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Coexpression cluster:C953: Difference between revisions

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{{Coexpression_clusters
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51,0.184705,0.411826,0.184047,0.425621,0.111096,0.18548,0.148563,0.130525,0.0154718,7.419e-05,0.0104837,0.396522,0.318983,0.267772,0.291371,0.168254,0.0066405,0.40407,0.000127419,0.478764,0.328268,0.594172,0.302509,0.121102,0.40705,0.224725,0.00163014,0.520157,0.327588,0.1256,0.459324,0.201671,0.5923,0.597634,0.495225,0.51408,0.502377,0.00128464,0.474502,0.212719,0.309128,0.533737,0.571519,0.434445,0.488829,0.363467,0.00465698,0.0100798,0.399782,0.343945,0.224236,0.530537,0.432612,0.44213,0.263525,0.492092,0.00574492,0.628217,0.522084,0.226979,0.491955,0.0458962,0.152349,0.152802,0.0876512,0.216263,0.117262,0.152699,0.03013,0.0139744,0.50945,0.00385038,0.0471723,0.0262387,0.22458,0.266409,0.0011303,0.322962,0.179632,0.0441793,0.186072,0.211757,0.338622,0.29306,0.126579,0.187708,0.245457,0.106235,0.352719,0.496388,0.283342,0.269216,0.00998735,0.367773,0.000377013,0.000318181,0.488202,0.0438035,0.0230999,0.584019,0.11758,0.632399,0.601983,0.345488,0.408688,0.153347,0.486539,0.637365,0.554869,0.00137797,0.308763,0.521884,0.532407,0.307503,0.00446391,0.0268042,0.629431,0.263855,0.578048,0.102464,0.0420888,0.255282,0.00750903,0.53587,0.502814,0.260932,0.236266,0.108433,0.431685,0.404852,0.0160401,0.198522,0.611947,0.273479,0.0411991,1.79097e-12,0.00192586,0.517565,0.582826,0.152975,0.153513|tfbs_overrepresentation_for_novel_motifs=0.83884,0.0494815,0.305225,1.12193,0.267236,0.439064,0.511871,0.164003,0.487494,0.285547,0.410439,0.553754,0.127813,1.25117,0.266007,0.782718,0.728104,1.17081,0.842338,0.216842,0.823689,0.0355541,0.431698,0.262652,0.918075,0.575764,0.112018,0.429643,0.74357,0.329945,0.389837,0.764231,3.14828,0.406122,0.23642,4.22578,0.233607,0.440165,0.213144,0.451713,0.235191,0.374544,0.0412835,2.0705,0.149259,0.333541,0.51292,0.4002,0.0372068,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.100358,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.0724994,0.988898,0.124338,0.114787,0.342172,0.684401,0.750836,0.341765,0.858505,0.699894,0.532172,0.963219,0.937974,0.0150019,0.0591186,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,2.49908,0.423564,0.82268,0.619373,0.606171,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.846745,0.814459,0.300169,0.41935,1.12352,2.66855,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,1.33422,1.18405,0.636999,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,1.17257,0.641461,1.83907,0.37143,0.193834,0.50389,0.150327,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,1.27204,0.0121205|tfbs_overrepresentation_jaspar=MA0003.1;0.00371372,MA0004.1;1.06719,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.0324647,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,MA0027.1;2.48103,MA0028.1;1.40203,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.0764047,MA0050.1;1.04113,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.088427,MA0056.1;0,MA0057.1;0.539841,MA0058.1;2.37381,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;1.99244,MA0070.1;1.96957,MA0071.1;2.08432,MA0072.1;0.840664,MA0073.1;3.19635e-05,MA0074.1;0.509711,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;1.4402,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;1.35827,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.257174,MA0105.1;0.0643619,MA0106.1;0.554855,MA0107.1;0.592696,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.208403,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;2.35992,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.552298,MA0145.1;0.706237,MA0146.1;0.0045741,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.833414,MA0035.2;1.19307,MA0039.2;0.0006485,MA0138.2;0.608783,MA0002.2;0.46405,MA0137.2;0.780538,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.0433683,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;1.20819,MA0153.1;0.969315,MA0154.1;0.488402,MA0155.1;0.0402662,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;1.15068,MA0161.1;0,MA0162.1;0.0107891,MA0163.1;0.00648562,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;3.47892e-06,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0}}
|full_id=C953_Synoviocyte_Olfactory_Lens_embryonic_eye_rectum_tenocyte
|id=C953
}}

Latest revision as of 11:34, 17 September 2013


Full id: C953_Synoviocyte_Olfactory_Lens_embryonic_eye_rectum_tenocyte



Phase1 CAGE Peaks

Hg19::chr6:151670237..151670275,-p@chr6:151670237..151670275
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Hg19::chr6:151670325..151670388,-p@chr6:151670325..151670388
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Hg19::chr6:151670495..151670565,-p@chr6:151670495..151670565
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Hg19::chr6:151671044..151671077,-p@chr6:151671044..151671077
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Hg19::chr6:151671119..151671166,-p@chr6:151671119..151671166
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Hg19::chr6:151671321..151671355,-p@chr6:151671321..151671355
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Hg19::chr6:151671408..151671451,-p@chr6:151671408..151671451
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Hg19::chr6:151671486..151671529,-p@chr6:151671486..151671529
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Hg19::chr6:151678864..151678868,+p6@AKAP12


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
anatomical cluster3.87e-20373
cell layer1.23e-18309
epithelium6.21e-18306
multi-cellular organism3.17e-16656
multi-tissue structure2.94e-14342
anatomical system7.02e-14624
anatomical group1.30e-13625
anatomical conduit2.12e-13240
structure with developmental contribution from neural crest7.41e-12132
tube9.28e-12192
embryo2.80e-11592
vasculature3.12e-1178
vascular system3.12e-1178
mesenchyme2.78e-10160
entire embryonic mesenchyme2.78e-10160
nervous system2.02e-0989
central nervous system3.23e-0981
developing anatomical structure3.77e-09581
epithelial vesicle4.54e-0978
dense mesenchyme tissue5.92e-0973
paraxial mesoderm1.02e-0872
presumptive paraxial mesoderm1.02e-0872
unilaminar epithelium1.15e-08148
neural plate1.42e-0882
presumptive neural plate1.42e-0882
multilaminar epithelium1.61e-0883
somite2.02e-0871
presomitic mesoderm2.02e-0871
presumptive segmental plate2.02e-0871
dermomyotome2.02e-0871
trunk paraxial mesoderm2.02e-0871
organism subdivision2.32e-08264
vessel2.71e-0868
trunk3.40e-08199
neurectoderm3.91e-0886
muscle tissue4.35e-0864
musculature4.35e-0864
musculature of body4.35e-0864
trunk mesenchyme5.00e-08122
germ layer5.84e-08560
germ layer / neural crest5.84e-08560
embryonic tissue5.84e-08560
presumptive structure5.84e-08560
germ layer / neural crest derived structure5.84e-08560
epiblast (generic)5.84e-08560
skeletal muscle tissue9.07e-0862
striated muscle tissue9.07e-0862
myotome9.07e-0862
embryonic structure1.01e-07564
epithelial tube open at both ends2.20e-0759
blood vessel2.20e-0759
blood vasculature2.20e-0759
vascular cord2.20e-0759
brain2.58e-0768
future brain2.58e-0768
cardiovascular system3.17e-07109
circulatory system3.29e-07112
epithelial tube4.42e-07117
neural tube8.08e-0756
neural rod8.08e-0756
future spinal cord8.08e-0756
neural keel8.08e-0756
splanchnic layer of lateral plate mesoderm8.59e-0783


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)
MA0003.10.00371372
MA0004.11.06719
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.11.40203
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.04113
MA0051.10.510444
MA0052.10.795605
MA0055.10.088427
MA0056.10
MA0057.10.539841
MA0058.12.37381
MA0059.10.323879
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.11.99244
MA0070.11.96957
MA0071.12.08432
MA0072.10.840664
MA0073.13.19635e-05
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.4402
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.11.35827
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.592696
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.12.35992
MA0142.10.679161
MA0143.10.571113
MA0144.10.552298
MA0145.10.706237
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.833414
MA0035.21.19307
MA0039.20.0006485
MA0138.20.608783
MA0002.20.46405
MA0137.20.780538
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.488402
MA0155.10.0402662
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.0107891
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.23.47892e-06
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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

No analysis results for this cluster

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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