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MCL coexpression mm9:440: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!1.69e-12!46;UBERON:0002204!3.68e-09!32;UBERON:0002371!9.34e-09!16
|ontology_enrichment_uberon=UBERON:0002384!1.69e-12!46;UBERON:0002204!3.68e-09!32;UBERON:0002371!9.34e-09!16
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.0322544,0.157426,0.593409,1.03515,0.618816,0.782043,0.165361,0.177198,0.1389,0.252112,0.760086,0.165655,0.804507,0.322172,0,0.46143,0.285124,0.964807,0.157913,0.133242,0.585659,0.296055,1.02912,0.489022,0.319311,0.322606,0.655992,0.74011,0.230852,0.22152,0.552579,0.281806,0.279585,0.66368,0.242788,0.0778621,0.274364,0.0668978,0.43804,0.0860512,0.225414,0.182703,0.667769,0.616787,0.197508,0.391673,0.244272,0.896328,0.116163,0.445973,0.341665,0.681799,0.683824,0.700221,0.302599,0.385691,0.26711,0.878517,0.300938,0.534331,0.349585,0.192373,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.144846,0.692376,0.106553,0.731855,0.120421,0.108578,0.279429,0.381898,0.518764,0.422405,1.07599,0.476893,0.348372,0.361155,0.623727,0.390032,1.47685,0.231141,0.395899,1.32869,0.896685,0.62835,0.564287,0.0914951,0.231442,0.455703,0.370414,0.56686,1.01594,0.1892,0.0779031,0.552324,0.667487,1.13461,0.445567,0.225081,0.498793,0.241171,0.139088,0.134388,0.170493,0.669156,0.838495,0.256145,0.903482,1.01241,0.205053,0.208431,0.462587,0.55693,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.310322,0.651613,0.200314,0.799981,0.313768,0.92434,0.204108,0.534959,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,1.12026,0.225756,0.394362,1.65442,0.539014,0.622526,0.726489,0.0270799,0.685297,0.215456,0.841089,0.762455,0.342508,0.340691,0.516355,0.534479,0.886073,0.622933,0.522515,0.168927,0.436947,0.306938,0.0772819,0.757197,0.871674
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.0322544,0.157426,0.593409,1.03515,0.618816,0.782043,0.165361,0.177198,0.1389,0.252112,0.760086,0.165655,0.804507,0.322172,0,0.46143,0.285124,0.964807,0.157913,0.133242,0.585659,0.296055,1.02912,0.489022,0.319311,0.322606,0.655992,0.74011,0.230852,0.22152,0.552579,0.281806,0.279585,0.66368,0.242788,0.0778621,0.274364,0.0668978,0.43804,0.0860512,0.225414,0.182703,0.667769,0.616787,0.197508,0.391673,0.244272,0.896328,0.116163,0.445973,0.341665,0.681799,0.683824,0.700221,0.302599,0.385691,0.26711,0.878517,0.300938,0.534331,0.349585,0.192373,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.144846,0.692376,0.106553,0.731855,0.120421,0.108578,0.279429,0.381898,0.518764,0.422405,1.07599,0.476893,0.348372,0.361155,0.623727,0.390032,1.47685,0.231141,0.395899,1.32869,0.896685,0.62835,0.564287,0.0914951,0.231442,0.455703,0.370414,0.56686,1.01594,0.1892,0.0779031,0.552324,0.667487,1.13461,0.445567,0.225081,0.498793,0.241171,0.139088,0.134388,0.170493,0.669156,0.838495,0.256145,0.903482,1.01241,0.205053,0.208431,0.462587,0.55693,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.310322,0.651613,0.200314,0.799981,0.313768,0.92434,0.204108,0.534959,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,1.12026,0.225756,0.394362,1.65442,0.539014,0.622526,0.726489,0.0270799,0.685297,0.215456,0.841089,0.762455,0.342508,0.340691,0.516355,0.534479,0.886073,0.622933,0.522515,0.168927,0.436947,0.306938,0.0772819,0.757197,0.871674
|tfbs_overrepresentation_jaspar=MA0003.1;0.0741826,MA0004.1;0.594255,MA0006.1;0.0950487,MA0007.1;0.195085,MA0009.1;0.576798,MA0014.1;0.465689,MA0017.1;0.356464,MA0019.1;0.413421,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.331378,MA0029.1;0.51708,MA0030.1;1.2985,MA0031.1;0.490954,MA0038.1;0.319246,MA0040.1;0.588314,MA0041.1;0.464691,MA0042.1;0.442876,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.191487,MA0050.1;0.662757,MA0051.1;0.871644,MA0052.1;1.45222,MA0055.1;0.0774805,MA0056.1;0,MA0057.1;0.0134783,MA0058.1;0.431697,MA0059.1;0.147666,MA0060.1;0.0544856,MA0061.1;0.887454,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.0143498,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.234437,MA0072.1;0.579318,MA0073.1;1.66351,MA0074.1;0.281183,MA0076.1;0.386726,MA0077.1;0.559443,MA0078.1;0.354249,MA0081.1;0.950346,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.383684,MA0089.1;0,MA0090.1;0.534933,MA0091.1;1.81222,MA0092.1;0.535473,MA0093.1;0.700866,MA0095.1;0,MA0098.1;0,MA0100.1;0.271974,MA0101.1;0.466845,MA0103.1;0.373479,MA0105.1;0.502472,MA0106.1;0.360817,MA0107.1;0.73481,MA0108.2;0.433384,MA0109.1;0,MA0111.1;0.191411,MA0113.1;0.337108,MA0114.1;0.238352,MA0115.1;0.669167,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;0.467825,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;1.67153,MA0136.1;0.297196,MA0139.1;0.367034,MA0140.1;0.271883,MA0141.1;0.805726,MA0142.1;1.20233,MA0143.1;0.925469,MA0144.1;0.242681,MA0145.1;0.420675,MA0146.1;0.266647,MA0147.1;0.0750034,MA0148.1;0.218033,MA0149.1;0.157322,MA0062.2;0.521029,MA0035.2;0.275617,MA0039.2;1.01082,MA0138.2;0.402586,MA0002.2;1.03486,MA0137.2;0.127311,MA0104.2;0.408321,MA0047.2;0.318614,MA0112.2;0.24038,MA0065.2;0.656619,MA0150.1;1.07872,MA0151.1;0,MA0152.1;0.318703,MA0153.1;0.716409,MA0154.1;0.609154,MA0155.1;0.0502893,MA0156.1;0.77202,MA0157.1;1.14109,MA0158.1;0,MA0159.1;0.0802352,MA0160.1;0.220282,MA0161.1;0,MA0162.1;0.327867,MA0163.1;0.29229,MA0164.1;0.297489,MA0080.2;1.76688,MA0018.2;0.305372,MA0099.2;1.02741,MA0079.2;0.818468,MA0102.2;1.27355,MA0258.1;0.478272,MA0259.1;0.524511,MA0442.1;0
}}
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Revision as of 11:45, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80962341..80962353,-p@chr10:80962341..80962353
-
Mm9::chr14:103379325..103379344,+p@chr14:103379325..103379344
+
Mm9::chr16:91406066..91406089,+p9@Il10rb
Mm9::chr18:62316324..62316329,-p@chr18:62316324..62316329
-
Mm9::chr19:32329718..32329755,+p@chr19:32329718..32329755
+
Mm9::chr1:130602320..130602335,+p@chr1:130602320..130602335
+
Mm9::chr1:87505064..87505089,+p@chr1:87505064..87505089
+
Mm9::chr1:89523255..89523265,+p@chr1:89523255..89523265
+
Mm9::chr1:89749728..89749742,-p@chr1:89749728..89749742
-
Mm9::chr4:130470264..130470268,+p@chr4:130470264..130470268
+
Mm9::chr5:108117177..108117198,+p@chr5:108117177..108117198
+
Mm9::chr5:65883638..65883674,-p@chr5:65883638..65883674
-
Mm9::chr5:73194336..73194339,+p@chr5:73194336..73194339
+
Mm9::chr5:99765762..99765773,+p@chr5:99765762..99765773
+
Mm9::chr7:25230809..25230816,+p@chr7:25230809..25230816
+
Mm9::chr8:26178393..26178407,-p@chr8:26178393..26178407
-
Mm9::chr9:107904389..107904396,+p@chr9:107904389..107904396
+


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:0004920interleukin-10 receptor activity0.000986139264778393
GO:0019969interleukin-10 binding0.000986139264778393
GO:0004907interleukin receptor activity0.0118336711773407
GO:0019965interleukin binding0.0118336711773407
GO:0019838growth factor binding0.0118336711773407
GO:0007596blood coagulation0.0118336711773407
GO:0007599hemostasis0.0118336711773407
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0118336711773407
GO:0050817coagulation0.0118336711773407
GO:0019955cytokine binding0.0125508633699068
GO:0050878regulation of body fluid levels0.0125508633699068
GO:0042060wound healing0.0129841669862488
GO:0009611response to wounding0.043693555116335



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic cell6.13e-1932
hematopoietic oligopotent progenitor cell6.13e-1932
hematopoietic stem cell6.13e-1932
angioblastic mesenchymal cell6.13e-1932
hematopoietic multipotent progenitor cell6.13e-1932
common myeloid progenitor1.23e-1219
connective tissue cell1.69e-1246
mesenchymal cell1.69e-1246
stem cell6.07e-1297
hematopoietic lineage restricted progenitor cell1.05e-1125
megakaryocyte progenitor cell3.07e-116
megakaryocyte3.07e-116
motile cell2.58e-1054
myeloid cell9.34e-0916
somatic stem cell1.23e-0891
multi fate stem cell1.23e-0891
lymphoid lineage restricted progenitor cell4.68e-0812
CD4-positive, alpha-beta T cell8.64e-088
megakaryocyte-erythroid progenitor cell1.58e-079
lymphocyte2.02e-0713
common lymphoid progenitor2.02e-0713
mature alpha-beta T cell6.12e-079
alpha-beta T cell6.12e-079
immature T cell6.12e-079
mature T cell6.12e-079
immature alpha-beta T cell6.12e-079

Uber Anatomy
Ontology termp-valuen
connective tissue1.69e-1246
musculoskeletal system3.68e-0932
bone marrow9.34e-0916

Disease
Ontology termp-valuen
musculoskeletal system cancer2.41e-133
muscle cancer2.41e-133
organ system cancer6.80e-076


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)
MA0003.10.0741826
MA0004.10.594255
MA0006.10.0950487
MA0007.10.195085
MA0009.10.576798
MA0014.10.465689
MA0017.10.356464
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.10.331378
MA0029.10.51708
MA0030.11.2985
MA0031.10.490954
MA0038.10.319246
MA0040.10.588314
MA0041.10.464691
MA0042.10.442876
MA0043.10.666547
MA0046.10.609938
MA0048.10.191487
MA0050.10.662757
MA0051.10.871644
MA0052.11.45222
MA0055.10.0774805
MA0056.10
MA0057.10.0134783
MA0058.10.431697
MA0059.10.147666
MA0060.10.0544856
MA0061.10.887454
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.0143498
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.11.66351
MA0074.10.281183
MA0076.10.386726
MA0077.10.559443
MA0078.10.354249
MA0081.10.950346
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.383684
MA0089.10
MA0090.10.534933
MA0091.11.81222
MA0092.10.535473
MA0093.10.700866
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.466845
MA0103.10.373479
MA0105.10.502472
MA0106.10.360817
MA0107.10.73481
MA0108.20.433384
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.10.238352
MA0115.10.669167
MA0116.10.0949327
MA0117.10.639033
MA0119.10.467825
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.11.67153
MA0136.10.297196
MA0139.10.367034
MA0140.10.271883
MA0141.10.805726
MA0142.11.20233
MA0143.10.925469
MA0144.10.242681
MA0145.10.420675
MA0146.10.266647
MA0147.10.0750034
MA0148.10.218033
MA0149.10.157322
MA0062.20.521029
MA0035.20.275617
MA0039.21.01082
MA0138.20.402586
MA0002.21.03486
MA0137.20.127311
MA0104.20.408321
MA0047.20.318614
MA0112.20.24038
MA0065.20.656619
MA0150.11.07872
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.10.609154
MA0155.10.0502893
MA0156.10.77202
MA0157.11.14109
MA0158.10
MA0159.10.0802352
MA0160.10.220282
MA0161.10
MA0162.10.327867
MA0163.10.29229
MA0164.10.297489
MA0080.21.76688
MA0018.20.305372
MA0099.21.02741
MA0079.20.818468
MA0102.21.27355
MA0258.10.478272
MA0259.10.524511
MA0442.10
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