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Coexpression cluster:C1460: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.94918,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,1.92111,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,2.90447,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,0.939587,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.664116,0.390088,0.0393783,0.468392,1.59472,1.33909,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,1.82745,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,1.68655,0.84426,0.913168,0.477584,1.94676,0.86037,0.684313,1.37357,1.10535,0.0481066,0.398737,1.02636,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,2.06841,1.90697,0.548668,0.877269,0.647343,0.483695,2.62193,0.44815,0.978783,0.430775,1.38333,1.29401,0.352243,2.24955,0.529546,0.824029,0.312699,1.14892,1.81315,0.581628,2.79485,1.40534,1.96935,3.87911,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.175219,2.24213,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,3.15765,0.136746,1.06652,1.07915,0.258882,1.59875,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,4.07199,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.0360157,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,1.94918,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,1.92111,0.402028,0.436569,0.0880431,0.576478,0.387783,0.483957,2.90447,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.640661,0.939587,0.316592,0.35388,0.585658,0.329602,0.248856,0.355745,0.513952,0.664116,0.390088,0.0393783,0.468392,1.59472,1.33909,0.0909286,0.396429,0.745008,0.675919,0.149032,1.00488,1.15929,0.653901,1.82745,0.62023,1.04504,0.619193,0.968558,0.666252,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.624519,0.206105,1.68655,0.84426,0.913168,0.477584,1.94676,0.86037,0.684313,1.37357,1.10535,0.0481066,0.398737,1.02636,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.864356,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,2.06841,1.90697,0.548668,0.877269,0.647343,0.483695,2.62193,0.44815,0.978783,0.430775,1.38333,1.29401,0.352243,2.24955,0.529546,0.824029,0.312699,1.14892,1.81315,0.581628,2.79485,1.40534,1.96935,3.87911,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.175219,2.24213,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,3.15765,0.136746,1.06652,1.07915,0.258882,1.59875,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,4.07199,0.83286,0.683502,0.29379,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.176622,MA0004.1;0.558729,MA0006.1;0.391183,MA0007.1;0.539222,MA0009.1;1.03681,MA0014.1;0.0254709,MA0017.1;0.432438,MA0019.1;0.7124,MA0024.1;0.929647,MA0025.1;1.17262,MA0027.1;2.65688,MA0028.1;0.408079,MA0029.1;0.949428,MA0030.1;0.937696,MA0031.1;0.871496,MA0038.1;0.665566,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;1.45353,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;18.1594,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;0.457555,MA0060.1;0.267412,MA0061.1;0.23892,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;1.09642,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;0.00076337,MA0074.1;0.660398,MA0076.1;0.475586,MA0077.1;0.997832,MA0078.1;0.763954,MA0081.1;0.457725,MA0083.1;1.04447,MA0084.1;1.5477,MA0087.1;1.00322,MA0088.1;0.0971959,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;0.394379,MA0095.1;0,MA0098.1;0,MA0100.1;0.679972,MA0101.1;0.397846,MA0103.1;0.381434,MA0105.1;0.134725,MA0106.1;0.70837,MA0107.1;0.320267,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.314898,MA0115.1;1.28169,MA0116.1;3.26878,MA0117.1;1.07516,MA0119.1;0.440684,MA0122.1;1.10154,MA0124.1;1.23968,MA0125.1;1.15445,MA0130.1;0,MA0131.1;0.782708,MA0132.1;0,MA0133.1;0,MA0135.1;1.06778,MA0136.1;0.672893,MA0139.1;2.62599,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.107156,MA0146.1;0.0213085,MA0147.1;0.327615,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;5.77199,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;0.26661,MA0047.2;0.695777,MA0112.2;0.332548,MA0065.2;1.7308,MA0150.1;0.484557,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.819655,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.150673,MA0163.1;1.18186,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.000444266,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1460_neuroectodermal_amygdala_neuroblastoma_medial_frontal_non_occipital



Phase1 CAGE Peaks

Hg19::chr1:102462374..102462385,-p5@OLFM3
Hg19::chr1:102462460..102462469,-p10@OLFM3
Hg19::chr1:102462475..102462493,-p1@OLFM3
Hg19::chr1:102462503..102462522,-p3@OLFM3
Hg19::chr1:102462565..102462591,-p2@OLFM3
Hg19::chr2:166984486..166984506,-p2@ENST00000507401


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nervous system4.71e-8289
neural tube2.29e-8156
neural rod2.29e-8156
future spinal cord2.29e-8156
neural keel2.29e-8156
central nervous system1.73e-8081
regional part of nervous system1.15e-7553
regional part of brain1.15e-7553
brain1.08e-6668
future brain1.08e-6668
regional part of forebrain1.65e-6241
forebrain1.65e-6241
anterior neural tube1.65e-6241
future forebrain1.65e-6241
neurectoderm1.05e-6086
telencephalon1.07e-5634
brain grey matter1.18e-5634
gray matter1.18e-5634
neural plate1.51e-5382
presumptive neural plate1.51e-5382
cerebral hemisphere2.39e-5332
regional part of telencephalon1.11e-5232
ectoderm-derived structure4.17e-46171
ectoderm4.17e-46171
presumptive ectoderm4.17e-46171
regional part of cerebral cortex1.67e-4522
ecto-epithelium5.15e-43104
neocortex1.46e-4120
pre-chordal neural plate6.37e-4161
cerebral cortex1.98e-3925
pallium1.98e-3925
adult organism2.67e-38114
organ system subdivision3.13e-34223
structure with developmental contribution from neural crest1.99e-32132
posterior neural tube4.44e-1915
chordal neural plate4.44e-1915
basal ganglion9.25e-199
nuclear complex of neuraxis9.25e-199
aggregate regional part of brain9.25e-199
collection of basal ganglia9.25e-199
cerebral subcortex9.25e-199
neural nucleus1.65e-189
nucleus of brain1.65e-189
tube6.74e-17192
gyrus7.26e-156
telencephalic nucleus1.18e-147
segmental subdivision of hindbrain5.87e-1412
hindbrain5.87e-1412
presumptive hindbrain5.87e-1412
anatomical cluster7.62e-14373
brainstem4.74e-136
segmental subdivision of nervous system9.91e-1313
parietal lobe3.73e-125
occipital lobe4.57e-125
temporal lobe6.38e-126
limbic system8.75e-125
anatomical conduit7.15e-11240
corpus striatum8.78e-104
striatum8.78e-104
ventral part of telencephalon8.78e-104
future corpus striatum8.78e-104
organ part1.59e-09218
regional part of metencephalon4.70e-099
metencephalon4.70e-099
future metencephalon4.70e-099
frontal cortex1.95e-083
epithelium7.62e-08306
pons8.77e-083
caudate-putamen1.20e-073
dorsal striatum1.20e-073
cell layer1.21e-07309
diencephalon1.40e-077
future diencephalon1.40e-077
germ layer2.16e-07560
germ layer / neural crest2.16e-07560
embryonic tissue2.16e-07560
presumptive structure2.16e-07560
germ layer / neural crest derived structure2.16e-07560
epiblast (generic)2.16e-07560
embryo2.37e-07592
embryonic structure3.33e-07564
spinal cord5.17e-073
dorsal region element5.17e-073
dorsum5.17e-073
medulla oblongata6.12e-073
myelencephalon6.12e-073
future myelencephalon6.12e-073
sympathetic nervous system6.12e-075
autonomic nervous system6.12e-075
Disease
Ontology termp-valuen
neuroectodermal tumor4.54e-1310


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)
MA0003.10.176622
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.0254709
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.11.45353
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.118.1594
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.11.09642
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.0971959
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.10.134725
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.13.26878
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.12.62599
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.0213085
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.25.77199
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.332548
MA0065.21.7308
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.819655
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.150673
MA0163.11.18186
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.000444266
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
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
CTCF#1066465.360256373075034.21437267579784e-050.000755354158036126
NANOG#79923524.37064873417722.72082401016006e-071.39911442046828e-05
REST#597858.041690596773356.54774545315482e-050.00106202824566243



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1460&oldid=2569971"