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Coexpression cluster:C1241: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=2.69543,4.21052,0.384703,0.529489,1.62733,0.52784,2.50145,0.226729,0.224331,1.18097,1.24425,0.647852,0.541517,0.592674,0.341795,0.365029,0.827563,0.28906,1.08139,0.0986842,0.384762,0.23059,0.520063,0.338096,1.09974,0.670692,0.164928,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.546594,0.309012,0.232776,2.27897,0.529001,0.282922,5.09012,0.307642,1.16235,1.91266,3.37087,0.0257952,0.415364,0.60533,0.486696,0.511111,1.63856,0.684981,0.617179,1.79619,0.941629,1.09491,0.595623,0.350547,0.562713,1.44118,0.561701,0.905643,0.60771,1.19465,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.369103,1.0929,0.531388,0.503161,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.649554,1.04131,2.24329,0.097572,2.03804,1.69317,1.65172,1.27705,1.01423,0.881388,0.26423,0.910085,0.277058,1.69423,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,1.78098,0.493026,0.815341,0.589207,0.43012,2.38505,3.70924,0.915771,0.379203,0.507004,1.22894,0.304323,1.90797,0.474472,0.762789,1.35329,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,2.05416,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,0.554217,0.738579,1.94751,1.15519,0.26104,5.32038,0.887646,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.212606
|tfbs_overrepresentation_jaspar=MA0003.1;3.86995,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.367415,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;2.46653,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;1.01052,MA0056.1;0,MA0057.1;11.3064,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;1.09187,MA0063.1;0,MA0066.1;10.5966,MA0067.1;1.29359,MA0068.1;7.33233,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;16.2663,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;0.405093,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;1.37625,MA0089.1;0,MA0090.1;0.436918,MA0091.1;0.505453,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.347695,MA0103.1;0.332048,MA0105.1;2.29445,MA0106.1;0.648997,MA0107.1;0.274127,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;0.269076,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;1.65047,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.254954,MA0145.1;7.27104,MA0146.1;2.9475,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.193221,MA0035.2;0.564239,MA0039.2;4.63638,MA0138.2;0.704862,MA0002.2;0.213296,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;4.65133,MA0065.2;0.282161,MA0150.1;0.430951,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.335384,MA0155.1;6.12689,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;1.40717,MA0160.1;0.543522,MA0161.1;0,MA0162.1;1.13878,MA0163.1;5.04376,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;0.650405,MA0099.2;0.572,MA0079.2;58.2692,MA0102.2;1.51913,MA0258.1;3.62283,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:47, 22 January 2013


Full id: C1241_neuroblastoma_small_Skeletal_Dendritic_Pericytes_merkel_mesenchymal



Phase1 CAGE Peaks

Hg19::chr19:4279244..4279280,+p1@SHD
Hg19::chr19:4279282..4279293,+p11@SHD
Hg19::chr19:4279314..4279337,+p5@SHD
Hg19::chr19:4279360..4279365,+p16@SHD
Hg19::chr19:4279396..4279410,+p7@SHD
Hg19::chr19:4279450..4279459,+p8@SHD
Hg19::chr19:4279462..4279473,+p13@SHD


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>disease_data<br>

Cell Type
Ontology termp-valuen
plasmacytoid dendritic cell3.25e-153
cell of skeletal muscle8.73e-139
Uber Anatomy
Ontology termp-valuen
neural tube3.45e-1856
neural rod3.45e-1856
future spinal cord3.45e-1856
neural keel3.45e-1856
regional part of nervous system5.89e-1753
regional part of brain5.89e-1753
nervous system3.14e-1689
neocortex1.89e-1520
telencephalon2.08e-1534
brain5.32e-1468
future brain5.32e-1468
regional part of cerebral cortex5.70e-1422
cerebral hemisphere8.62e-1432
brain grey matter6.41e-1334
gray matter6.41e-1334
central nervous system7.89e-1381
regional part of forebrain1.95e-1241
forebrain1.95e-1241
anterior neural tube1.95e-1241
future forebrain1.95e-1241
cerebral cortex3.53e-1225
pallium3.53e-1225
regional part of telencephalon2.13e-1132
neural plate2.63e-1182
presumptive neural plate2.63e-1182
neurectoderm1.29e-1086
ecto-epithelium2.11e-09104
sympathetic nervous system2.59e-095
autonomic nervous system2.59e-095
parietal lobe2.38e-085
pre-chordal neural plate1.15e-0761
ectoderm-derived structure2.83e-07171
ectoderm2.83e-07171
presumptive ectoderm2.83e-07171
adult organism3.36e-07114
posterior neural tube3.64e-0715
chordal neural plate3.64e-0715
brainstem5.19e-076
gyrus5.66e-076
Disease
Ontology termp-valuen
neuroendocrine tumor7.98e-086


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)
MA0003.13.86995
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.367415
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.12.46653
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.11.01052
MA0056.10
MA0057.111.3064
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.09187
MA0063.10
MA0066.110.5966
MA0067.11.29359
MA0068.17.33233
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.116.2663
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.11.37625
MA0089.10
MA0090.10.436918
MA0091.10.505453
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.347695
MA0103.10.332048
MA0105.12.29445
MA0106.10.648997
MA0107.10.274127
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.65047
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.17.27104
MA0146.12.9475
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.24.63638
MA0138.20.704862
MA0002.20.213296
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.24.65133
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.335384
MA0155.16.12689
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.11.40717
MA0160.10.543522
MA0161.10
MA0162.11.13878
MA0163.15.04376
MA0164.10.678332
MA0080.20.344472
MA0018.20.650405
MA0099.20.572
MA0079.258.2692
MA0102.21.51913
MA0258.13.62283
MA0259.10.289405
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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