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MCL coexpression mm9:343: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002193!5.73e-26!48;UBERON:0002405!5.73e-26!48;UBERON:0002390!1.01e-25!45;UBERON:0003061!1.01e-25!45;UBERON:0004177!2.63e-23!29;UBERON:0005057!2.63e-23!29;UBERON:0002370!2.16e-21!23;UBERON:0000974!2.16e-21!23;UBERON:0004807!2.16e-21!23;UBERON:0005058!2.16e-21!23;UBERON:0003351!2.16e-21!23;UBERON:0009113!2.16e-21!23;UBERON:0003295!2.16e-21!23;UBERON:0009722!2.16e-21!23;UBERON:0005562!2.16e-21!23;UBERON:0007690!2.16e-21!23;UBERON:0000077!8.14e-21!35;UBERON:0006562!2.41e-20!24;UBERON:0003408!2.41e-20!24;UBERON:0001557!2.41e-20!24;UBERON:0001042!2.41e-20!24;UBERON:0008814!2.41e-20!24;UBERON:0009145!2.41e-20!24;UBERON:0002384!8.10e-19!46;UBERON:0000072!1.15e-17!27;UBERON:0000063!8.88e-13!35;UBERON:0003081!1.04e-12!87;UBERON:0007811!2.54e-12!36;UBERON:0000065!7.59e-12!41;UBERON:0001004!1.80e-11!42;UBERON:0000153!9.99e-10!43;UBERON:0003929!6.37e-08!55;UBERON:0000926!1.54e-07!120;UBERON:0004120!1.54e-07!120;UBERON:0006603!1.54e-07!120;UBERON:0001041!2.15e-07!80;UBERON:0002368!5.90e-07!60
|ontology_enrichment_uberon=UBERON:0002193!5.73e-26!48;UBERON:0002405!5.73e-26!48;UBERON:0002390!1.01e-25!45;UBERON:0003061!1.01e-25!45;UBERON:0004177!2.63e-23!29;UBERON:0005057!2.63e-23!29;UBERON:0002370!2.16e-21!23;UBERON:0000974!2.16e-21!23;UBERON:0004807!2.16e-21!23;UBERON:0005058!2.16e-21!23;UBERON:0003351!2.16e-21!23;UBERON:0009113!2.16e-21!23;UBERON:0003295!2.16e-21!23;UBERON:0009722!2.16e-21!23;UBERON:0005562!2.16e-21!23;UBERON:0007690!2.16e-21!23;UBERON:0000077!8.14e-21!35;UBERON:0006562!2.41e-20!24;UBERON:0003408!2.41e-20!24;UBERON:0001557!2.41e-20!24;UBERON:0001042!2.41e-20!24;UBERON:0008814!2.41e-20!24;UBERON:0009145!2.41e-20!24;UBERON:0002384!8.10e-19!46;UBERON:0000072!1.15e-17!27;UBERON:0000063!8.88e-13!35;UBERON:0003081!1.04e-12!87;UBERON:0007811!2.54e-12!36;UBERON:0000065!7.59e-12!41;UBERON:0001004!1.80e-11!42;UBERON:0000153!9.99e-10!43;UBERON:0003929!6.37e-08!55;UBERON:0000926!1.54e-07!120;UBERON:0004120!1.54e-07!120;UBERON:0006603!1.54e-07!120;UBERON:0001041!2.15e-07!80;UBERON:0002368!5.90e-07!60
|tfbs_overrepresentation_for_novel_motifs=0.379825,0.119746,0.341317,1.40483,0.191527,0.466956,0.615468,0.0918969,0.752205,0.11695,1.0366,0.206436,0.0209655,0.636202,0.463829,0,0.374352,0.719963,0.202974,0.16663,0.604268,0.321305,0.223092,0.189689,0.108863,0.243873,0.612988,0.50041,0.248458,0.122724,0.928995,0.460285,0.0475156,0.157141,0.806589,0.0464706,0.382826,0.2039,0.336224,0.823236,0.186742,0.161379,0.636444,0.468447,0.290064,0.426921,0.833552,0.52593,0.340931,0.0722351,0.359925,0.729809,0.417327,0.586014,0.601849,0.22892,0.559359,0.197526,0.173818,0.644883,0.442975,0.271204,0.111304,0.350689,0.237053,0.384144,0.727642,1.06142,0.438956,0.919268,0.0946191,0.0971174,0.20691,0.632466,0.325879,0.145958,0.157028,0.300684,0.428247,0.614637,0.0981933,0.388829,0.270104,0.217876,0.5282,0.0985324,0.66191,0.122924,0.842295,1.21975,0.793151,0.532634,0.471416,0.198642,0.594936,0.855124,0.0897681,0.473864,0.834007,0.0321057,0.168895,0.460042,0.570262,0.360414,0.359547,0.485402,0.409409,0.519389,0.0900536,0.29175,0.369309,0.57187,0.296684,0.187937,0.799811,0.184628,0.0842419,0.450125,0.375433,0.668337,0.637418,0.333667,0.245224,0.811709,0.851175,0.43141,0.62924,0.465518,0.726225,0.202267,0.554981,0.432886,0.698665,0.238902,0.820264,0.314435,1.8569,0.162291,0.773792,1.58317,1.18855,0.732048,0.707182,0.469382,0.35423,0.486829,0.31213,1.54387,0.125637,0.193635,0.261373,0.43405,0.587436,0.30395,0.238221,0.662158,0.731564,0.847,0.117954,0.124089,0.782756,0.527439,1.10281,0.365959,0.927041,0.657421,0.380389,0.205322,0.0723599
|tfbs_overrepresentation_for_novel_motifs=0.379825,0.119746,0.341317,1.40483,0.191527,0.466956,0.615468,0.0918969,0.752205,0.11695,1.0366,0.206436,0.0209655,0.636202,0.463829,0,0.374352,0.719963,0.202974,0.16663,0.604268,0.321305,0.223092,0.189689,0.108863,0.243873,0.612988,0.50041,0.248458,0.122724,0.928995,0.460285,0.0475156,0.157141,0.806589,0.0464706,0.382826,0.2039,0.336224,0.823236,0.186742,0.161379,0.636444,0.468447,0.290064,0.426921,0.833552,0.52593,0.340931,0.0722351,0.359925,0.729809,0.417327,0.586014,0.601849,0.22892,0.559359,0.197526,0.173818,0.644883,0.442975,0.271204,0.111304,0.350689,0.237053,0.384144,0.727642,1.06142,0.438956,0.919268,0.0946191,0.0971174,0.20691,0.632466,0.325879,0.145958,0.157028,0.300684,0.428247,0.614637,0.0981933,0.388829,0.270104,0.217876,0.5282,0.0985324,0.66191,0.122924,0.842295,1.21975,0.793151,0.532634,0.471416,0.198642,0.594936,0.855124,0.0897681,0.473864,0.834007,0.0321057,0.168895,0.460042,0.570262,0.360414,0.359547,0.485402,0.409409,0.519389,0.0900536,0.29175,0.369309,0.57187,0.296684,0.187937,0.799811,0.184628,0.0842419,0.450125,0.375433,0.668337,0.637418,0.333667,0.245224,0.811709,0.851175,0.43141,0.62924,0.465518,0.726225,0.202267,0.554981,0.432886,0.698665,0.238902,0.820264,0.314435,1.8569,0.162291,0.773792,1.58317,1.18855,0.732048,0.707182,0.469382,0.35423,0.486829,0.31213,1.54387,0.125637,0.193635,0.261373,0.43405,0.587436,0.30395,0.238221,0.662158,0.731564,0.847,0.117954,0.124089,0.782756,0.527439,1.10281,0.365959,0.927041,0.657421,0.380389,0.205322,0.0723599
|tfbs_overrepresentation_jaspar=MA0003.1;0.0142031,MA0004.1;0.444991,MA0006.1;0.789557,MA0007.1;0.135697,MA0009.1;0.483331,MA0014.1;0.0690682,MA0017.1;0.515383,MA0019.1;0.329708,MA0024.1;0.445298,MA0025.1;0.694475,MA0027.1;2.07936,MA0028.1;0.477663,MA0029.1;0.426655,MA0030.1;1.10385,MA0031.1;0.402033,MA0038.1;0.243815,MA0040.1;0.494317,MA0041.1;2.25336,MA0042.1;1.07583,MA0043.1;0.569356,MA0046.1;0.514989,MA0048.1;0.206983,MA0050.1;0.506524,MA0051.1;0.250459,MA0052.1;0.501416,MA0055.1;0.00826433,MA0056.1;0,MA0057.1;0.180412,MA0058.1;0.628633,MA0059.1;0.659185,MA0060.1;0.281866,MA0061.1;0.618873,MA0063.1;0,MA0066.1;0.235725,MA0067.1;0.798606,MA0068.1;0.543816,MA0069.1;0.501715,MA0070.1;1.23487,MA0071.1;0.505175,MA0072.1;1.21895,MA0073.1;8.90733,MA0074.1;0.603526,MA0076.1;0.560918,MA0077.1;0.466808,MA0078.1;0.275441,MA0081.1;0.353705,MA0083.1;0.568641,MA0084.1;1.11388,MA0087.1;0.530004,MA0088.1;0.100554,MA0089.1;0,MA0090.1;0.124244,MA0091.1;0.153118,MA0092.1;0.124428,MA0093.1;0.496926,MA0095.1;0,MA0098.1;0,MA0100.1;0.201797,MA0101.1;0.681587,MA0103.1;0.253989,MA0105.1;0.303135,MA0106.1;0.281418,MA0107.1;0.526347,MA0108.2;0.348212,MA0109.1;0,MA0111.1;1.33098,MA0113.1;0.259904,MA0114.1;0.338149,MA0115.1;0.571881,MA0116.1;0.206147,MA0117.1;0.542889,MA0119.1;0.683064,MA0122.1;0.560692,MA0124.1;1.77049,MA0125.1;0.67944,MA0130.1;0,MA0131.1;0.326061,MA0132.1;0,MA0133.1;0,MA0135.1;0.602346,MA0136.1;0.637057,MA0139.1;0.0885364,MA0140.1;0.201717,MA0141.1;0.280405,MA0142.1;0.389844,MA0143.1;0.27232,MA0144.1;0.621329,MA0145.1;0.222364,MA0146.1;0.0248607,MA0147.1;0.162533,MA0148.1;0.470482,MA0149.1;0.104621,MA0062.2;0.536836,MA0035.2;0.205003,MA0039.2;0.407918,MA0138.2;0.319705,MA0002.2;0.706893,MA0137.2;0.581412,MA0104.2;0.254432,MA0047.2;0.243248,MA0112.2;0.22235,MA0065.2;0.223525,MA0150.1;0.421594,MA0151.1;0,MA0152.1;0.243327,MA0153.1;0.617506,MA0154.1;0.093399,MA0155.1;0.267894,MA0156.1;0.94766,MA0157.1;0.363212,MA0158.1;0,MA0159.1;0.174007,MA0160.1;0.475244,MA0161.1;0,MA0162.1;0.222445,MA0163.1;0.768601,MA0164.1;1.85886,MA0080.2;0.90228,MA0018.2;0.231394,MA0099.2;0.314682,MA0079.2;1.47575,MA0102.2;1.16504,MA0258.1;0.895773,MA0259.1;0.347953,MA0442.1;0
}}
}}

Revision as of 11:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:114799630..114799648,+p@chr10:114799630..114799648
+
Mm9::chr10:95861444..95861457,+p@chr10:95861444..95861457
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Mm9::chr11:98805740..98805771,+p@chr11:98805740..98805771
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Mm9::chr12:85328750..85328777,+p4@Acot2
Mm9::chr12:85534937..85534948,-p10@C130039O16Rik
Mm9::chr13:112587461..112587466,+p@chr13:112587461..112587466
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Mm9::chr13:112597992..112598030,+p@chr13:112597992..112598030
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Mm9::chr15:72983928..72983956,+p@chr15:72983928..72983956
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Mm9::chr16:57471448..57471461,+p@chr16:57471448..57471461
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Mm9::chr17:71202982..71202985,-p7@Tgif1
Mm9::chr19:12870212..12870222,+p@chr19:12870212..12870222
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Mm9::chr19:53515961..53515969,-p@chr19:53515961..53515969
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Mm9::chr1:179187574..179187585,+p@chr1:179187574..179187585
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Mm9::chr2:126500931..126500953,-p@chr2:126500931..126500953
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Mm9::chr2:58013196..58013216,-p8@Cytip
Mm9::chr3:21976400..21976421,-p@chr3:21976400..21976421
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Mm9::chr3:87945689..87945693,+p@chr3:87945689..87945693
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Mm9::chr4:133176650..133176677,-p@chr4:133176650..133176677
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Mm9::chr4:140256984..140257004,-p@chr4:140256984..140257004
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Mm9::chr6:87776511..87776514,-p@chr6:87776511..87776514
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Mm9::chr7:82517026..82517029,-p@chr7:82517026..82517029
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Mm9::chrX:104284650..104284676,+p3@P2ry10


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

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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
hematopoietic cell1.65e-2632
hematopoietic oligopotent progenitor cell1.65e-2632
hematopoietic stem cell1.65e-2632
angioblastic mesenchymal cell1.65e-2632
hematopoietic multipotent progenitor cell1.65e-2632
lymphoid lineage restricted progenitor cell6.14e-2412
mature alpha-beta T cell3.90e-229
alpha-beta T cell3.90e-229
immature T cell3.90e-229
mature T cell3.90e-229
immature alpha-beta T cell3.90e-229
lymphocyte6.76e-2213
common lymphoid progenitor6.76e-2213
T cell1.58e-2111
pro-T cell1.58e-2111
CD4-positive, alpha-beta T cell9.91e-208
hematopoietic lineage restricted progenitor cell2.16e-1925
connective tissue cell8.10e-1946
mesenchymal cell8.10e-1946
nucleate cell2.64e-1716
leukocyte3.89e-1617
nongranular leukocyte3.89e-1617
motile cell2.98e-1554
thymocyte6.34e-156
double negative thymocyte6.34e-156
naive T cell6.34e-156
double-positive, alpha-beta thymocyte6.34e-156
CD4-positive, alpha-beta thymocyte6.34e-156
naive thymus-derived CD4-positive, alpha-beta T cell6.34e-156
DN4 thymocyte6.34e-156
DN1 thymic pro-T cell6.34e-156
DN2 thymocyte6.34e-156
DN3 thymocyte6.34e-156
immature single positive thymocyte6.34e-156
early T lineage precursor6.34e-156
mature CD4 single-positive thymocyte6.34e-156
resting double-positive thymocyte6.34e-156
double-positive blast6.34e-156
CD69-positive double-positive thymocyte6.34e-156
CD69-positive, CD4-positive single-positive thymocyte6.34e-156
CD4-positive, CD8-intermediate double-positive thymocyte6.34e-156
CD24-positive, CD4 single-positive thymocyte6.34e-156
stem cell4.44e-0997
common myeloid progenitor1.52e-0819
somatic stem cell5.33e-0791
multi fate stem cell5.33e-0791

Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.73e-2648
immune system5.73e-2648
hematopoietic system1.01e-2545
blood island1.01e-2545
hemopoietic organ2.63e-2329
immune organ2.63e-2329
thymus2.16e-2123
neck2.16e-2123
respiratory system epithelium2.16e-2123
hemolymphoid system gland2.16e-2123
pharyngeal epithelium2.16e-2123
thymic region2.16e-2123
pharyngeal gland2.16e-2123
entire pharyngeal arch endoderm2.16e-2123
thymus primordium2.16e-2123
early pharyngeal endoderm2.16e-2123
mixed endoderm/mesoderm-derived structure8.14e-2135
pharynx2.41e-2024
gland of gut2.41e-2024
upper respiratory tract2.41e-2024
chordate pharynx2.41e-2024
pharyngeal arch system2.41e-2024
pharyngeal region of foregut2.41e-2024
connective tissue8.10e-1946
segment of respiratory tract1.15e-1727
organ segment8.88e-1335
lateral plate mesoderm1.04e-1287
craniocervical region2.54e-1236
respiratory tract7.59e-1241
respiratory system1.80e-1142
anterior region of body9.99e-1043
gut epithelium6.37e-0855
mesoderm1.54e-07120
mesoderm-derived structure1.54e-07120
presumptive mesoderm1.54e-07120
foregut2.15e-0780
endocrine gland5.90e-0760


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)
MA0003.10.0142031
MA0004.10.444991
MA0006.10.789557
MA0007.10.135697
MA0009.10.483331
MA0014.10.0690682
MA0017.10.515383
MA0019.10.329708
MA0024.10.445298
MA0025.10.694475
MA0027.12.07936
MA0028.10.477663
MA0029.10.426655
MA0030.11.10385
MA0031.10.402033
MA0038.10.243815
MA0040.10.494317
MA0041.12.25336
MA0042.11.07583
MA0043.10.569356
MA0046.10.514989
MA0048.10.206983
MA0050.10.506524
MA0051.10.250459
MA0052.10.501416
MA0055.10.00826433
MA0056.10
MA0057.10.180412
MA0058.10.628633
MA0059.10.659185
MA0060.10.281866
MA0061.10.618873
MA0063.10
MA0066.10.235725
MA0067.10.798606
MA0068.10.543816
MA0069.10.501715
MA0070.11.23487
MA0071.10.505175
MA0072.11.21895
MA0073.18.90733
MA0074.10.603526
MA0076.10.560918
MA0077.10.466808
MA0078.10.275441
MA0081.10.353705
MA0083.10.568641
MA0084.11.11388
MA0087.10.530004
MA0088.10.100554
MA0089.10
MA0090.10.124244
MA0091.10.153118
MA0092.10.124428
MA0093.10.496926
MA0095.10
MA0098.10
MA0100.10.201797
MA0101.10.681587
MA0103.10.253989
MA0105.10.303135
MA0106.10.281418
MA0107.10.526347
MA0108.20.348212
MA0109.10
MA0111.11.33098
MA0113.10.259904
MA0114.10.338149
MA0115.10.571881
MA0116.10.206147
MA0117.10.542889
MA0119.10.683064
MA0122.10.560692
MA0124.11.77049
MA0125.10.67944
MA0130.10
MA0131.10.326061
MA0132.10
MA0133.10
MA0135.10.602346
MA0136.10.637057
MA0139.10.0885364
MA0140.10.201717
MA0141.10.280405
MA0142.10.389844
MA0143.10.27232
MA0144.10.621329
MA0145.10.222364
MA0146.10.0248607
MA0147.10.162533
MA0148.10.470482
MA0149.10.104621
MA0062.20.536836
MA0035.20.205003
MA0039.20.407918
MA0138.20.319705
MA0002.20.706893
MA0137.20.581412
MA0104.20.254432
MA0047.20.243248
MA0112.20.22235
MA0065.20.223525
MA0150.10.421594
MA0151.10
MA0152.10.243327
MA0153.10.617506
MA0154.10.093399
MA0155.10.267894
MA0156.10.94766
MA0157.10.363212
MA0158.10
MA0159.10.174007
MA0160.10.475244
MA0161.10
MA0162.10.222445
MA0163.10.768601
MA0164.11.85886
MA0080.20.90228
MA0018.20.231394
MA0099.20.314682
MA0079.21.47575
MA0102.21.16504
MA0258.10.895773
MA0259.10.347953
MA0442.10
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