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MCL coexpression mm9:317: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0043283;biopolymer metabolic process;0.045164440216554;77805,19877,16451,68592,20585,72102,67345,78610,66660,30843,18193,269254!GO:0006259;DNA metabolic process;0.045164440216554;78610,77805,18193,20585,269254!GO:0006281;DNA repair;0.045164440216554;78610,77805,269254!GO:0030331;estrogen receptor binding;0.045164440216554;18193!GO:0046966;thyroid hormone receptor binding;0.045164440216554;18193!GO:0046975;histone lysine N-methyltransferase activity (H3-K36 specific);0.045164440216554;18193!GO:0019992;diacylglycerol binding;0.045164440216554;19877,13139!}}
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metabolic process;0.045164440216554;77805,19877,16451,68592,20585,72102,67345,78610,66660,30843,18193,269254!GO:0006259;DNA metabolic process;0.045164440216554;78610,77805,18193,20585,269254!GO:0006281;DNA repair;0.045164440216554;78610,77805,269254!GO:0030331;estrogen receptor binding;0.045164440216554;18193!GO:0046966;thyroid hormone receptor binding;0.045164440216554;18193!GO:0046975;histone lysine N-methyltransferase activity (H3-K36 specific);0.045164440216554;18193!GO:0019992;diacylglycerol binding;0.045164440216554;19877,13139!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004119!9.14e-13!118;UBERON:0000925!9.14e-13!118;UBERON:0006595!9.14e-13!118;UBERON:0001007!1.25e-12!116;UBERON:0001555!1.25e-12!116;UBERON:0007026!1.25e-12!116;UBERON:0004921!2.75e-12!114;UBERON:0000077!5.45e-11!35;UBERON:0004177!1.10e-09!29;UBERON:0005057!1.10e-09!29;UBERON:0001004!3.91e-09!42;UBERON:0005911!5.09e-09!69;UBERON:0000065!9.35e-09!41;UBERON:0003408!1.17e-08!24;UBERON:0006562!1.71e-08!24;UBERON:0001557!1.71e-08!24;UBERON:0001042!1.71e-08!24;UBERON:0008814!1.71e-08!24;UBERON:0009145!1.71e-08!24;UBERON:0002370!2.93e-08!23;UBERON:0000974!2.93e-08!23;UBERON:0004807!2.93e-08!23;UBERON:0005058!2.93e-08!23;UBERON:0003351!2.93e-08!23;UBERON:0009113!2.93e-08!23;UBERON:0003295!2.93e-08!23;UBERON:0009722!2.93e-08!23;UBERON:0005562!2.93e-08!23;UBERON:0007690!2.93e-08!23;UBERON:0001041!4.22e-08!80;UBERON:0002193!5.54e-08!48;UBERON:0002405!5.54e-08!48;UBERON:0007023!9.08e-08!51;UBERON:0002390!3.24e-07!45;UBERON:0003061!3.24e-07!45;UBERON:0003929!6.19e-07!55;UBERON:0000072!6.69e-07!27|tfbs_overrepresentation_for_novel_motifs=0.653885,0.813349,0.591347,0.118279,0.343185,0.126473,0.1827,0.0647981,0.364548,0.927281,1.46477,0.174808,0.569961,1.06233,0.165983,0,0.88698,0.140166,1.10025,0.364023,0.0661203,0.734777,0.556548,0.0370733,0.0864761,1.1362,0.280346,0.847446,0.198293,0.53121,0.811481,0.416414,0.923713,0.641376,1.04451,0.440985,0.558216,0.988291,0.108255,0.212494,0.335087,0.416106,0.0176074,0.04385,0.87772,0.729854,0.747448,1.42729,0.0311015,0.776322,0.85605,1.88137,0.499975,1.33224,0.554419,1.702,0.464683,0.498914,0.124743,1.07598,0.39965,0.66335,0.396933,0.310832,1.1113,0.90792,0.678037,1.00855,0.395762,0.867464,0.547195,0.592153,0.569671,0.584436,0.243223,2.38712,0.111084,0.263199,0.38541,0.0679477,0.0698528,0.917924,0.234292,0.322554,0.48244,3.00549,0.130721,0.0839192,0.755897,1.16606,1.75844,0.486763,0.427209,0.154464,2.51183,0.0896384,0.332811,0.429584,2.10776,0.436104,0.0315985,0.416179,0.523506,0.320141,0.31931,1.93149,0.367229,0.447363,1.35283,1.31904,0.636848,0.525078,0.241499,0.477109,0.749248,0.331504,0.564331,1.25321,0.889294,0.125121,0.589296,0.294572,0.210922,0.262524,0.800032,0.388466,0.188119,0.421488,0.67664,0.157621,0.508573,0.73944,0.649498,0.205008,0.769462,0.216471,0.328991,0.134301,0.723554,1.52843,1.13499,0.682379,0.219341,0.425235,0.843813,0.133739,0.274066,1.4892,0.332285,2.97146,2.21864,2.84506,0.540306,1.06407,1.75011,0.613593,0.229288,1.54788,0.0944954,3.61674,0.732404,0.481698,0.388835,0.304588,0.311631,0.199302,0.302433,0.173777,3.34934|tfbs_overrepresentation_jaspar=MA0003.1;3.61728,MA0004.1;0.118549,MA0006.1;1.02271,MA0007.1;0.356106,MA0009.1;0.438777,MA0014.1;1.72609,MA0017.1;0.0511807,MA0019.1;0.290797,MA0024.1;0.401898,MA0025.1;0.645374,MA0027.1;2.02409,MA0028.1;2.01624,MA0029.1;0.383872,MA0030.1;0.389298,MA0031.1;0.360121,MA0038.1;0.209603,MA0040.1;0.449452,MA0041.1;0.0795363,MA0042.1;0.0734808,MA0043.1;0.522621,MA0046.1;0.469568,MA0048.1;0.441352,MA0050.1;0.435264,MA0051.1;0.215828,MA0052.1;0.456356,MA0055.1;0.305767,MA0056.1;0,MA0057.1;0.390656,MA0058.1;0.0704409,MA0059.1;0.0759876,MA0060.1;3.95872,MA0061.1;0.803721,MA0063.1;0,MA0066.1;0.20204,MA0067.1;0.748059,MA0068.1;0.130537,MA0069.1;0.456647,MA0070.1;0.448343,MA0071.1;0.140522,MA0072.1;0.44111,MA0073.1;0.140558,MA0074.1;0.178027,MA0076.1;2.86851,MA0077.1;0.422739,MA0078.1;0.672666,MA0081.1;0.611511,MA0083.1;0.521922,MA0084.1;1.0607,MA0087.1;0.484199,MA0088.1;1.94606,MA0089.1;0,MA0090.1;0.100075,MA0091.1;0.125983,MA0092.1;0.100239,MA0093.1;0.0482497,MA0095.1;0,MA0098.1;0,MA0100.1;0.508591,MA0101.1;0.274567,MA0103.1;0.203213,MA0105.1;1.57663,MA0106.1;0.244965,MA0107.1;0.434379,MA0108.2;0.308463,MA0109.1;0,MA0111.1;0.107549,MA0113.1;0.638437,MA0114.1;0.265028,MA0115.1;0.525089,MA0116.1;0.657566,MA0117.1;1.24255,MA0119.1;0.97823,MA0122.1;0.514153,MA0124.1;0.698593,MA0125.1;1.52529,MA0130.1;0,MA0131.1;1.42773,MA0132.1;0,MA0133.1;0,MA0135.1;0.554905,MA0136.1;0.191208,MA0139.1;0.836525,MA0140.1;0.170444,MA0141.1;0.0633664,MA0142.1;0.34839,MA0143.1;0.236381,MA0144.1;0.111883,MA0145.1;2.89144,MA0146.1;5.03883,MA0147.1;0.293895,MA0148.1;0.127756,MA0149.1;0.590986,MA0062.2;4.03657,MA0035.2;0.173482,MA0039.2;2.46861,MA0138.2;0.281269,MA0002.2;0.0641248,MA0137.2;0.223304,MA0104.2;0.375225,MA0047.2;0.209072,MA0112.2;0.604468,MA0065.2;1.39802,MA0150.1;0.355945,MA0151.1;0,MA0152.1;0.209147,MA0153.1;0.569763,MA0154.1;0.43148,MA0155.1;0.9573,MA0156.1;0.805459,MA0157.1;0.322822,MA0158.1;0,MA0159.1;1.29831,MA0160.1;0.129493,MA0161.1;0,MA0162.1;3.0509,MA0163.1;0.392466,MA0164.1;0.191451,MA0080.2;0.197063,MA0018.2;1.09054,MA0099.2;0.276491,MA0079.2;2.59925,MA0102.2;1.11159,MA0258.1;0.240529,MA0259.1;0.813577,MA0442.1;0}}

Latest revision as of 15:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128180889..128180901,-p5@Dgka
Mm9::chr10:128181070..128181141,-p1@Dgka
Mm9::chr10:62706636..62706712,+p1@Herc4
Mm9::chr11:60591033..60591065,+p1@Smcr8
Mm9::chr12:4599798..4599893,+p1@Itsn2
Mm9::chr12:52930268..52930344,-p1@Hectd1
Mm9::chr12:72116953..72117050,+p1@Arid4a
Mm9::chr13:55312285..55312319,+p4@Nsd1
Mm9::chr17:21625946..21626024,+p1@Zfp53
Mm9::chr18:10182126..10182149,-p5@Rock1
Mm9::chr18:10610046..10610114,-p1@Esco1
Mm9::chr2:28980663..28980698,+p1@Setx
Mm9::chr3:19957802..19957857,+p1@Hltf
Mm9::chr4:100937841..100937859,-p2@Jak1
Mm9::chr4:134486861..134486912,+p1@Syf2
Mm9::chr4:142752000..142752037,-p@chr4:142752000..142752037
-
Mm9::chr4:44769481..44769554,+p1@Zcchc7
Mm9::chr6:85911625..85911665,-p1@Dusp11
Mm9::chr6:85911666..85911677,-p4@Dusp11
Mm9::chr7:106289578..106289659,-p1@Uvrag
Mm9::chr7:99818398..99818422,-p1@Pcf11
Mm9::chr8:26212579..26212641,-p2@Plekha2
Mm9::chr9:110434942..110434971,+p3@Setd2
Mm9::chr9:20449170..20449233,-p1@Fbxl12
Mm9::chr9:70390679..70390727,+p1@Sltm


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

GO IDGO nameFDR corrected p-value
GO:0043283biopolymer metabolic process0.045164440216554
GO:0006259DNA metabolic process0.045164440216554
GO:0006281DNA repair0.045164440216554
GO:0030331estrogen receptor binding0.045164440216554
GO:0046966thyroid hormone receptor binding0.045164440216554
GO:0046975histone lysine N-methyltransferase activity (H3-K36 specific)0.045164440216554
GO:0019992diacylglycerol binding0.045164440216554



Relative expression of the co-expression cluster over median <br>Analyst:




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
endoderm-derived structure9.14e-13118
endoderm9.14e-13118
presumptive endoderm9.14e-13118
digestive system1.25e-12116
digestive tract1.25e-12116
primitive gut1.25e-12116
subdivision of digestive tract2.75e-12114
mixed endoderm/mesoderm-derived structure5.45e-1135
hemopoietic organ1.10e-0929
immune organ1.10e-0929
respiratory system3.91e-0942
endo-epithelium5.09e-0969
respiratory tract9.35e-0941
gland of gut1.17e-0824
pharynx1.71e-0824
upper respiratory tract1.71e-0824
chordate pharynx1.71e-0824
pharyngeal arch system1.71e-0824
pharyngeal region of foregut1.71e-0824
thymus2.93e-0823
neck2.93e-0823
respiratory system epithelium2.93e-0823
hemolymphoid system gland2.93e-0823
pharyngeal epithelium2.93e-0823
thymic region2.93e-0823
pharyngeal gland2.93e-0823
entire pharyngeal arch endoderm2.93e-0823
thymus primordium2.93e-0823
early pharyngeal endoderm2.93e-0823
foregut4.22e-0880
hemolymphoid system5.54e-0848
immune system5.54e-0848
adult organism9.08e-0851
hematopoietic system3.24e-0745
blood island3.24e-0745
gut epithelium6.19e-0755
segment of respiratory tract6.69e-0727


TFBS overrepresentation<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)
MA0003.13.61728
MA0004.10.118549
MA0006.11.02271
MA0007.10.356106
MA0009.10.438777
MA0014.11.72609
MA0017.10.0511807
MA0019.10.290797
MA0024.10.401898
MA0025.10.645374
MA0027.12.02409
MA0028.12.01624
MA0029.10.383872
MA0030.10.389298
MA0031.10.360121
MA0038.10.209603
MA0040.10.449452
MA0041.10.0795363
MA0042.10.0734808
MA0043.10.522621
MA0046.10.469568
MA0048.10.441352
MA0050.10.435264
MA0051.10.215828
MA0052.10.456356
MA0055.10.305767
MA0056.10
MA0057.10.390656
MA0058.10.0704409
MA0059.10.0759876
MA0060.13.95872
MA0061.10.803721
MA0063.10
MA0066.10.20204
MA0067.10.748059
MA0068.10.130537
MA0069.10.456647
MA0070.10.448343
MA0071.10.140522
MA0072.10.44111
MA0073.10.140558
MA0074.10.178027
MA0076.12.86851
MA0077.10.422739
MA0078.10.672666
MA0081.10.611511
MA0083.10.521922
MA0084.11.0607
MA0087.10.484199
MA0088.11.94606
MA0089.10
MA0090.10.100075
MA0091.10.125983
MA0092.10.100239
MA0093.10.0482497
MA0095.10
MA0098.10
MA0100.10.508591
MA0101.10.274567
MA0103.10.203213
MA0105.11.57663
MA0106.10.244965
MA0107.10.434379
MA0108.20.308463
MA0109.10
MA0111.10.107549
MA0113.10.638437
MA0114.10.265028
MA0115.10.525089
MA0116.10.657566
MA0117.11.24255
MA0119.10.97823
MA0122.10.514153
MA0124.10.698593
MA0125.11.52529
MA0130.10
MA0131.11.42773
MA0132.10
MA0133.10
MA0135.10.554905
MA0136.10.191208
MA0139.10.836525
MA0140.10.170444
MA0141.10.0633664
MA0142.10.34839
MA0143.10.236381
MA0144.10.111883
MA0145.12.89144
MA0146.15.03883
MA0147.10.293895
MA0148.10.127756
MA0149.10.590986
MA0062.24.03657
MA0035.20.173482
MA0039.22.46861
MA0138.20.281269
MA0002.20.0641248
MA0137.20.223304
MA0104.20.375225
MA0047.20.209072
MA0112.20.604468
MA0065.21.39802
MA0150.10.355945
MA0151.10
MA0152.10.209147
MA0153.10.569763
MA0154.10.43148
MA0155.10.9573
MA0156.10.805459
MA0157.10.322822
MA0158.10
MA0159.11.29831
MA0160.10.129493
MA0161.10
MA0162.13.0509
MA0163.10.392466
MA0164.10.191451
MA0080.20.197063
MA0018.21.09054
MA0099.20.276491
MA0079.22.59925
MA0102.21.11159
MA0258.10.240529
MA0259.10.813577
MA0442.10
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