Algorithms for high-density oligonucleotide array
- PMID: 12833666
Algorithms for high-density oligonucleotide array
Abstract
As a global gene expression-monitoring tool, high-density oligonucleotide arrays (HDAs), accelerate biological and drug discovery processes. Computational considerations affect several key issues, from array design and accurate gene expression level determination to various aspects of the biological analysis of cell functions and gene networks. This review highlights recent progress in ideas and algorithms that are specific to HDAs. Replacing a large number of specific 'mismatch' oligonucleotides by a small number of general noise control oligonucleotides and using dynamic probe-to-gene mapping were some of the ideas proposed. Several novel mismatch-free probe-to-gene condensation algorithms have demonstrated the ability to take advantage of such designs, and provide higher density and equivalent or better calculation accuracy than previous algorithms. Algorithms to be developed in the future should significantly increase both the quality and quantity of information revealed by a single array; therefore, a single array containing the whole mammalian genome or even multiple genomes could soon become a standard tool.
Similar articles
-
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.Bioinformatics. 2004 Nov 1;20(16):2534-44. doi: 10.1093/bioinformatics/bth280. Epub 2004 Apr 29. Bioinformatics. 2004. PMID: 15117752
-
Resource and hardware options for microarray-based experimentation.Brief Funct Genomic Proteomic. 2003 Apr;2(1):7-20. doi: 10.1093/bfgp/2.1.7. Brief Funct Genomic Proteomic. 2003. PMID: 15239939 Review.
-
Platform technologies for microarray analysis.Brief Funct Genomic Proteomic. 2003 Apr;2(1):4-6. doi: 10.1093/bfgp/2.1.4. Brief Funct Genomic Proteomic. 2003. PMID: 15239938 No abstract available.
-
High-density genechip oligonucleotide probe arrays.Adv Biochem Eng Biotechnol. 2002;77:21-42. doi: 10.1007/3-540-45713-5_2. Adv Biochem Eng Biotechnol. 2002. PMID: 12227735 Review.
-
Growing applications and advancements in microarray technology and analysis tools.Cell Biochem Biophys. 2005;43(1):149-66. doi: 10.1385/CBB:43:1:149. Cell Biochem Biophys. 2005. PMID: 16043891 Review.
Cited by
-
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.BMC Bioinformatics. 2004 Apr 20;5:42. doi: 10.1186/1471-2105-5-42. BMC Bioinformatics. 2004. PMID: 15099405 Free PMC article.
-
Development of low-density oligonucleotide microarrays for detecting mutations causing Wilson's disease.Indian J Med Res. 2015 Feb;141(2):175-86. doi: 10.4103/0971-5916.155548. Indian J Med Res. 2015. PMID: 25900953 Free PMC article.
-
Framework for Parallel Preprocessing of Microarray Data Using Hadoop.Adv Bioinformatics. 2018 Mar 29;2018:9391635. doi: 10.1155/2018/9391635. eCollection 2018. Adv Bioinformatics. 2018. PMID: 29796018 Free PMC article.
-
In vivo transcriptional profiling of Plasmodium falciparum.Malar J. 2004 Aug 5;3:30. doi: 10.1186/1475-2875-3-30. Malar J. 2004. PMID: 15296511 Free PMC article.
-
Algorithm-driven artifacts in median polish summarization of microarray data.BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553. BMC Bioinformatics. 2010. PMID: 21070630 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Other Literature Sources
Research Materials