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Coexpression cluster:C2941: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.44014,0.620826,2.42852,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,1.68405,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,8.0291,0.740899,0.463978,0.371755,0.493145,1.59701,0.183156,0.53106,0.314427,2.53981,0.822818,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,8.80903,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,4.31432,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,2.50078,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,13.1086,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266
|tfbs_overrepresentation_for_novel_motifs=1.44014,0.620826,2.42852,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,1.68405,0.867962,1.62243,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,1.53003,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,8.0291,0.740899,0.463978,0.371755,0.493145,1.59701,0.183156,0.53106,0.314427,2.53981,0.822818,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,1.82985,0.297448,0.776148,1.13655,1.92893,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,8.80903,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,4.31432,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,2.50078,1.14983,1.05974,0.979006,2.81371,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.785429,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,13.1086,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.91266
|tfbs_overrepresentation_jaspar=MA0003.1;1.45381,MA0004.1;0.71247,MA0006.1;1.31813,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;2.45009,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;4.04183,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;5.70469,MA0056.1;0,MA0057.1;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;1.92841,MA0067.1;1.53181,MA0068.1;1.52107,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;31.7729,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;1.57689,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;1.66396,MA0035.2;0.778873,MA0039.2;3.66694,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;3.12566,MA0065.2;1.09513,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;2.30186,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;4.10107,MA0160.1;0.756582,MA0161.1;0,MA0162.1;6.73484,MA0163.1;0.918944,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;8.14977,MA0102.2;1.75932,MA0258.1;1.88931,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 21:01, 22 January 2013


Full id: C2941_parietal_medulloblastoma_lung_occipital_Neural_temporal_small



Phase1 CAGE Peaks

Hg19::chr9:14313893..14313908,-p7@NFIB
Hg19::chr9:14314066..14314075,-p11@NFIB
Hg19::chr9:14314106..14314119,-p5@NFIB
Hg19::chr9:14314131..14314147,-p2@NFIB


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 cluster1.63e-53373
anatomical conduit1.46e-37240
tube1.08e-34192
epithelium3.55e-32306
cell layer3.83e-32309
multi-tissue structure5.47e-32342
structure with developmental contribution from neural crest8.37e-27132
nervous system1.28e-2589
organ system subdivision2.91e-25223
neurectoderm8.17e-2586
neural plate4.86e-2482
presumptive neural plate4.86e-2482
multi-cellular organism4.95e-24656
central nervous system5.68e-2481
ectoderm-derived structure4.57e-23171
ectoderm4.57e-23171
presumptive ectoderm4.57e-23171
anatomical system2.54e-22624
embryo5.44e-22592
anatomical group5.70e-22625
neural tube9.73e-2256
neural rod9.73e-2256
future spinal cord9.73e-2256
neural keel9.73e-2256
brain6.45e-2168
future brain6.45e-2168
adult organism1.09e-20114
developing anatomical structure1.29e-20581
regional part of nervous system1.51e-2053
regional part of brain1.51e-2053
embryonic structure2.10e-20564
germ layer2.93e-20560
germ layer / neural crest2.93e-20560
embryonic tissue2.93e-20560
presumptive structure2.93e-20560
germ layer / neural crest derived structure2.93e-20560
epiblast (generic)2.93e-20560
ecto-epithelium3.06e-20104
pre-chordal neural plate1.83e-1761
regional part of forebrain3.74e-1641
forebrain3.74e-1641
anterior neural tube3.74e-1641
future forebrain3.74e-1641
telencephalon1.48e-1534
organ part2.26e-15218
brain grey matter2.35e-1534
gray matter2.35e-1534
cerebral hemisphere2.94e-1532
regional part of telencephalon5.41e-1532
epithelial tube1.61e-13117
cerebral cortex5.15e-1325
pallium5.15e-1325
vasculature8.54e-1378
vascular system8.54e-1378
splanchnic layer of lateral plate mesoderm1.13e-1283
primordium3.67e-12160
regional part of cerebral cortex2.09e-1122
vessel2.27e-1168
circulatory system6.79e-11112
organ1.52e-10503
epithelial tube open at both ends1.72e-1059
blood vessel1.72e-1059
blood vasculature1.72e-1059
vascular cord1.72e-1059
neocortex2.79e-1020
cardiovascular system3.65e-10109
organism subdivision1.40e-09264
compound organ1.26e-0868
primary circulatory organ5.05e-0827
blood vessel endothelium1.53e-0718
endothelium1.53e-0718
cardiovascular system endothelium1.53e-0718
simple squamous epithelium3.48e-0722
heart3.57e-0724
primitive heart tube3.57e-0724
primary heart field3.57e-0724
anterior lateral plate mesoderm3.57e-0724
heart tube3.57e-0724
heart primordium3.57e-0724
cardiac mesoderm3.57e-0724
cardiogenic plate3.57e-0724
heart rudiment3.57e-0724
squamous epithelium5.59e-0725
organ segment5.63e-0798
posterior neural tube7.85e-0715
chordal neural plate7.85e-0715


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)
MA0003.11.45381
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.10.873355
MA0024.14.04183
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.15.70469
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.131.7729
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.23.66694
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.23.12566
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.14.10107
MA0160.10.756582
MA0161.10
MA0162.16.73484
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.28.14977
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
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
E2F1#186944.907389214879320.001724022357361790.010688304106643
E2F6#187645.017155731697390.00157802193473060.00999860661538124
MYC#460945.22228187160940.001344309395272740.00890287437748189
REST#597849.650028716128020.0001152825614219170.0015765346906303



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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