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Coexpression cluster:C638: Difference between revisions

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{{Coexpression_clusters
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7,1.00468e-10,0.0195084,3.57414e-05,0.274743,0.275462,0.0291418,0.848665,9.41353e-07,0.233234,8.6248e-16,0.29108,0.595703,0.315097,0.000971939,0.657795,0.147894,0.257401,0.166003,0.254446,0.00046488,0.420552,0.201283,0.260326,0.56424,0.685278,0.663217,0.356279,0.373564,0.571642,0.156002,0.0258013,0.747657,0.0246822,2.46347e-07,0.602579,0.633647,0.688046,5.56869e-26,0.857865,0.252359,2.70866e-05,0.276474,0.619012,0.024543,0.000104735,0.14327,0.366902,0.00372834,0.603657,0.337649,0.0687843,0.341247,0.481022,0.29746,0.149274,0.690717,0.00450421,0.664123,2.09865e-05,0.108935,1.10083e-06,0.00817644,0.56202,0.123426,0.577896,0.167392,0.27322,0.22134,0.195528,0.767906,0.0222551,2.12792e-21,0.544167,0.449866,0.384185,0.00224526,0.249171,3.58451e-08,0.553004,3.16033e-11,0.269217,0.46149,0.754102,0.820512,0.238348,0.556477,0.40406,0.533477,0.680896,0.127655,0.0714674,0.0164399,0.295569,0.165459,0.757358,0.654735,0.104189,0.000905322,0.51031,0.264557,0.011907,0.437434,3.42603e-05,0.732422,0.00219843,0.647906,0.504741,0.27326,0.000374563,0.547991,0.00458504,0.749937,0.69157,0.000308107,0.013851,1.07384e-05,0.651396,0.517352,0.0706501,0.682887,0.329999,0.65125,0.409482,0.226719,0.227361,0.00778871,0.315496,0.0165557,0.227215,0.108583,0.757328,0.0263299,0.25332,0.129686,0.624999,0.00769537,0.382401,0.266095,0.454858,0.265087,0.402864,0.0415444,0.309364,0.474347,0.416949,0.189841,0.276311,0.354746,0.160298,0.0313599,0.655972,0.00670687,1.3893e-08,3.52383e-18,0.000853348,1.86949e-05,0.0514651,0.279669,0.00152865,0.0863771,0.395816,0.598612,0.001144,0.761425,0.482811,1.74761e-08,0.00087282,0.64545,0.210944,0.716075,0.547561,0.0206641,0.682681,0.693478,0.0204019,0.0825511,0.628086,0.786522,0.00526642,0.388065,0.568069,0.331954,0.367768,2.46443e-05,0.00759152,0.00517598,0.375214,0.342479,0.831075,0.584807,0.553916,0.771635,0.291242,0.432933,0.391636,0.00022113,4.43161e-05,0.550009,0.678211,0.743325,2.10269e-08,0.160064|tfbs_overrepresentation_for_novel_motifs=0.554539,2.91984,1.03473,0.297884,0.153879,0.296522,0.360887,0.270053,0.953813,0.208748,0.271739,1.03072,0.0551804,0.350994,0.465119,0.506197,1.37708,1.79539,0.480243,0.663557,0.184,3.07871,0.789382,0.150321,0.218509,0.418678,1.51997,0.288329,0.472898,0.352289,0.254115,1.44899,1.09533,0.788265,0.130292,8.12702,0.12818,0.806075,1.20525,0.881025,0.129369,0.241157,1.4336,0.46248,0.171538,0.206995,0.361827,0.262957,1.00268,0.921037,1.10173,0.372023,0.780607,1.59963,0.811691,0.353512,0.15913,0.325599,0.352007,0.324748,1.52924,0.363871,0.564331,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.230809,0.0817196,0.254168,0.80977,1.164,0.047312,1.45323,0.519091,0.581542,1.15217,0.493088,0.533593,0.37913,0.274429,0.760489,0.218798,0.20656,0.961931,0.454557,1.35556,0.98765,1.74203,0.609873,0.101133,0.468794,0.109261,0.0605346,1.56542,0.458696,6.7938,0.113893,0.6046,0.644537,0.563483,0.492631,0.268065,0.548871,0.348037,0.623411,0.142849,0.19228,0.641937,0.179896,0.279418,0.940917,0.12714,0.271646,1.30184,0.500972,0.336456,0.801818,1.1473,0.294241,0.388967,1.04884,0.519787,0.935668,0.614537,0.842806,0.109858,0.735394,0.712269,0.856671,1.77669,1.00021,0.0344783,0.695928,0.786388,0.95886,1.80749,1.40745,0.922589,0.356906,0.646464,0.494226,0.318465,0.47912,1.64894,1.2469,0.0991414,0.712398,0.466341,0.735758,0.0728391,0.363452,1.12781,0.440071,0.443316,0.623978,0.196611,0.921409,0.718143,0.580811,0.577588,0.508869,1.75041,1.06123,0.945224,1.04415|tfbs_overrepresentation_jaspar=MA0003.1;0.568865,MA0004.1;0.275994,MA0006.1;0.152601,MA0007.1;1.32983,MA0009.1;0.695988,MA0014.1;0.450273,MA0017.1;3.88524,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.0262025,MA0050.1;0.265714,MA0051.1;0.359609,MA0052.1;0.623986,MA0055.1;0.671485,MA0056.1;0,MA0057.1;0.10396,MA0058.1;0.200063,MA0059.1;0.199079,MA0060.1;1.42755,MA0061.1;0.841286,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;1.99958,MA0069.1;0.681911,MA0070.1;0.671241,MA0071.1;1.58009,MA0072.1;0.666958,MA0073.1;0.0088374,MA0074.1;1.68271,MA0076.1;0.212295,MA0077.1;1.58596,MA0078.1;1.98692,MA0081.1;1.09529,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.491738,MA0089.1;0,MA0090.1;0.635809,MA0091.1;0.278153,MA0092.1;0.247341,MA0093.1;0.154754,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.92504,MA0103.1;0.448026,MA0105.1;0.430023,MA0106.1;0.399649,MA0107.1;0.348426,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;0.414278,MA0114.1;3.68475,MA0115.1;5.03209,MA0116.1;0.354243,MA0117.1;0.732,MA0119.1;0.18693,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.0564547,MA0140.1;0.327488,MA0141.1;0.574537,MA0142.1;0.514195,MA0143.1;1.06513,MA0144.1;1.08559,MA0145.1;0.827687,MA0146.1;1.84907,MA0147.1;0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|full_id=C638_skeletal_tongue_Adipocyte_diaphragm_penis_throat_Smooth
|id=C638
}}

Latest revision as of 11:27, 17 September 2013


Full id: C638_skeletal_tongue_Adipocyte_diaphragm_penis_throat_Smooth



Phase1 CAGE Peaks

Hg19::chr9:35684475..35684520,+p@chr9:35684475..35684520
+
Hg19::chr9:35684538..35684558,-p@chr9:35684538..35684558
-
Hg19::chr9:35685273..35685313,+p@chr9:35685273..35685313
+
Hg19::chr9:35685418..35685431,+p@chr9:35685418..35685431
+
Hg19::chr9:35685445..35685517,+p@chr9:35685445..35685517
+
Hg19::chr9:35685537..35685548,-p9@TPM2
Hg19::chr9:35685631..35685657,+p@chr9:35685631..35685657
+
Hg19::chr9:35685667..35685687,-p7@TPM2
Hg19::chr9:35685751..35685774,-p5@TPM2
Hg19::chr9:35689148..35689192,+p@chr9:35689148..35689192
+
Hg19::chr9:35689172..35689190,-p@chr9:35689172..35689190
-
Hg19::chr9:35689196..35689218,-p@chr9:35689196..35689218
-
Hg19::chr9:35689248..35689267,-p@chr9:35689248..35689267
-
Hg19::chr9:35689915..35689930,-p1@TPM2


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
dense mesenchyme tissue6.04e-2773
somite7.84e-2771
presomitic mesoderm7.84e-2771
presumptive segmental plate7.84e-2771
dermomyotome7.84e-2771
trunk paraxial mesoderm7.84e-2771
epithelial vesicle1.73e-2678
paraxial mesoderm2.41e-2672
presumptive paraxial mesoderm2.41e-2672
muscle tissue6.97e-2564
musculature6.97e-2564
musculature of body6.97e-2564
skeletal muscle tissue2.62e-2462
striated muscle tissue2.62e-2462
myotome2.62e-2462
multilaminar epithelium4.45e-2283
trunk mesenchyme1.08e-19122
mesenchyme5.29e-19160
entire embryonic mesenchyme5.29e-19160
organism subdivision3.54e-16264
trunk8.81e-14199
multi-tissue structure4.21e-13342
artery2.18e-1242
arterial blood vessel2.18e-1242
arterial system2.18e-1242
unilaminar epithelium2.46e-12148
multi-cellular organism8.92e-12656
splanchnic layer of lateral plate mesoderm2.77e-1183
epithelial tube open at both ends3.37e-1059
blood vessel3.37e-1059
blood vasculature3.37e-1059
vascular cord3.37e-1059
systemic artery7.59e-1033
systemic arterial system7.59e-1033
mesoderm1.77e-09315
mesoderm-derived structure1.77e-09315
presumptive mesoderm1.77e-09315
vasculature2.72e-0978
vascular system2.72e-0978
epithelial tube1.53e-08117
surface structure2.13e-0899
anatomical system5.62e-08624
anatomical group9.15e-08625
vessel1.78e-0768
primary circulatory organ1.96e-0727
circulatory system4.31e-07112
embryonic structure8.48e-07564
embryo9.08e-07592
heart9.48e-0724
primitive heart tube9.48e-0724
primary heart field9.48e-0724
anterior lateral plate mesoderm9.48e-0724
heart tube9.48e-0724
heart primordium9.48e-0724
cardiac mesoderm9.48e-0724
cardiogenic plate9.48e-0724
heart rudiment9.48e-0724


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)
MA0003.10.568865
MA0004.10.275994
MA0006.10.152601
MA0007.11.32983
MA0009.10.695988
MA0014.10.450273
MA0017.13.88524
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.10.671485
MA0056.10
MA0057.10.10396
MA0058.10.200063
MA0059.10.199079
MA0060.11.42755
MA0061.10.841286
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.11.99958
MA0069.10.681911
MA0070.10.671241
MA0071.11.58009
MA0072.10.666958
MA0073.10.0088374
MA0074.11.68271
MA0076.10.212295
MA0077.11.58596
MA0078.11.98692
MA0081.11.09529
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.491738
MA0089.10
MA0090.10.635809
MA0091.10.278153
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.92504
MA0103.10.448026
MA0105.10.430023
MA0106.10.399649
MA0107.10.348426
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.13.68475
MA0115.15.03209
MA0116.10.354243
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.10.327488
MA0141.10.574537
MA0142.10.514195
MA0143.11.06513
MA0144.11.08559
MA0145.10.827687
MA0146.11.84907
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.20.326883
MA0039.20.0280647
MA0138.20.44894
MA0002.20.248488
MA0137.20.504333
MA0104.20.0769208
MA0047.20.388882
MA0112.20.0554275
MA0065.24.11878
MA0150.10.218956
MA0151.10
MA0152.10.886132
MA0153.10.790794
MA0154.10.219649
MA0155.13.2564
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.13.06752
MA0160.10.833266
MA0161.10
MA0162.10.03301
MA0163.12.12087
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.20.0619564
MA0102.21.22472
MA0258.10.624652
MA0259.10.117259
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
TFAP2A#702044.719609820869990.008221727346191040.0324491339395679



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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