The current excitement in bioinformatics - Analysis of whole-genome expression data: How does it relate to protein structure and function?

Current Opinion in Structural Biology

Volumn 10, Issue 5, 2000, Pages 574-584

  Gerstein, Mark ^a   Jansen, Ronald ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION; DATA ANALYSIS; DATA BASE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION; INFORMATION SCIENCE; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW;

EID: 0033783651     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00134-2     Document Type: Review

References (76)

1. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization
2. Expression monitoring by hybridization to high-density oligonucleotide arrays
3. Characterization of the yeast transcriptome
4. Expression profiling using cDNA microarrays
5. Exploring the new world of the genome with DNA microarrays
6. High density synthetic oligonucleotide arrays
7. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression
8. The transcriptional program of sporulation in budding yeast
9. Exploring the metabolic and genetic control of gene expression on a genomic scale
10. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
11. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays
12. Genome-wide expression profiling in Escherichia coli K-12
13. A global profile of germ line gene expression in C. elegans
14. Microarray analysis of Drosophila development during metamorphosis
15. Gene expression profile of aging and its retardation by caloric restriction
16. The transcriptional program in the response of human fibroblasts to serum
17. Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis
18. A genome-wide transcriptional analysis of the mitotic cell cycle
19. Ratio-based decisions and the quantitative analysis of cDNA microarray images
20. Computational methods for the identification of differential and coordinated gene expression
21. Systematic management and analysis of yeast gene expression data
22. One-stop shop for microarray data
23. Cluster analysis and display of genome-wide expression patterns
24. Cluster analysis and data visualization of large-scale gene expression data
25. Knowledge-based analysis of microarray gene expression data by using support vector machines
26. Large-scale temporal gene expression mapping of central nervous system development
27. Exploring expression data: Identification and analysis of coexpressed genes
28. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
29. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
30. Systematic determination of genetic network architecture
31. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
32. Analysis of gene expression data using self-organizing maps
33. Clustering gene expression patterns
34. Principal component analysis to summarize microarray experiments: Application to sporulation time series
35. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
36. Systematic variation in gene expression patterns in human cancer cell lines
37. Analysis of gene expression microarrays for phenotype classification
38. Systems for categorizing functions of gene products
39. Genes and proteins of Escherichia coli K-12
40. MIPS: A database for genomes and protein sequences
41. The ENZYME database in 2000
42. The EcoCyc and MetaCyc databases
43. MPW: The metabolic pathways database
44. KEGG: Kyoto encyclopedia of genes and genomes
45. Gene ontology: Tool for the unification of biology
46. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
47. Measuring shifts in function and evolutionary opportunity using variability profiles: A case study of the globins
48. EUCLID: Automatic classification of proteins in functional classes by their database annotations
49. Moonlighting proteins
50. Characterization of a functional thrombin receptor. Issues and opportunities
51. Prediction of enzyme classification from protein sequence without the use of sequence similarity
52. Conserved clusters of functionally related genes in two bacterial genomes
53. Synexpression groups in eukaryotes
54. A combined algorithm for genome-wide prediction of protein function
55. Using Bayesian networks to analyze expression data
56. SCOP: A structural classification of proteins database
57. Assigning genomic sequences to CATH
58. Touring protein fold space with Dali/FSSP
59. Population statistics of protein structures: Lessons from structural classifications
60. The relation between the divergence of sequence and structure in proteins
61. Evolution of protein sequences and structures
62. Protein folds and functions
63. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
64. Analysis of the yeast transcriptome with structural and functional categories
65. Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census
66. Regulatory elements and expression profiles
67. Predicting gene regulatory elements in silico on a genomic scale
68. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
69. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
70. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
71. The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): Comprehensive resources for the organization and comparison of model organism protein information
72. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
73. Genome-wide analysis relating expression level with protein subcellular organization
74. A Bayesian system integrating expression data with sequence patterns for localizing proteins: Comprehensive application to the yeast genome
75. Dissecting the regulatory circuitry of a eukaryotic genome