Threshold selection in gene co-expression networks using spectral graph theory techniques

BMC Bioinformatics

Volumn 10, Issue SUPPL. 11, 2009, Pages

  Perkins, Andy D ^a   Langston, Michael A ^b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b University of Tennessee Knoxville   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; CLUSTERING ALGORITHMS; COMPUTATION THEORY; EIGENVALUES AND EIGENFUNCTIONS; GENES; HIGH PASS FILTERS; LINEAR TRANSFORMATIONS; YEAST;

CO-EXPRESSION NETWORKS; CONSERVATIVE APPROACHES; EIGENVALUES AND EIGENVECTORS; GENE-GENE RELATIONSHIPS; MEASURE OF SIMILARITIES; SPECTRAL CLUSTERING METHODS; SPECTRAL GRAPH THEORY; STATISTICAL SIGNIFICANCE;

GRAPH THEORY;

ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; COMMUNITY STRUCTURE; CONTROLLED STUDY; GENE EXPRESSION; GENETIC SELECTION; HUMAN; MICROARRAY ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; REFERENCE VALUE; SACCHAROMYCES CEREVISIAE;

HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

EID: 70449448956     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S11-S4     Document Type: Article

References (26)

1. Wolfe CJ, Kohane IS, Butte AJ. Systematic survey revals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics 2005, 6(79). 1239911, 16162296.
2. Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ. Construction, visualization, and clustering of transcription networks from microarray expression data. PLoS Computational Biology 2007, 3(10):e206.
3. Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Cunto FD. Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Computational Biology 2008, 4(3):e1000043. 2268251, 18369433, 10.1371/journal.pcbi.1000043.
4. Butte AJ, Tamayo P, Slonim D, Golub TR, Kohane IS. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America 2000, 97(22):12182-12186. 17315, 11027309, 10.1073/pnas.220392197.
5. Voy BH, Scharff JA, Perkins AD, Saxton AM, Borate B, Chesler EJ, Branstetter LK, Langston MA. Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Computational Biology 2006, 2(7):e89. 1513268, 16854212, 10.1371/journal.pcbi.0020089.
6. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14:1085-1094. 10.1101/gr.1910904, 15173114, 419787.
7. Moriyama M, Hoshida Y, Otsuka M, Nishimura S, Kato N, Goto T, Taniguchi H, Shiratori Y, Seki N, Omata M. Relevance network between chemosensitivity and transcriptome in human hepatoma cells. Molecular Cancer Therapeutics 2003, 2:199-205.
8. Chung FRK. Spectral Graph Theory. Regional Conference Series in Mathematics, Providence: American Mathematical Society 1994, 92.
9. Alpert CJ, Kahng AB, Yao SZ. Spectral partitioning with multiple eigenvectors. Discrete Applied Mathematics 1999, 90(1-3):3-26.
10. Ding CHQ, He X, Zha H. A spectral method to separate disconnected and nearly-disconnected web graph components. Proceedings of the Seventh ACM International Conference on Knowledge Discovery and Data Mining: 26-29 August 2001; San Francisco 2001,
11. Ng AY, Jordan MI, Weiss Y. On spectral clustering: analysis and an algorithm. Advances in Neural and Information Processing Systems: 3-8 December 2001; Vancouver 2001,
12. Ruan J, Zhang W. Identifying network communities with a high resolution. Physical Review E 2008, 77(016104).
13. Perkins AD. Addressing challenges in a graph-based analysis of high-throughput biological data. PhD thesis 2008, University of Tennessee, Department of Electrical Engineering and Computer Science.
14. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccaromyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 1998, 9(12):3273-3297. 25624, 9843569.
15. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(16):6062-6067. 395923, 15075390, 10.1073/pnas.0400782101.
16. Shi J, Malik J. Normalized cuts and image segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2000, 22(8):888-905.
17. Chesler EJ, Langston MA. Combinatorial genetic regulatory network analysis tools for high throughput transcriptomic data. RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics: 2-4 December 2005; San Diego 2005,
18. Garey MR, Johnson DS. Computers and Intractability: A Guide to the Theory of NP-Completeness 1979, New York: W. H. Freeman.
19. Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson DK, Zhou J. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics 2007, 8:299. 2212665, 17697349, 10.1186/1471-2105-8-299.
20. Borate B. Comparative Analysis of Thresholding Algorithms for Microarray-derived Gene Correlation Matrices. Master's thesis 2008, The University of Tennessee.
21. Lai LC, Kosorukoff AL, Burke PV, Kwast KE. Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae. Eukaryotic Cell 2006, 5(9):1468-1489. 1563586, 16963631, 10.1128/EC.00107-06.
22. SGD Project Saccharomyces Genome Database. , http://www.yeastgenome.org
23. Newman MEJ, Girvan M. Finding and evaluating comunity struture in networks. Physical Review E 2004, 69(026113).
24. R Development Core Team R: A Language and Environment for Statistical Computing 2008, R Foundation for Statistical Computing, Vienna, Austria.
25. Gautier L, Cope L, Bolstad BM, Irizarry RA. affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20(3):307-315. 10.1093/bioinformatics/btg405, 14960456.
26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 2004, 5:R80. 545600, 15461798, 10.1186/gb-2004-5-10-r80.