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Coexpression cluster:C1540: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.12961,0.143275,0.436508,1.43205,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,1.36279,0.707204,0.223349,1.56773,0.391663,0.415981,0.889639,0.892779,0.236034,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,0.323162,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,1.43182,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,2.22199,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,2.06841,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,2.88157,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,1.66144,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,2.91904,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.0115686
|tfbs_overrepresentation_for_novel_motifs=1.12961,0.143275,0.436508,1.43205,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,1.36279,0.707204,0.223349,1.56773,0.391663,0.415981,0.889639,0.892779,0.236034,0.127969,0.436569,0.0880431,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.0334022,0.35388,0.585658,0.878269,0.248856,0.936389,0.513952,0.323162,0.390088,0.0393783,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,1.43182,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,2.22199,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.218784,0.206105,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.0481066,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,0.393853,0.32338,1.23175,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,2.06841,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,2.88157,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,1.66144,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,2.91904,2.17352,1.7705,1.27501,0.657956,0.983666,1.91065,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.79772,0.661335,0.0115686
|tfbs_overrepresentation_jaspar=MA0003.1;0.026277,MA0004.1;1.37419,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;2.02362,MA0038.1;0.665566,MA0040.1;2.19519,MA0041.1;1.41501,MA0042.1;0.544748,MA0043.1;1.03713,MA0046.1;1.02569,MA0048.1;0.152639,MA0050.1;1.34656,MA0051.1;0.661179,MA0052.1;0.959373,MA0055.1;0.465994,MA0056.1;0,MA0057.1;0.450439,MA0058.1;1.16137,MA0059.1;2.01959,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;1.09824,MA0089.1;0,MA0090.1;0.490736,MA0091.1;0.561458,MA0092.1;0.522012,MA0093.1;2.7063,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;6.4792,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;5.06785,MA0145.1;1.16614,MA0146.1;0.0213085,MA0147.1;2.3862,MA0148.1;0.584698,MA0149.1;0.612449,MA0062.2;0.23336,MA0035.2;0.621793,MA0039.2;0.00570825,MA0138.2;0.765223,MA0002.2;0.255126,MA0137.2;6.08217,MA0104.2;2.08061,MA0047.2;0.695777,MA0112.2;0.101413,MA0065.2;1.18263,MA0150.1;2.10974,MA0151.1;0,MA0152.1;0.629368,MA0153.1;1.13732,MA0154.1;0.413181,MA0155.1;0.0961854,MA0156.1;0.417278,MA0157.1;3.15651,MA0158.1;0,MA0159.1;2.38949,MA0160.1;0.600559,MA0161.1;0,MA0162.1;0.0383129,MA0163.1;0.0270301,MA0164.1;0.738243,MA0080.2;1.80563,MA0018.2;0.709805,MA0099.2;0.629739,MA0079.2;0.000444266,MA0102.2;1.58513,MA0258.1;0.289793,MA0259.1;0.893594,MA0442.1;0
}}
}}

Revision as of 20:00, 22 January 2013


Full id: C1540_gastric_pharyngeal_mucinous_smallcell_transitionalcell_rhabdomyosarcoma_somatostatinoma



Phase1 CAGE Peaks

Hg19::chr7:83277863..83277878,-p5@SEMA3E
Hg19::chr7:83277884..83277902,-p7@SEMA3E
Hg19::chr7:83278189..83278204,-p3@SEMA3E
Hg19::chr7:83278284..83278319,-p4@SEMA3E
Hg19::chr7:83278322..83278339,-p6@SEMA3E
Hg19::chr7:83278414..83278504,-p1@SEMA3E


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism5.34e-40114
neural plate2.71e-3082
presumptive neural plate2.71e-3082
neural tube3.52e-2956
neural rod3.52e-2956
future spinal cord3.52e-2956
neural keel3.52e-2956
regional part of nervous system3.80e-2853
regional part of brain3.80e-2853
neurectoderm7.91e-2886
central nervous system1.66e-2581
pre-chordal neural plate4.62e-2561
organ system subdivision1.70e-24223
ecto-epithelium3.79e-24104
regional part of forebrain6.03e-2441
forebrain6.03e-2441
anterior neural tube6.03e-2441
future forebrain6.03e-2441
brain9.08e-2468
future brain9.08e-2468
nervous system1.71e-2289
structure with developmental contribution from neural crest4.22e-21132
brain grey matter8.39e-2134
gray matter8.39e-2134
telencephalon1.64e-2034
cerebral hemisphere3.90e-1932
regional part of telencephalon4.84e-1932
ectoderm-derived structure4.93e-17171
ectoderm4.93e-17171
presumptive ectoderm4.93e-17171
anatomical cluster1.38e-15373
multi-tissue structure1.13e-14342
regional part of cerebral cortex1.83e-1422
cerebral cortex2.22e-1325
pallium2.22e-1325
neocortex7.49e-1320
organ4.92e-11503
neural nucleus2.60e-099
nucleus of brain2.60e-099
organ part3.40e-09218
anatomical conduit1.25e-08240
epithelium1.91e-08306
pigment epithelium of eye2.90e-0811
cell layer4.15e-08309
tube4.93e-08192
telencephalic nucleus1.70e-077
basal ganglion6.39e-079
nuclear complex of neuraxis6.39e-079
aggregate regional part of brain6.39e-079
collection of basal ganglia6.39e-079
cerebral subcortex6.39e-079
multi-cellular organism8.82e-07656


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)
MA0003.10.026277
MA0004.11.37419
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
MA0031.12.02362
MA0038.10.665566
MA0040.12.19519
MA0041.11.41501
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.450439
MA0058.11.16137
MA0059.12.01959
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
MA0088.11.09824
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.12.7063
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
MA0115.16.4792
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
MA0144.15.06785
MA0145.11.16614
MA0146.10.0213085
MA0147.12.3862
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.26.08217
MA0104.22.08061
MA0047.20.695777
MA0112.20.101413
MA0065.21.18263
MA0150.12.10974
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.13.15651
MA0158.10
MA0159.12.38949
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.0270301
MA0164.10.738243
MA0080.21.80563
MA0018.20.709805
MA0099.20.629739
MA0079.20.000444266
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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#1066443.573504248716680.01316635007238510.0466144762605454
FOXA1#316947.387613166256970.0008562625545346090.0064461331314813
USF1#739144.240999518138640.007005367750829420.0296100045541654
ZNF263#1012745.481227758007120.002675609380607230.0147484017575995



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:C1540&oldid=2570051"