Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data.
We have developed a new method for classifying 3D reconstructions with missing data obtained by electron microscopy techniques. The method is based on principal component analysis (PCA) combined with expectation maximization. The missing data, together with the principal components, are treated as hidden variables that are estimated by maximizing a likelihood function. PCA in 3D is similar to PCA for 2D image analysis. A lower dimensional subspace of significant features is selected, into which the data are projected, and if desired, subsequently classified. In addition, our new algorithm estimates the missing data for each individual volume within the lower dimensional subspace. Application to both a large model data set and cryo-electron microscopy experimental data demonstrates the good performance of the algorithm and illustrates its potential for studying macromolecular assemblies with continuous conformational variations.
Yu
Lingbo
L
University of Vermont, Department of Molecular Physiology and Biophysics, Burlington, VT 05405, USA.
Snapp
Robert R
RR
Ruiz
Teresa
T
Radermacher
Michael
M
D000465:Algorithms; D020285:Cryoelectron Microscopy; D021621:Imaging, Three-Dimensional; D015233:Models, Statistical; D025341:Principal Component Analysis; D011336:Probability
Ultramicroscopy. 1977 Apr;2(2-3):219-27
888241
Virology. 1964 Mar;22:342-59
14127832
J Struct Biol. 2001 Dec;136(3):167-80
12051897
J Electron Microsc Tech. 1988 Aug;9(4):359-94
3058896
J Microsc. 1987 May;146(Pt 2):113-36
3302267
Clin Chem. 1981 Jun;27(6):798-805
7237756
Biophys Chem. 2003;100(1-3):577-91
12646392
J Mol Biol. 1982 Oct 15;161(1):134-7
7154073
J Struct Biol. 2007 Jan;157(1):126-37
16973379
J Struct Biol. 2007 Sep;159(3):433-42
17591445
J Mol Biol. 1983 Jan 25;163(3):409-30
6339729
J Struct Biol. 2008 Jun;162(3):436-50
18440828
Ultramicroscopy. 1981;6(2):187-94
7268930
Psychometrika. 1967 Sep;32(3):241-54
5234703
Ultramicroscopy. 1987;21(2):111-23
12425301
J Struct Biol. 2008 Mar;161(3):276-86
17720536
Structure. 2009 Dec 9;17(12):1563-1572
20004160
J Microsc. 1990 Feb;157(Pt 2):187-203
2179560
Ultramicroscopy. 1994 Feb;53(2):121-36
8171751
J Struct Biol. 2007 Jul;159(1):135-43
17493831
J Struct Biol. 2006 Mar;153(3):284-99
16431136
J Theor Biol. 1973 Nov 5;42(1):1-32
4760662
J Microsc. 1986 Oct;144(Pt 1):1-14
3632765
J Struct Biol. 2003 Aug;143(2):124-34
12972349
J Microsc. 1986 Jan;141(Pt 1):RP1-2
3514918
J Mol Biol. 1983 Jan 25;163(3):431-50
6339730
Naturwissenschaften. 1968 Jul;55(7):333-6
5678030
Ultramicroscopy. 1978;3(3):283-90
32653
Proc R Soc Lond B Biol Sci. 1972 Jul 25;182(1066):89-102
4403086
Methods Cell Biol. 2007;79:741-67
17327182
J Struct Biol. 1997 Dec;120(3):387-95
9441941
J Struct Biol. 2006 Jun;154(3):269-79
16621601
Curr Top Cell Regul. 1981;19:77-101
6460594