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Coexpression cluster:C1472: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,2.90668,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,2.54809,1.36279,0.707204,0.223349,1.56773,0.391663,0.415981,0.889639,0.336106,1.92111,0.127969,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,1.10781,1.40695,0.396295,0.186644,0.530785,0.92701,0.302275,1.19786,0.939587,0.0334022,0.93226,0.585658,0.329602,0.248856,0.355745,0.513952,3.5838,0.390088,0.992846,1.18176,0.66382,0.542147,0.630853,0.396429,0.745008,0.675919,1.43182,1.00488,1.15929,0.653901,0.400834,2.55301,1.04504,0.619193,0.968558,2.7005,0.267534,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,1.25018,0.275507,0.146905,1.15727,0.624519,1.12235,0.192925,0.84426,0.913168,0.477584,1.25579,0.86037,0.684313,0.272514,1.10535,16.2549,0.126687,0.181871,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,0.234532,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,1.35291,0.877269,0.647343,0.483695,2.62193,0.44815,0.978783,0.430775,2.36793,1.29401,0.352243,2.24955,0.529546,1.9262,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,2.24213,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,1.48535,0.799467,2.01411,0.510514,0.306342,0.136746,0.639143,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,2.00817,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,6.49853
|tfbs_overrepresentation_jaspar=MA0003.1;8.45809,MA0004.1;0.558729,MA0006.1;1.79433,MA0007.1;1.33289,MA0009.1;1.03681,MA0014.1;13.0869,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;1.59836,MA0040.1;0.955415,MA0041.1;0.578072,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;0.545671,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.0586456,MA0056.1;0,MA0057.1;0.147053,MA0058.1;0.458909,MA0059.1;2.01959,MA0060.1;0.267412,MA0061.1;2.71441,MA0063.1;0,MA0066.1;0.66601,MA0067.1;1.35893,MA0068.1;0.578694,MA0069.1;1.02175,MA0070.1;1.01032,MA0071.1;0.625297,MA0072.1;1.00572,MA0073.1;20.1331,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;1.61871,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;3.72097,MA0103.1;0.381434,MA0105.1;3.35204,MA0106.1;0.70837,MA0107.1;6.34858,MA0108.2;0.868347,MA0109.1;0,MA0111.1;0.504913,MA0113.1;0.725375,MA0114.1;0.845337,MA0115.1;1.28169,MA0116.1;0.323925,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;0.226048,MA0140.1;0.622527,MA0141.1;0.455728,MA0142.1;0.838805,MA0143.1;0.725558,MA0144.1;0.299851,MA0145.1;0.707171,MA0146.1;1.8938,MA0147.1;3.2919,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;19.5364,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;0.414885,MA0104.2;3.79531,MA0047.2;0.695777,MA0112.2;1.65732,MA0065.2;0.718489,MA0150.1;3.12199,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.132326,MA0155.1;8.67446,MA0156.1;0.417278,MA0157.1;0.810597,MA0158.1;0,MA0159.1;0.328286,MA0160.1;0.600559,MA0161.1;0,MA0162.1;12.4774,MA0163.1;10.5765,MA0164.1;0.738243,MA0080.2;0.394469,MA0018.2;2.83905,MA0099.2;0.629739,MA0079.2;30.6205,MA0102.2;1.58513,MA0258.1;1.43672,MA0259.1;0.336472,MA0442.1;0
}}
}}

Revision as of 19:57, 22 January 2013


Full id: C1472_nonsmall_neuroblastoma_small_tubular_carcinoid_smallcell_merkel



Phase1 CAGE Peaks

Hg19::chr1:235813008..235813019,-p8@GNG4
Hg19::chr1:235813034..235813097,-p1@GNG4
Hg19::chr1:235813117..235813120,-p11@GNG4
Hg19::chr1:235813272..235813285,-p6@GNG4
Hg19::chr1:235813290..235813323,-p2@GNG4
Hg19::chr1:235813325..235813360,-p3@GNG4


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
neural cell3.78e-1325
neuronal stem cell9.50e-098
neuron3.70e-076
neuroblast3.70e-076
electrically signaling cell3.70e-076
neurectodermal cell5.41e-0759
neuron associated cell6.64e-0717
neuron associated cell (sensu Vertebrata)6.64e-0717
Uber Anatomy
Ontology termp-valuen
nervous system1.32e-3789
central nervous system1.65e-3681
neural tube6.38e-2756
neural rod6.38e-2756
future spinal cord6.38e-2756
neural keel6.38e-2756
organ system subdivision6.61e-27223
brain7.53e-2768
future brain7.53e-2768
regional part of nervous system3.63e-2553
regional part of brain3.63e-2553
ectoderm-derived structure3.49e-20171
ectoderm3.49e-20171
presumptive ectoderm3.49e-20171
neurectoderm1.06e-1986
regional part of forebrain1.81e-1841
forebrain1.81e-1841
anterior neural tube1.81e-1841
future forebrain1.81e-1841
neural plate1.67e-1782
presumptive neural plate1.67e-1782
brain grey matter2.19e-1734
gray matter2.19e-1734
telencephalon2.67e-1734
cerebral hemisphere2.47e-1632
regional part of telencephalon4.88e-1632
ecto-epithelium1.25e-13104
cerebral cortex6.33e-1325
pallium6.33e-1325
pre-chordal neural plate3.33e-1261
neocortex1.15e-1120
regional part of cerebral cortex2.12e-1122
posterior neural tube1.01e-0915
chordal neural plate1.01e-0915
adult organism1.62e-09114
organ part6.76e-09218
structure with developmental contribution from neural crest2.18e-08132
segmental subdivision of hindbrain4.74e-0812
hindbrain4.74e-0812
presumptive hindbrain4.74e-0812
segmental subdivision of nervous system3.66e-0713
anatomical cluster8.34e-07373
Disease
Ontology termp-valuen
cell type cancer1.90e-18143
cancer8.51e-17235
disease of cellular proliferation9.52e-16239
germ cell and embryonal cancer1.91e-1122
germ cell cancer1.91e-1122
carcinoma1.44e-09106
neuroectodermal tumor3.86e-0910
gastrointestinal system cancer2.72e-0714


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)
MA0003.18.45809
MA0004.10.558729
MA0006.11.79433
MA0007.11.33289
MA0009.11.03681
MA0014.113.0869
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
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.12.01959
MA0060.10.267412
MA0061.12.71441
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.120.1331
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.11.61871
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.13.72097
MA0103.10.381434
MA0105.13.35204
MA0106.10.70837
MA0107.16.34858
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
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
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.11.8938
MA0147.13.2919
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.219.5364
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.23.79531
MA0047.20.695777
MA0112.21.65732
MA0065.20.718489
MA0150.13.12199
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.18.67446
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.112.4774
MA0163.110.5765
MA0164.10.738243
MA0080.20.394469
MA0018.22.83905
MA0099.20.629739
MA0079.230.6205
MA0102.21.58513
MA0258.11.43672
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
HEY1#2346264.040111043105710.0002298968555807510.00253245413985846
POLR2A#543062.147453176558070.01019570676818780.0380432089733036
SIN3A#2594265.408884726815143.99207083571449e-050.000743054510802327
TAF1#687263.343046285745290.0007162474284635620.00573343796898183



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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