Computational analysis of microarray gene expression profiles: Clustering, classification, and beyond

Chemometrics and Intelligent Laboratory Systems

Volumn 62, Issue 2, 2002, Pages 199-216

  Liang, Jie ^a   Kachalo, Seman ^a  

^a University of Illinois at Chicago   (United States)

Author keywords

Clustering; Computational analysis; Microarray gene expression profiles

Indexed keywords

ALGORITHM; ARTICLE; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; GENE SEQUENCE; GENE STRUCTURE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL;

EID: 0037188461     PISSN: 01697439     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-7439(02)00014-X     Document Type: Article

References (60)

1. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
2. Distinctive gene expression patterns in human mammary epithelial cells and breast cancers
3. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
4. Classification of small cell lung cancer and pulmonary carcinoid by gene expression profiles
5. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
6. Expression monitoring by hybridization to high-density oligonucleotide arrays
7. Use of a cDNA microarray to analyse gene expression patterns in human cancer
8. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array
9. Genome-wide expression monitoring in Saccharomyces cerevisiae
10. Exploring the metabolic and genetic control of gene expression on a genomic scal
11. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
12. Cluster analysis and data visualization of large-scale gene expression data
13. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
14. Cluster analysis and display of genome-wide expression patterns
15. Large-scale temporal gene expression mapping of central nervous system development
16. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
17. Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
18. Assessing reliability of gene clusters from gene expression data
19. Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments
20. A generalized inverse for matrices
21. An improved training algorithm for support vector machines
22. Fast training of support vector machines using sequential minimal optimization
23. Tissue classification with gene expression profiles
24. Knowledge-based analysis of microarray gene expression data by using support vector machines
25. Classification of biologically active compounds by support vector machines
26. Protein sorting signals and prediction of subcellular localization
27. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
28. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
29. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
30. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
31. Extracting protein alignment models from the sequence database
32. Bayesian adaptive alignment and inference
33. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
34. Finding regulatory elements using joint likelihoods for sequence and expression profile data
35. BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
36. Bayesian inference on biopolymer models
37. A gene expression database for the molecular pharmacology of cancer
38. An information-intensive approach to the molecular pharmacology of cancer
39. A protein expression database for the molecular pharmacology of cancer
40. Mining the NCI anticancer drug discovery databases: Genetic function approximation for the qsar study of anticancer ellipticine analogues
41. Mining and visualizing large anticancer drug discovery databases
42. Characterization of anticancer agents by their growth inhibitory activity and relationships to mechanism of action and structure