Comparing the similarity of time-series gene expression using signal processing metrics

Journal of Biomedical Informatics

Volumn 34, Issue 6, 2001, Pages 396-405

  Butte, Atul J ^a   Bao, Ling ^a   Reis, Ben Y ^a   Watkins, Timothy W ^a   Kohane, Isaac S ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

Bioinformatics; Dynamics; Gene expression; Time series; Yeast

Indexed keywords

RNA;

ALGORITHM; ARTICLE; BIOMEDICINE; COMPARATIVE STUDY; CORRELATION COEFFICIENT; CORRELATION FUNCTION; DENSITY; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC COMPATIBILITY; GENETIC ENGINEERING; GENETIC TRAIT; HUMAN; MEASUREMENT; MEDICAL LITERATURE; NONHUMAN; POWER SPECTRUM; PRIORITY JOURNAL; SIGNAL PROCESSING; TECHNIQUE; TIME SERIES ANALYSIS;

EID: 0035552015     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1006/jbin.2002.1037     Document Type: Article

References (50)

1. Large-scale temporal gene expression mapping of central nervous system development
2. Differential regulation of circadian pacemaker output by separate clock genes in Drosophila
3. Problems associated with the study of cellular oscillations
4. A test case of correlation metric construction of a reaction pathway from measurements
5. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy
6. The transcriptional program in the response of human fibroblasts to serum
7. Gene expression profile of aging and its retardation by caloric restriction
8. Gene microarray identification of redox and mitochondrial elements that control resistance or sensitivity to apoptosis
9. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
10. Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation
11. How the host 'sees' pathogens: Global gene expression responses to infection
12. Systematic determination of genetic network architecture
13. Cluster analysis and display of genome-wide expression patterns
14. An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis
15. Large scale gene expression analysis of cholesterol-loaded macrophages
16. Genomic-scale gene expression profiling of normal and malignant immune cells
17. Reveal, a general reverse engineering algorithm for inference of genetic network architectures
18. Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in S. cerevisiae
19. Clustering gene expression patterns
20. Super-paramagnetic clustering of yeast gene expression profiles
21. Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters
22. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
23. Extracting knowledge from dynamics in gene expression
24. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
25. Transcriptional regulation and function during the human cell cycle
26. Global analysis of the genetic network controlling a bacterial cell cycle
27. Principal components analysis to summarize microarray experiments: Application to sporulation time series
28. Dynamic modeling of gene expression data
29. Transfer function analysis of autonomic regulation. I. Canine atrial rate response
30. Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes
31. Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2
32. Role of the putative zinc finger domain of Saccharomyces cerevisiae DNA polymerase epsilon in DNA replication and the S/M checkpoint pathway
33. Regulation of translation initiation by amino acids in eukaryotic cells
34. Oxidative stress induces neuronal death by recruiting a protease and phosphatase-gated mechanism
35. Differential ubiquitin-dependent degradation of the yeast apo-cytochrome c isozymes
36. An essential Saccharomyces cerevisiae single-stranded DNA binding protein is homologous to the large subunit of human RP-A
37. Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants
38. Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
39. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast
40. Genomic expression programs in the response of yeast cells to environmental changes
41. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock
42. The core meiotic transcriptome in budding yeasts
43. Temporal gene regulation during HIV-1 infection of human CD4+ T cells
44. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p
45. Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis
46. Microarray analysis and organization of circadian gene expression in Drosophila
47. Circadian regulation of gene expression systems in the Drosophila head