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Coexpression cluster:C340: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.143948,0.0233656,0.321347,0.0875053,0.101662,0.292862,0.124514,0.0305595,0.0883366,0.00339967,0.0735689,0.148731,0.00249308,0.377328,1.10261,0.842971,1.34778,0.167515,0.0190937,2.9528,0.0341522,0.0740958,0.0832693,0.241549,0.407145,0.162121,0.0920886,0.0823079,0.254829,0.601202,0.0647008,0.292383,0.00877736,0.124205,0.0166732,1.13649,0.191651,0.613203,0.538548,2.46866,0.378503,0.212479,1.63094,1.95289,0.000230864,0.0432796,0.394651,2.44217,1.23913,0.770831,0.509118,1.91744,0.0369143,0.925826,0.475837,0.119953,0.262028,0.103222,0.411545,0.336051,0.32323,0.126376,0.0297555,0.68786,0.423138,0.222166,0.551996,0.889382,0.284717,0.737624,0.0536708,1.50888,0.0029804,0.474142,0.00227848,0.324522,0.00130349,0.234122,0.282332,0.395197,0.0649382,0.245107,0.136039,0.093723,0.431067,1.68665e-05,0.286473,0.0262235,3.11647,0.984017,0.634935,0.408872,3.14861,2.22414,0.0238196,0.151139,0.137698,0.337414,1.05847,0.0192233,0.543149,0.300686,0.333104,0.739294,0.214431,0.250761,0.256823,0.116603,0.0481039,0.0202481,0.0373322,0.881325,0.0326221,0.565106,0.592003,0.0731252,0.0100728,0.0642305,1.8385,0.741282,0.467142,0.185428,0.0855095,0.14239,0.691757,0.234645,0.121127,0.30868,0.503421,0.307146,0.409436,0.0658293,0.515797,1.99086,0.646547,0.000840633,0.223949,0.0825583,0.608436,1.42699,1.03434,0.575287,2.48489,0.334687,0.61701,2.23216,1.75116,1.27059,0.0572348,0.0092535,0.028005,0.000391854,0.409747,0.323402,0.126114,0.765951,0.176807,0.0909941,0.0482085,0.039044,1.40688,0.394694,0.770374,0.0400133,0.226459,0.135598,0.946231,0.123801,0.00150999
|tfbs_overrepresentation_for_novel_motifs=0.143948,0.0233656,0.321347,0.0875053,0.101662,0.292862,0.124514,0.0305595,0.0883366,0.00339967,0.0735689,0.148731,0.00249308,0.377328,1.10261,0.842971,1.34778,0.167515,0.0190937,2.9528,0.0341522,0.0740958,0.0832693,0.241549,0.407145,0.162121,0.0920886,0.0823079,0.254829,0.601202,0.0647008,0.292383,0.00877736,0.124205,0.0166732,1.13649,0.191651,0.613203,0.538548,2.46866,0.378503,0.212479,1.63094,1.95289,0.000230864,0.0432796,0.394651,2.44217,1.23913,0.770831,0.509118,1.91744,0.0369143,0.925826,0.475837,0.119953,0.262028,0.103222,0.411545,0.336051,0.32323,0.126376,0.0297555,0.68786,0.423138,0.222166,0.551996,0.889382,0.284717,0.737624,0.0536708,1.50888,0.0029804,0.474142,0.00227848,0.324522,0.00130349,0.234122,0.282332,0.395197,0.0649382,0.245107,0.136039,0.093723,0.431067,1.68665e-05,0.286473,0.0262235,3.11647,0.984017,0.634935,0.408872,3.14861,2.22414,0.0238196,0.151139,0.137698,0.337414,1.05847,0.0192233,0.543149,0.300686,0.333104,0.739294,0.214431,0.250761,0.256823,0.116603,0.0481039,0.0202481,0.0373322,0.881325,0.0326221,0.565106,0.592003,0.0731252,0.0100728,0.0642305,1.8385,0.741282,0.467142,0.185428,0.0855095,0.14239,0.691757,0.234645,0.121127,0.30868,0.503421,0.307146,0.409436,0.0658293,0.515797,1.99086,0.646547,0.000840633,0.223949,0.0825583,0.608436,1.42699,1.03434,0.575287,2.48489,0.334687,0.61701,2.23216,1.75116,1.27059,0.0572348,0.0092535,0.028005,0.000391854,0.409747,0.323402,0.126114,0.765951,0.176807,0.0909941,0.0482085,0.039044,1.40688,0.394694,0.770374,0.0400133,0.226459,0.135598,0.946231,0.123801,0.00150999
|tfbs_overrepresentation_jaspar=MA0003.1;3.23213e-07,MA0004.1;0.0757747,MA0006.1;0.246818,MA0007.1;0.0679494,MA0009.1;0.375925,MA0014.1;6.64619e-07,MA0017.1;0.0330569,MA0019.1;2.78537,MA0024.1;2.22122,MA0025.1;0.487069,MA0027.1;1.90579,MA0028.1;0.027018,MA0029.1;0.308904,MA0030.1;0.300221,MA0031.1;0.252799,MA0038.1;0.792032,MA0040.1;0.313366,MA0041.1;0.0839596,MA0042.1;0.070122,MA0043.1;0.376179,MA0046.1;0.367181,MA0048.1;0.0398014,MA0050.1;0.0704881,MA0051.1;0.12372,MA0052.1;0.316327,MA0055.1;1.27577,MA0056.1;0,MA0057.1;0.985115,MA0058.1;0.0404315,MA0059.1;0.0400338,MA0060.1;0.088709,MA0061.1;0.658355,MA0063.1;0,MA0066.1;0.126249,MA0067.1;0.649823,MA0068.1;0.00151483,MA0069.1;0.364099,MA0070.1;0.355189,MA0071.1;0.7003,MA0072.1;0.351626,MA0073.1;8.05477,MA0074.1;0.123313,MA0076.1;1.51726,MA0077.1;0.345539,MA0078.1;0.182227,MA0081.1;0.358793,MA0083.1;0.381987,MA0084.1;0.823032,MA0087.1;0.922978,MA0088.1;0.00048777,MA0089.1;0,MA0090.1;0.0504181,MA0091.1;0.076904,MA0092.1;0.0614105,MA0093.1;0.0239335,MA0095.1;0,MA0098.1;0,MA0100.1;9.7516,MA0101.1;0.482318,MA0103.1;0.440826,MA0105.1;0.863849,MA0106.1;0.14939,MA0107.1;0.508128,MA0108.2;0.250614,MA0109.1;0,MA0111.1;0.202948,MA0113.1;0.159148,MA0114.1;0.0103097,MA0115.1;0.581155,MA0116.1;0.519984,MA0117.1;0.406527,MA0119.1;0.140833,MA0122.1;0.42795,MA0124.1;0.544476,MA0125.1;0.471774,MA0130.1;0,MA0131.1;0.193896,MA0132.1;0,MA0133.1;0,MA0135.1;1.03495,MA0136.1;0.129893,MA0139.1;0.00262644,MA0140.1;0.104326,MA0141.1;0.355203,MA0142.1;0.230443,MA0143.1;0.934001,MA0144.1;2.13031,MA0145.1;0.00369633,MA0146.1;0.000772138,MA0147.1;0.0120199,MA0148.1;1.02524,MA0149.1;0.0995233,MA0062.2;0.0183194,MA0035.2;0.103973,MA0039.2;0.000784269,MA0138.2;0.183007,MA0002.2;0.0252114,MA0137.2;0.0286334,MA0104.2;0.00528131,MA0047.2;0.142334,MA0112.2;5.97705e-05,MA0065.2;8.82601e-05,MA0150.1;0.0483839,MA0151.1;0,MA0152.1;0.349115,MA0153.1;0.457467,MA0154.1;0.000222686,MA0155.1;0.0222112,MA0156.1;0.0292146,MA0157.1;0.607927,MA0158.1;0,MA0159.1;2.40093,MA0160.1;0.645549,MA0161.1;0,MA0162.1;0.000781013,MA0163.1;7.66935e-06,MA0164.1;0.166704,MA0080.2;0.0239532,MA0018.2;0.150204,MA0099.2;1.17065,MA0079.2;0.194472,MA0102.2;0.858102,MA0258.1;0.0390558,MA0259.1;0.846411,MA0442.1;0
}}
}}

Revision as of 19:05, 22 January 2013


Full id: C340_hepatocellular_skeletal_breast_putamen_mucinous_pituitary_hepatoblastoma



Phase1 CAGE Peaks

Hg19::chr7:94285674..94285689,+p1@PEG10
Hg19::chr7:94292678..94292708,-p@chr7:94292678..94292708
-
Hg19::chr7:94292685..94292712,+p3@PEG10
Hg19::chr7:94292726..94292754,-p@chr7:94292726..94292754
-
Hg19::chr7:94292734..94292850,+p2@PEG10
Hg19::chr7:94292773..94292786,-p@chr7:94292773..94292786
-
Hg19::chr7:94292829..94292871,-p@chr7:94292829..94292871
-
Hg19::chr7:94293053..94293080,+p1@CU690760
Hg19::chr7:94293245..94293269,+p2@CU690760
Hg19::chr7:94293817..94293830,+p14@PEG10
Hg19::chr7:94293846..94293857,+p27@PEG10
Hg19::chr7:94293862..94293872,+p24@PEG10
Hg19::chr7:94293938..94293949,+p18@PEG10
Hg19::chr7:94294066..94294084,+p13@PEG10
Hg19::chr7:94294134..94294144,+p22@PEG10
Hg19::chr7:94294191..94294215,+p8@PEG10
Hg19::chr7:94294239..94294250,+p25@PEG10
Hg19::chr7:94294286..94294316,+p6@PEG10
Hg19::chr7:94294313..94294347,-p1@CU690761
Hg19::chr7:94294329..94294346,+p16@PEG10
Hg19::chr7:94294370..94294381,-p@chr7:94294370..94294381
-
Hg19::chr7:94294382..94294404,+p11@PEG10
Hg19::chr7:94294389..94294434,-p@chr7:94294389..94294434
-
Hg19::chr7:94294417..94294461,+p1@AB384093
Hg19::chr7:94294477..94294489,+p@chr7:94294477..94294489
+
Hg19::chr7:94294495..94294511,+p@chr7:94294495..94294511
+
Hg19::chr7:94294567..94294582,+p9@PEG10
Hg19::chr7:94294623..94294645,+p4@PEG10
Hg19::chr7:94294932..94294973,-p@chr7:94294932..94294973
-
Hg19::chr7:94294939..94294976,+p7@PEG10
Hg19::chr7:94295525..94295551,+p15@PEG10
Hg19::chr7:94297514..94297599,+p5@PEG10
Hg19::chr7:94298287..94298339,+p@chr7:94298287..94298339
+
Hg19::chr7:94298512..94298534,+p@chr7:94298512..94298534
+


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
organ system subdivision1.32e-23223
neural tube7.60e-2356
neural rod7.60e-2356
future spinal cord7.60e-2356
neural keel7.60e-2356
central nervous system1.46e-2281
regional part of nervous system2.93e-2253
regional part of brain2.93e-2253
nervous system3.59e-2189
brain1.44e-1968
future brain1.44e-1968
neurectoderm6.03e-1786
brain grey matter7.79e-1634
gray matter7.79e-1634
regional part of forebrain1.17e-1541
forebrain1.17e-1541
anterior neural tube1.17e-1541
future forebrain1.17e-1541
telencephalon4.30e-1534
neural plate1.35e-1482
presumptive neural plate1.35e-1482
regional part of telencephalon1.49e-1432
cerebral hemisphere2.78e-1432
multi-tissue structure1.97e-13342
organ part9.20e-13218
ectoderm-derived structure2.82e-12171
ectoderm2.82e-12171
presumptive ectoderm2.82e-12171
cerebral cortex2.24e-1125
pallium2.24e-1125
ecto-epithelium3.15e-11104
anatomical cluster3.62e-11373
pre-chordal neural plate7.22e-1161
regional part of cerebral cortex2.37e-1022
structure with developmental contribution from neural crest3.46e-10132
neocortex4.47e-0920
cell layer1.18e-08309
posterior neural tube1.58e-0815
chordal neural plate1.58e-0815
epithelium1.90e-08306
segmental subdivision of hindbrain3.88e-0812
hindbrain3.88e-0812
presumptive hindbrain3.88e-0812
respiratory primordium1.93e-0738
endoderm of foregut1.93e-0738
larynx2.73e-079
segmental subdivision of nervous system3.13e-0713
embryo4.07e-07592
Disease
Ontology termp-valuen
cell type cancer8.18e-14143
carcinoma2.29e-10106


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)
MA0003.13.23213e-07
MA0004.10.0757747
MA0006.10.246818
MA0007.10.0679494
MA0009.10.375925
MA0014.16.64619e-07
MA0017.10.0330569
MA0019.12.78537
MA0024.12.22122
MA0025.10.487069
MA0027.11.90579
MA0028.10.027018
MA0029.10.308904
MA0030.10.300221
MA0031.10.252799
MA0038.10.792032
MA0040.10.313366
MA0041.10.0839596
MA0042.10.070122
MA0043.10.376179
MA0046.10.367181
MA0048.10.0398014
MA0050.10.0704881
MA0051.10.12372
MA0052.10.316327
MA0055.11.27577
MA0056.10
MA0057.10.985115
MA0058.10.0404315
MA0059.10.0400338
MA0060.10.088709
MA0061.10.658355
MA0063.10
MA0066.10.126249
MA0067.10.649823
MA0068.10.00151483
MA0069.10.364099
MA0070.10.355189
MA0071.10.7003
MA0072.10.351626
MA0073.18.05477
MA0074.10.123313
MA0076.11.51726
MA0077.10.345539
MA0078.10.182227
MA0081.10.358793
MA0083.10.381987
MA0084.10.823032
MA0087.10.922978
MA0088.10.00048777
MA0089.10
MA0090.10.0504181
MA0091.10.076904
MA0092.10.0614105
MA0093.10.0239335
MA0095.10
MA0098.10
MA0100.19.7516
MA0101.10.482318
MA0103.10.440826
MA0105.10.863849
MA0106.10.14939
MA0107.10.508128
MA0108.20.250614
MA0109.10
MA0111.10.202948
MA0113.10.159148
MA0114.10.0103097
MA0115.10.581155
MA0116.10.519984
MA0117.10.406527
MA0119.10.140833
MA0122.10.42795
MA0124.10.544476
MA0125.10.471774
MA0130.10
MA0131.10.193896
MA0132.10
MA0133.10
MA0135.11.03495
MA0136.10.129893
MA0139.10.00262644
MA0140.10.104326
MA0141.10.355203
MA0142.10.230443
MA0143.10.934001
MA0144.12.13031
MA0145.10.00369633
MA0146.10.000772138
MA0147.10.0120199
MA0148.11.02524
MA0149.10.0995233
MA0062.20.0183194
MA0035.20.103973
MA0039.20.000784269
MA0138.20.183007
MA0002.20.0252114
MA0137.20.0286334
MA0104.20.00528131
MA0047.20.142334
MA0112.25.97705e-05
MA0065.28.82601e-05
MA0150.10.0483839
MA0151.10
MA0152.10.349115
MA0153.10.457467
MA0154.10.000222686
MA0155.10.0222112
MA0156.10.0292146
MA0157.10.607927
MA0158.10
MA0159.12.40093
MA0160.10.645549
MA0161.10
MA0162.10.000781013
MA0163.17.66935e-06
MA0164.10.166704
MA0080.20.0239532
MA0018.20.150204
MA0099.21.17065
MA0079.20.194472
MA0102.20.858102
MA0258.10.0390558
MA0259.10.846411
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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C340&oldid=2568851"