Factor Analysis
Data Base

Factor Analysis in Genetics and Molecular Biology

1. D. Bharanidharan and N. Gautham "Principal component analysis of DNA oligonucleotide structural data" Biochemical and Biophysical Research Communications 340, 4, 1229-1237 (2006)
2. J.M. Caddick, A.C. Hilton, R.A. Armstrong, P.A. Lambert, T. Worthington, and T.S.J. Elliott "Description and critical appraisal of principal components analysis (PCA) methodology applied to pulsed-field gel electrophoresis profiles of methicillin-resistant Staphylococcus aureus isolates" Journal of Microbiological Methods 65, 1, 87-95 (2006)
3. A.P.G. Crijns, F. Gerbens, A.E.D. Plantinga, G.J. Meersma, S. de Jong, R.M.W. Hofstra, E.G.E. de Vries, A.G.J. van der Zee, G.H. de Bock, and G.J. te Meerman "A biological question and a balanced (orthogonal) design: the ingredients to efficiently analyze two-color microarrays with Confirmatory Factor Analysis" BMC Genomics 7, 232 (2006)
4. J. Fostel, R. Boneva, and Lloyd "Exploration of the gene expression correlates of chronic unexplained fatigue using factor analysis" Pharmacogenomics 7, 3, 441-454 (2006)
5. G. Hasler, D. Kazuba, and D.L.Murphy "Factor analysis of obsessive-compulsive disorder YBOCS-SC symptoms and association with 5-HTTLPR SERT polymorphism." American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics 141, 4, 403-408 (2006)
6. R. Kustra, Romy Shioda, and Mu Zhu "A factor analysis model for functional genomics" BMC Bioinformatics 7, 216 (2006)
7. J.C. Roden, B.W. King, D. Trout, A. Mortazavi, B.J. Wold, and C.E. Hart "Mining gene expression data by interpreting principal components" BMC Bioinformatics 7, 194 (2006)
8. M.J. van der Werf, B. Pieterse, N. van Luijk, F. Schuren, B. van der Werff-van der Vat, K. Overkamp and R.H. Jellema "Multivariate analysis of microarray data by principal component discriminant analysis: prioritizing relevant transcripts linked to the degradation of different carbohydrates in Pseudomonas putida S12" Microbiology 152, 1, 257-272 (2006)

1. H. Hamzehzarghani, A.C. Kushalappa, Y. Dion, S. Rioux, A. Comeau, V. Yaylayan, W.D. Marshall and D.E. Mather "Metabolic profiling and factor analysis to discriminate quantitative resistance in wheat cultivars against fusarium head blight" Physiological and Molecular Plant Pathology 66, 4, 119-133 (2005)
2. L. Lancashire, O. Schmid, H. Shah, and G. Ball "Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis" Bioinformatics 21, 10, 2191-2199 (2005)
3. G. Liu, M.T. Swihart, and S. Neelamegham "Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling" Bioinformatics 21, 7, 1194-1202 (2005)
4. Y. Liu, M.P. Vincenti, and H. Yokota "Principal component analysis for predicting transcription-factor binding motifs from array-derived data" BMC Bioinformatics 6, 276 (2005)
5. Z. Liu, D. Chen, and H. Bensmail "Gene expression data classification with Kernel principal component analysis" Journal of Biomedicine and Biotechnology 2005, 2, 155-159 (2005)
6. K. Meyer and M. Kirkpatrick "Restricted maximum likelihood estimation of genetic principal components and smoothed covariance matrices" Genetic Selection Evolution 37, 1, 1-30 (2005)
7. Y. Mu, P.H. Nguyen and G. Stock "Energy landscape of a small peptide revealed by dihedral angle principal component analysis" Proteins: Structure, Function, and Bioinformatics 58, 1, 45-52 (2005)
8. Y. Pittelkow and S.R. Wilson "Use of principal component analysis and the GE-biplot for the graphical exploration of gene expression data" Biometrics 61, 2, 630-634 (2005)
9. P.L. Roubertoux, P-V. Guillot, S. Mortaud, M. Pratte, M. Jamon, C. Cohen-Salmon and S. Tordjman "Attack behaviors in mice: From factorial structure to quantitative trait loci mapping" European Journal of Pharmacology 526, 1-3, 172-185 (2005)
10. A.A. Sharov, D.B. Dudekula and M.S.H. Ko "A web-based tool for principal component and significance analysis of microarray data" Bioinformatics 21, 10, 2548-2549 (2005)
11. A. Wang and E.A. Gehan "Gene selection for microarray data analysis using principal component analysis" Statistics in Medicine 24, 13, 2069-2087 (2005)
12. T. Yu and K-C. Li "Inference of transcriptional regulatory network by two-stage constrained space factor analysis" Bioinformatics 21, 21, 4033-4038 (2005)

1. V. Barra "Analysis of gene expression data using functional principal components" Computer Methods and Programs in Biomedicine 75, 1, 1-9 (2004)
2. C.C.C.R. de Carvalho and M.M.R. da Fonseca "Principal component analysis applied to bacterial cell behaviour in the presence of organic solvents" Biocatalysis and Biotransformation 22, 3, 203-214 (2004)
3. M. Girolami and R. Breitling "Biologically valid linear factor models of gene expression" Bioinformatics 20, 17, 3021-3033 (2004)
4. B.D. Horne and N.J. Camp "Principal component analysis for selection of optimal SNP-sets that capture intragenic genetic variation" Genetic Epidemiology 26, 1, 11-21 (2004)
5. M. Hubert and S. Engelen "Robust PCA and classification in biosciences" Bioinformatics 20, 11, 1728-1736 (2004)
6. A. Ishikawa and T. Namikawa "Mapping major quantitative trait loci for postnatal growth in an intersubspecific backcross between C57BL/6J and Philippine wild mice by using principal component analysis" Genes & Genetic Systems 79, 1, 27-39 (2004)
7. W-C. Lee and Y-H Shu "Mapping Disease-Susceptibility Genes in Admixed Populations Using Interval Principal Component Tests" Behavior Genetics 25, 34, 5, 525-531 (2004)
8. Z.R. Li, X. Han and G.R. Liu "Protein designability analysis in sequence principal component space using 2D lattice model" Computer Methods and Programs in Biomedicine 76, 1, 21-29 (2004)
9. Z. Lin and R.B. Altman "Finding Haplotype Tagging SNPs by Use of Principal Components Analysis" American Journal of Human Genetics 75, 5, 850-861 (2004)
10. R. Stoyanova, T.D. Querec, T.R. Brown and C. Patriotis "Normalization of single-channel DNA array data by principal component analysis" Bioinformatics 20, 11, 1772-1784 (2004)
11. C. Toker and M.I. Cagirgan "The use of phenotypic correlations and factor analysis in determining characters for grain yield selection in chickpea (Cicer arietinum L.)" Hereditas 140, 3, 226-228 (2004)
12. M. Wang, S. Ahrne, M. Antonsson, and G. Molin "T-RFLP combined with principal component analysis and 16S rRNA gene sequencing: an effective strategy for comparison of fecal microbiota in infants of different ages" Journal of Microbiological Methods 59, 1, 53-69 (2004)

1. A. Ben-Hur and I. Guyon "Detecting stable clusters using principal component analysis" In: Functional Genomics, Methods and Protocols. Series: Methods in Molecular Biology 224, 159-182 (Humana Press, Totowa, NJ, USA, 2003)
2. S. Bicciato, A. Luchini and C. Di Bello "PCA disjoint models for multiclass cancer analysis using gene expression data" Bioinformatics 19, 5, 571-578 (2003)
3. N. Delaunay-Bertoncini, V. Pichon, and M.C. Hennion "Experimental comparison of three monoclonal antibodies for the class-selective immunoextraction of triazines. Correlation with molecular modeling and principal component analysis studies" Journal of Chromatography A 999, 1-2, 3-15 (2003)
4. E.D. Dorn, G.D. McDonald, M.C. Storrie-Lombardi and K.H. Nealson "Principal component analysis and neural networks for detection of amino acid biosignatures" Icarus 166, 2, 403-409 (2003)
5. E. Marengo, R. Leardi, E. Robotti, P.G. Righetti, F. Antonucci, and D. Cecconi "Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics" Journal of Proteome Research 2, 4, 351-360 (2003)
6. L.E. Peterson "Partitioning large-sample microarray-based gene expression profiles using principal components analysis" Computer Methods and Programs in Biomedicine 70, 2, 107-119 (2003)
7. R.L. Sapra and S.K. Lal "A strategy for selecting diverse accessions using Principal Component Analysis from a large germplasm collection of soybean" Plant Genetic Resources 1, 2/3, 151-156 (2003)
8. T. Tsunoda, Y. Koh, F. Koizumi, S. Tsukiyama, H. Ueda, F. Taguchi, H. Yamaue, N. Saijo, and K. Nishio "Differential gene expression profiles and identification of the genes relevant to clinicopathologic factors in colorectal cancer selected by cDNA array method in combination with principal component analysis" International Journal of Oncology 23, 1, 49-59 (2003)
9. B.A. Wagner, M.D. Salman, D.A. Dargatz, P.S. Morley, T.E. Wittum and T.J. Keefe "Factor analysis of minimum-inhibitory concentrations for Escherichia coli isolated from feedlot cattle to model relationships among antimicrobial-resistance outcomes" Preventive Veterinary Medicine 57, 3, 127-139 (2003)
10. B. Wu, B. Quilot, J. Kervella, M. Génard and S. Li "Analysis of genotypic variation of sugar and acid contents in peaches and nectarines through the Principle Component Analysis" Euphytica 132, 3, 375-384 (2003)

1. K. Chase, D.R. Carrier, F.R. Adler, T. Jarvik, E.A. Ostrander, T.D. Lorentzen and K.G. Lark "Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton" Proceedings of the National Academy of Sciences 99, 15, 9930-9935 (2002)
2. P. de B. Harrington, K.J. Voorhees, F. Basile and A.D. Hendricker "Validation using sensitivity and target transform factor analyses of neuralnetwork models for classifying bacteria from mass spectra" Journal of the American Society for Mass Spectrometry 13, 1, 10-21 (2002)
3. M. Hörnquist, J. Hertz and M. Wahde "Effective dimensionality of large-scale expression data using principal component analysis" Biosystems 65, 2-3, 147-156 (2002)
4. D. Houle, J. Mezey and P. Galpern "Interpretation of the results of common principal components analyses" Evolution. International Journal of Organic Evolution 56, 3, 433-440 (2002)
5. J. Landgrebe, W. Wurst and G. Welzl "Permutation-validated principal components analysis of microarray data" Genome Biology 3, 4, research0019 (2002)
6. M. Mähler, C. Most, S. Schmidtke, J.P. Sundberg, R. Li, H.J. Hedrich and G.A. Churchill "Genetics of Colitis Susceptibility in IL-10-Deficient Mice: Backcross versus F2 Results Contrasted by Principal Component Analysis" Genomics 80, 3, 274-282 (2002)
7. F. Martin, M-S. Kim, B. Hovemann and E. Alcorta "Factor Analysis of Olfactory Responses in Drosophila melanogaster Enhancer-Trap Lines as a Method for Ascertaining Common Reception Components for Different Odorants" Behavior Genetics 32, 1, 79-88 (2002)
8. S. Murata, K. Mochizuki, T. Nakazawa, T. Kondo, N. Nakamura, H. Yamashita, Y. Urata, T. Ashihara and R. Katoh "Detection of underlying characteristics of nuclear chromatin patterns of thyroid tumor cells using texture and factor analyses" Cytometry 49, 3, 91-95 (2002)
9. L.E. Peterson "Factor analysis of cluster-specific gene expression levels from cDNA microarrays" Computer Methods and Programs in Biomedicine 69, 3, 179-188 (2002)
10. K.J. Preacher and R.C. MacCallum "Exploratory Factor Analysis in Behavior Genetics Research: Factor Recovery with Small Sample Sizes" Behavior Genetics 32, 2, 153-161 (2002)

1. S. Brosse, J.L. Giraudel and S. Lek "Utilisation of non-supervised neural networks and principal component analysis to study fish assemblages" Ecological Modelling 146, 1-3, 159-166 (2001)
2. M. Crescenzi and A Giuliani "The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data" FEBS Letters 507, 1, 114-118 (2001)
3. S.L. Dollhopf, S.A. Hashsham and J.M. Tiedje "Interpreting 16S rDNA T-RFLP Data: Application of Self-Organizing Maps and Principal Component Analysis to Describe Community Dynamics and Convergence" Microbial Ecology 42, 4, 495-505 (2001)
4. K.L. Moser, C.M. Jedrey, D. Conti, J.H. Schick, C. Gray-McGuire, S.K. Nath, D. Daley and J.M. Olson "Comparison of three methods for obtaining principal components from family data in genetic analysis of complex disease" Genetic Epidemiology 21, Suppl.1, S726-S731 (2001)
5. N. Ota and D.A. Agard "Enzyme specificity under dynamic control II: Principal component analysis of a-lytic protease using global and local solvent boundary conditions" Protein Science 10, 7, 1403-1414 (2001)
6. T.H. Reijmers, R. Wehrens and L.M.C. Buydens "Circular effects in representations of an RNA nucleotides data set in relation with principal components analysis" Chemometrics and Intelligent Laboratory Systems 56, 2, 61-71 (2001)
7. R. Takors, M. Gerigk, H. Paschold and C. Wandrey "Principal-component analysis for microbial L-phenylalanine production" Bioprocess and Biosystems Engineering 24, 2, 93-99 (2001)
8. A.J. de la Vega and S.C. Chapman "Genotype by environment interaction and indirect selection for yield in sunflower - II. Three-mode principal component analysis of oil and biomass yield across environments in Argentina" Field Crops Research 72, 1, 39-50 (2001)
9. K.Y. Yeung and W.L. Ruzzo "Principal component analysis for clustering gene expression data" Bioinformatics 17, 9, 763-774 (2001)

1. A. Gogos, D. Jantz, S. Sentürker, D. Richardson, M. Dizdaroglu and N.D. Clarke "Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: An experimental test using DNA glycosylase homologs" Proteins: Structure, Function, and Genetics 40, 1, 98-105 (2000)
2. S. Raychaudhuri, J.M. Stuart and R.B. Altman "Principal components analysis to summarize microarray experiments: application to sporulation time series" Pacific Symposium on Biocomputing 5, 455-466 (2000)
3. M.J.H. Rietveld, G.C.M. van Baal, C.V. Dolan and D.I. Boomsma "Genetic Factor Analyses of Specific Cognitive Abilities in 5-Year-Old Dutch Children" Behavior Genetics 30, 1, 29-40 (2000)
4. L. Xue and J. Bajorath "Molecular descriptors for effective classification of biologically active compounds based on principal component analysis identified by a genetic algorithm" Journal of Chemical Information and Computer Sciences 40, 3, 801-809 (2000)

1. R. Kazmierkiewicz, C. Czaplewski, B. Lammek and J. Ciarkowski "Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories" Journal of Computer-Aided Molecular Design 13, 1, 21-33 (1999)
2. J.M. Koshi and W.J. Bruno "Major structural determinants of transmembrane proteins identified by principal component analysis" Proteins: Structure, Function, and Genetics 34, 3, 333-340 (1999)
3. J. Otsuka, N. Kikuchi and S. Kojima "Similarity relations of DNA and RNA polymerases investigated by the principal component analysis of amino acid sequences" Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1434, 2, 221-247 (1999)
4. J. Ott and D. Rabinowitz "A principal-components approach based on heritability for combining phenotype information" Human Heredity 49, 2, 106-111 (1999)
5. M. Scholz, S. Schmidt, S. Loesgen and H. Bickeboller "Analysis of principal component based quantitative phenotypes for alcoholism" Genetic Epidemiology 17, Suppl. 1, S313-S318 (1999)
6. P. Wikström, A-C. Andersson and M. Forsman "Biomonitoring complex microbial communities using random amplified polymorphic DNA and principal component analysis" FEMS Microbiology Ecology 28, 2, 131-139 (1999)

1. H-P. Piepho "Empirical best linear unbiased prediction in cultivar trials using factor-analytic variance-covariance structures" TAG Theoretical and Applied Genetics 97, 1-2, 195 - 201 (1998)

1. M. Teitelman and F.H. Eeckman "Principal component analysis and large-scale correlations in non-coding sequences of human DNA" Journal of Computational Biology 3, 4, 573-576 (1996)

1. F. Calafell and J. Bertranpetit "Principal component analysis of gene frequencies and the origin of Basques" American Journal of Physical Anthropology 93, 2, 201-215 (1994)

1. J. Taylor and C.S. Giometti "Use of principal components analysis for mutation detection with two-dimensional electrophoresis protein separations" Electrophoresis 13, 3, 162-168 (1992)

1. L.L. Vasil'eva and L.N. Trut "[The use of the method of principal components for phenogenetic analysis of the integral domestication trait]" Genetika 26, 3, 516-524 (1990)

1. P.M. Kroonenberg and K.E. Basford "An investigation of multi-attribute genotype response across environments using three-mode principal component analysis" Euphytica 44, 1-2, 109-123 (1989)

1. A.C. Heath, R. Jardine, L.J. Eaves and N.G. Martin "The genetic structure of personality I. Phenotypic factor structure of the EPQ in an Australian sample" Personality and Individual Differences 9, 1, 59-67 (1988)
2. M. Sieber, A.E. Freeman and P.N. Hinz "Comparison between factor analysis from a phenotypic and genetic correlation matrix using linear type traits of Holstein dairy cows" Journal of Dairy Science 71, 2, 477-484 (1988)

1. M. Joncas, S. Michaud, J.P. Carmichael and M.C. Lavoie "Detection of false-positives among total and fecal coliform counts by factorial analysis of correspondence" Applied and Environmental Microbiology 49, 1, 229-231 (1985)

1. G.V.S. Rao and R.S. Paroda "Factor analysis in clusterbean (Cyamopsis tetragonoloba (L.) Taub)" TAG Theoretical and Applied Genetics 62, 3, 273-276 (1982)

1. M.S. Eppel' "[Factor analysis of immunogenetic data]" Molecularnaya Biologia (Moscow) 15, 1, 96-102 (1981)

1. B.R. Murty, V. Arunachalam and O.P. Jain "Factor analysis in relation to breeding system" Genetica 41, 1, 179-189 (1970)