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Coexpression cluster:C733: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.253158,0.306045,0.246925,0.975357,0.21227,0.371921,0.44126,0.384145,0.762093,0.0713737,0.344881,0.481459,0.0905352,0.430675,0.606477,0.230406,0.650562,0.168654,0.0986515,0.14663,0.246975,0.423587,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.24094,0.325512,0.685875,0.14393,0.0919867,0.184525,0.285028,0.182011,0.372963,0.492146,0.706689,0.540033,0.311187,0.471149,0.209923,0.00493315,0.273032,0.442265,0.335245,1.8813,0.214901,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.218374,0.40339,0.0681812,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,1.28337,0.0464399,0.906867,0.0876634,0.576459,0.071925,0.607953,0.672773,0.280653,0.333602,0.623044,1.16527,0.123028,0.856604,0.0372554,3.53066,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.456075,0.212875,1.49285,1.10159,0.743159,0.544807,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.712243,0.735091,0.242288,0.353283,1.04009,0.180771,0.0096263,0.324453,0.58906,0.901377,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,1.54623,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,1.7524,0.582016,0.395692,0.566218,1.75262,0.830443,0.146851,0.0413159,0.0216333,1.94121,0.113748,0.444001,1.22899,0.525224,0.582239,0.286011,0.261307,1.02032,0.813307,1.6118,0.264042,0.597299,0.459987,0.137885,0.440034,0.000550667
|tfbs_overrepresentation_for_novel_motifs=0.253158,0.306045,0.246925,0.975357,0.21227,0.371921,0.44126,0.384145,0.762093,0.0713737,0.344881,0.481459,0.0905352,0.430675,0.606477,0.230406,0.650562,0.168654,0.0986515,0.14663,0.246975,0.423587,0.36495,0.20812,0.779948,0.50266,0.267398,0.363006,0.214796,0.24094,0.325512,0.685875,0.14393,0.0919867,0.184525,0.285028,0.182011,0.372963,0.492146,0.706689,0.540033,0.311187,0.471149,0.209923,0.00493315,0.273032,0.442265,0.335245,1.8813,0.214901,0.515974,0.453148,0.179579,0.760015,0.908824,0.433372,0.218374,0.40339,0.0681812,0.402472,0.725346,0.444449,0.119615,0.624068,0.461047,0.591283,0.99547,1.35949,0.675894,1.19869,0.299692,1.28337,0.0464399,0.906867,0.0876634,0.576459,0.071925,0.607953,0.672773,0.280653,0.333602,0.623044,1.16527,0.123028,0.856604,0.0372554,3.53066,0.0654897,0.540459,1.45821,1.08742,0.830286,0.702047,0.456075,0.212875,1.49285,1.10159,0.743159,0.544807,0.792069,0.164861,0.696605,0.737766,0.654073,0.580349,0.340854,0.638916,0.427507,0.285742,0.199366,0.712243,0.735091,0.242288,0.353283,1.04009,0.180771,0.0096263,0.324453,0.58906,0.901377,0.898765,0.538171,0.966635,0.471181,1.14929,0.608677,0.435413,0.706859,0.940494,0.159968,0.830959,0.328039,0.954592,0.468088,1.10012,1.26269,1.54623,0.363513,1.05827,1.9115,1.51034,1.02151,0.437004,1.7524,0.582016,0.395692,0.566218,1.75262,0.830443,0.146851,0.0413159,0.0216333,1.94121,0.113748,0.444001,1.22899,0.525224,0.582239,0.286011,0.261307,1.02032,0.813307,1.6118,0.264042,0.597299,0.459987,0.137885,0.440034,0.000550667
|tfbs_overrepresentation_jaspar=MA0003.1;0.000970254,MA0004.1;0.349539,MA0006.1;0.210781,MA0007.1;0.332734,MA0009.1;0.79061,MA0014.1;0.0144431,MA0017.1;0.682686,MA0019.1;0.486183,MA0024.1;0.688373,MA0025.1;0.921763,MA0027.1;2.39404,MA0028.1;0.224112,MA0029.1;0.707146,MA0030.1;0.696006,MA0031.1;0.633489,MA0038.1;0.443833,MA0040.1;0.712837,MA0041.1;0.366339,MA0042.1;0.337481,MA0043.1;0.790919,MA0046.1;0.779945,MA0048.1;0.0494179,MA0050.1;0.338274,MA0051.1;0.439895,MA0052.1;0.716602,MA0055.1;0.00989454,MA0056.1;0,MA0057.1;0.176435,MA0058.1;0.732537,MA0059.1;0.2641,MA0060.1;0.119532,MA0061.1;0.100525,MA0063.1;0,MA0066.1;0.444231,MA0067.1;1.1037,MA0068.1;0.943943,MA0069.1;0.776171,MA0070.1;0.765217,MA0071.1;0.40788,MA0072.1;0.760818,MA0073.1;1.08342,MA0074.1;0.439193,MA0076.1;0.278993,MA0077.1;0.753278,MA0078.1;0.533387,MA0081.1;0.26424,MA0083.1;0.79797,MA0084.1;1.28962,MA0087.1;0.758426,MA0088.1;0.248289,MA0089.1;0,MA0090.1;0.291627,MA0091.1;0.351901,MA0092.1;0.852371,MA0093.1;0.61153,MA0095.1;0,MA0098.1;0,MA0100.1;0.456802,MA0101.1;0.216017,MA0103.1;0.587485,MA0105.1;0.0403209,MA0106.1;0.482519,MA0107.1;0.156959,MA0108.2;0.630531,MA0109.1;0,MA0111.1;0.303543,MA0113.1;0.498009,MA0114.1;0.908082,MA0115.1;1.02805,MA0116.1;0.159642,MA0117.1;0.827487,MA0119.1;0.250314,MA0122.1;0.852927,MA0124.1;0.98702,MA0125.1;0.904129,MA0130.1;0,MA0131.1;0.550695,MA0132.1;0,MA0133.1;0,MA0135.1;0.820382,MA0136.1;0.450422,MA0139.1;0.0922451,MA0140.1;1.84316,MA0141.1;0.2626,MA0142.1;1.46715,MA0143.1;0.498176,MA0144.1;0.438224,MA0145.1;0.02761,MA0146.1;0.00165539,MA0147.1;0.162359,MA0148.1;0.372124,MA0149.1;0.396509,MA0062.2;0.0969238,MA0035.2;1.04409,MA0039.2;0.00136845,MA0138.2;0.534556,MA0002.2;0.358551,MA0137.2;0.229531,MA0104.2;0.118985,MA0047.2;0.47109,MA0112.2;0.260758,MA0065.2;0.839576,MA0150.1;0.286461,MA0151.1;0,MA0152.1;0.411494,MA0153.1;0.887528,MA0154.1;0.0391503,MA0155.1;0.0230394,MA0156.1;0.231442,MA0157.1;0.576556,MA0158.1;0,MA0159.1;1.51416,MA0160.1;0.386031,MA0161.1;0,MA0162.1;0.00470038,MA0163.1;0.122012,MA0164.1;0.509774,MA0080.2;0.611699,MA0018.2;0.483823,MA0099.2;0.411824,MA0079.2;0.311083,MA0102.2;1.32663,MA0258.1;0.420151,MA0259.1;0.168926,MA0442.1;0
}}
}}

Revision as of 19:24, 22 January 2013


Full id: C733_pineal_neuroectodermal_anaplastic_epithelioid_papillary_parietal_middle



Phase1 CAGE Peaks

Hg19::chr11:126565298..126565302,-p@chr11:126565298..126565302
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Hg19::chr11:126605112..126605121,-p@chr11:126605112..126605121
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Hg19::chr11:126669389..126669406,-p@chr11:126669389..126669406
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Hg19::chr11:126724227..126724237,-p@chr11:126724227..126724237
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Hg19::chr11:126792092..126792107,-p@chr11:126792092..126792107
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Hg19::chr11:126792108..126792125,-p@chr11:126792108..126792125
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Hg19::chr11:126794867..126794870,-p@chr11:126794867..126794870
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Hg19::chr11:126794895..126794906,-p@chr11:126794895..126794906
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Hg19::chr11:126798945..126798948,-p@chr11:126798945..126798948
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Hg19::chr11:126824157..126824162,-p@chr11:126824157..126824162
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Hg19::chr11:126842992..126842996,-p@chr11:126842992..126842996
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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
skin fibroblast2.29e-1123
Uber Anatomy
Ontology termp-valuen
neural tube1.71e-6856
neural rod1.71e-6856
future spinal cord1.71e-6856
neural keel1.71e-6856
regional part of nervous system1.12e-6253
regional part of brain1.12e-6253
regional part of forebrain9.87e-5641
forebrain9.87e-5641
anterior neural tube9.87e-5641
future forebrain9.87e-5641
brain3.99e-5368
future brain3.99e-5368
central nervous system3.49e-5281
brain grey matter3.72e-5234
gray matter3.72e-5234
telencephalon9.89e-5234
nervous system2.23e-5089
neurectoderm1.11e-4986
regional part of telencephalon7.46e-4832
neural plate1.01e-4782
presumptive neural plate1.01e-4782
cerebral hemisphere1.23e-4732
pre-chordal neural plate2.57e-3961
regional part of cerebral cortex6.28e-3822
ecto-epithelium1.10e-36104
neocortex1.81e-3320
cerebral cortex7.46e-3325
pallium7.46e-3325
structure with developmental contribution from neural crest2.26e-29132
adult organism5.73e-26114
ectoderm-derived structure1.35e-23171
ectoderm1.35e-23171
presumptive ectoderm1.35e-23171
basal ganglion1.15e-219
nuclear complex of neuraxis1.15e-219
aggregate regional part of brain1.15e-219
collection of basal ganglia1.15e-219
cerebral subcortex1.15e-219
neural nucleus1.94e-219
nucleus of brain1.94e-219
telencephalic nucleus3.89e-177
organ system subdivision1.34e-16223
tube4.72e-14192
posterior neural tube9.60e-1415
chordal neural plate9.60e-1415
limbic system7.71e-135
parietal lobe1.92e-125
temporal lobe1.92e-126
corpus striatum9.34e-114
striatum9.34e-114
ventral part of telencephalon9.34e-114
future corpus striatum9.34e-114
segmental subdivision of nervous system1.01e-1013
brainstem1.08e-096
gyrus1.26e-096
anatomical conduit5.89e-09240
segmental subdivision of hindbrain7.33e-0912
hindbrain7.33e-0912
presumptive hindbrain7.33e-0912
caudate-putamen1.14e-083
dorsal striatum1.14e-083
pons6.85e-083
occipital lobe8.12e-085
epithelium1.10e-07306
organ part1.34e-07218
cell layer1.70e-07309
spinal cord2.13e-073
dorsal region element2.13e-073
dorsum2.13e-073
organ6.97e-07503
regional part of diencephalon9.56e-074
Disease
Ontology termp-valuen
musculoskeletal system disease4.19e-115
myotonic disease4.19e-115
muscle tissue disease4.19e-115
myopathy4.19e-115
muscular disease4.19e-115
myotonic dystrophy4.19e-115


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)
MA0003.10.000970254
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.0144431
MA0017.10.682686
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.224112
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.0494179
MA0050.10.338274
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.10.176435
MA0058.10.732537
MA0059.10.2641
MA0060.10.119532
MA0061.10.100525
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.943943
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.11.08342
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.26424
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.248289
MA0089.10
MA0090.10.291627
MA0091.10.351901
MA0092.10.852371
MA0093.10.61153
MA0095.10
MA0098.10
MA0100.10.456802
MA0101.10.216017
MA0103.10.587485
MA0105.10.0403209
MA0106.10.482519
MA0107.10.156959
MA0108.20.630531
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.908082
MA0115.11.02805
MA0116.10.159642
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.10.450422
MA0139.10.0922451
MA0140.11.84316
MA0141.10.2626
MA0142.11.46715
MA0143.10.498176
MA0144.10.438224
MA0145.10.02761
MA0146.10.00165539
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.21.04409
MA0039.20.00136845
MA0138.20.534556
MA0002.20.358551
MA0137.20.229531
MA0104.20.118985
MA0047.20.47109
MA0112.20.260758
MA0065.20.839576
MA0150.10.286461
MA0151.10
MA0152.10.411494
MA0153.10.887528
MA0154.10.0391503
MA0155.10.0230394
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.11.51416
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.122012
MA0164.10.509774
MA0080.20.611699
MA0018.20.483823
MA0099.20.411824
MA0079.20.311083
MA0102.21.32663
MA0258.10.420151
MA0259.10.168926
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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