,0.0017212,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,1.65118,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,2.27558,1.95911,0.599922,0.843849,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,2.78317,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,2.58159,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.99742,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,3.21962,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,3.30166,0.936473,1.96295|tfbs_overrepresentation_jaspar=MA0003.1;0.708947,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;2.16573,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;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,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;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;0.257905,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;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;2.26598,MA0145.1;0.752137,MA0146.1;0.707589,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;2.70092,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;1.39232,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;2.37721,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;0.481578,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial
|id=C4677
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4677_lung_mesothelioma_Renal_liposarcoma_pharyngeal_Nucleus_Endothelial



Phase1 CAGE Peaks

Hg19::chr7:27153185..27153215,+p1@ENST00000522193
Hg19::chr7:27153226..27153257,+p2@ENST00000522193
Hg19::chr7:27153269..27153285,+p3@ENST00000522193


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
trunk7.70e-25199
mesenchyme4.62e-24160
entire embryonic mesenchyme4.62e-24160
vessel3.53e-2068
trunk mesenchyme1.79e-19122
epithelial tube open at both ends4.84e-1859
blood vessel4.84e-1859
blood vasculature4.84e-1859
vascular cord4.84e-1859
epithelial tube5.13e-18117
unilaminar epithelium3.49e-17148
vasculature1.20e-1578
vascular system1.20e-1578
organism subdivision1.46e-15264
trunk region element4.75e-14101
muscle tissue8.48e-1464
musculature8.48e-1464
musculature of body8.48e-1464
skeletal muscle tissue3.04e-1362
striated muscle tissue3.04e-1362
myotome3.04e-1362
epithelial vesicle2.83e-1278
anatomical conduit3.69e-12240
splanchnic layer of lateral plate mesoderm3.91e-1283
artery5.87e-1242
arterial blood vessel5.87e-1242
arterial system5.87e-1242
anatomical cluster7.39e-12373
subdivision of trunk1.05e-11112
intermediate mesoderm1.82e-1028
somite2.39e-1071
presomitic mesoderm2.39e-1071
presumptive segmental plate2.39e-1071
dermomyotome2.39e-1071
trunk paraxial mesoderm2.39e-1071
immaterial anatomical entity3.44e-10117
paraxial mesoderm5.57e-1072
presumptive paraxial mesoderm5.57e-1072
dense mesenchyme tissue1.26e-0973
subdivision of digestive tract1.92e-09118
epithelium2.08e-09306
anatomical space2.14e-0995
renal system3.87e-0948
cell layer5.93e-09309
multi-tissue structure8.13e-09342
blood vessel endothelium1.05e-0818
endothelium1.05e-0818
cardiovascular system endothelium1.05e-0818
urinary system structure1.41e-0847
cavitated compound organ1.78e-0831
systemic artery1.80e-0833
systemic arterial system1.80e-0833
tube2.28e-08192
abdomen element2.62e-0854
abdominal segment element2.62e-0854
simple squamous epithelium2.97e-0822
body cavity precursor3.24e-0854
mesoderm3.83e-08315
mesoderm-derived structure3.83e-08315
presumptive mesoderm3.83e-08315
abdominal segment of trunk4.81e-0860
abdomen4.81e-0860
multilaminar epithelium5.01e-0883
reproductive structure5.09e-0859
reproductive system5.09e-0859
cardiovascular system1.85e-07109
digestive system2.67e-07145
digestive tract2.67e-07145
primitive gut2.67e-07145
circulatory system3.53e-07112
squamous epithelium5.04e-0725
anatomical cavity7.64e-0761
aorta7.99e-0721
aortic system7.99e-0721
cloaca8.79e-0714
anal region8.79e-0714
embryonic cloaca8.79e-0714
terminal part of digestive tract8.79e-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)
MA0003.10.708947
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
MA0038.12.16573
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
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
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
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0111.11.80901
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
MA0144.12.26598
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.432958
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
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
MA0159.12.37721
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
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
CTBP2#1488362.71700033932814.049570681927e-060.00013053491124993
FOS#235338.99795530889440.001372499272417130.00901808439836254
GATA2#2624312.7449317335540.0004829527704283790.00438982631773451
STAT3#6774310.51946499715420.0008589184530415310.00645496037398032
SUZ12#23512350.11578091106297.93834897779404e-060.000223409654780876
TCF7L2#6934310.77017656313730.0008003181298398380.00617269220606623
YY1#752834.911170749853860.008441455341808260.0331210892795519
ZNF263#1012738.221841637010680.001799043925565870.0110122112614098



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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