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LRBase × scTensorで細胞間コミュニケーションの検出

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Mishima.syk#13の発表資料

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LRBase × scTensorで細胞間コミュニケーションの検出

  1. 1. 

  2. 2. 
 

  3. 3. 
 Chen S, 2015
  4. 4. Togo picture gallery by DBCLS is Licensed under a Creative Commons 2.1 (c)
  5. 5. 
 Pavilicev M, 2017 Ramilowski J A, 2015 Li L, 2017 Skelly D A, 2018
  6. 6. Togo picture gallery by DBCLS is Licensed under a Creative Commons 2.1 (c)
  7. 7. X
  8. 8. X X1 X2 X3 ^ ^ ^
  9. 9. X u1'◦v1' u2'◦v2' u3'◦v3' X1 X2 X3 ^ ^ ^
  10. 10. X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1 u2◦v2 u3◦v3 X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
  11. 11. 
X u1'◦v1' u2'◦v2' u3'◦v3' u1◦v1 u2◦v2 u3◦v3 UΛVT X1 X2 X3 ^ ^ ^ λ1 λ2 λ3
  12. 12. χ A(1) A(2) A(3) S
  13. 13. χ S S
  14. 14. 
 
 

  15. 15. 1 Tsuyuzaki K. et. al., 2019 (in prep.)
  16. 16. 2 Tsuyuzaki K. et. al., 2019 (in prep.)
  17. 17. 3 Tsuyuzaki K. et. al., 2019 (in prep.)
  18. 18. 4 Tsuyuzaki K. et. al., 2019 (in prep.)
  19. 19. 
 
 
 

  20. 20. library(scTensor) library(SingleCellExperiment) library(LRBase.Hsa.eg.db) data(“GermMale”) # Data matrix (486genes × 852cells, 7class, 3.5MB) data(“tsneGermMale”) # The result of Rtsne (21kb) data(“labelGermMale”) # Celltype label (15kb) sce <- SingleCellExperiment(assays = list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE = tsneGermMale$Y) cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) rks <- cellCellRanks(sce) 
 cellCellDecomp(sce, ranks=rks$selected) 
 cellCellReport(sce, reducedDimNames="TSNE", out.dir=tmp, title="Cell-cell interaction within Germline, Male, GSE86146", author="Koki Tsuyuzaki", thr=80)
  21. 21. 
 

  22. 22. Tsuyuzaki K. et. al., 2018
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  24. 24. 
 
 Tsuyuzaki K. et. al., 2018
  25. 25. 
 
 
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  26. 26. 
 1/4 
 Himmelstein, D S et al., 2017
  27. 27. 
 
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  28. 28. 2/4 Cichonska, A et al., 2015
  29. 29. 3/4
  30. 30. 3/4 Gusev A. et. al., 2016Sun S. et. al., 2018 

  31. 31. 4/4 
 

  32. 32. 4/4 Butler A et. al., 2018Brown B C et. al., 2018 
 
 

  33. 33. = Raquel Urtasun, 2008Laurens, 2008 Graph PCA, Bo Jiang, 2013 

  34. 34. PCA: 1 X
  35. 35. PLS/CCA/siNMF: 2 X,Y
  36. 36. PLS/CCA/siNMF: 2 X,Y
  37. 37. PLS/CCA/siNMF: 2 X,Y 
 

  38. 38. CMF: n 
 Marinka Zitnik, 2016
  39. 39. CMTF: n Ermis B, 2012 Suleiman A Khan, 2016 Evirm Acar, 2011
  40. 40. 
 
 


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