PUBLICATION
Zebrafish spotted-microarray for genome-wide expression profiling experiments: data acquisition and analysis
- Authors
- Lam, S.H., Krishna Murthy Karuturi, R., and Gong, Z.
- ID
- ZDB-PUB-090424-6
- Date
- 2009
- Source
- Methods in molecular biology (Clifton, N.J.) 546: 197-226 (Chapter)
- Registered Authors
- Gong, Zhiyuan, Lam, Siew Hong
- Keywords
- Zebrafish spotted-microarray, Transcriptome, Gene expression profiling, Data acquisition, Data processing, Data analysis, Data mining
- MeSH Terms
-
- Algorithms
- Animals
- Databases, Genetic
- Gene Expression Profiling/methods*
- Gene Regulatory Networks
- Genes
- Image Processing, Computer-Assisted/methods
- Oligonucleotide Array Sequence Analysis/methods*
- Pattern Recognition, Automated/methods
- Statistics as Topic/methods*
- Time Factors
- Zebrafish/genetics*
- PubMed
- 19378106 Full text @ Meth. Mol. Biol.
Citation
Lam, S.H., Krishna Murthy Karuturi, R., and Gong, Z. (2009) Zebrafish spotted-microarray for genome-wide expression profiling experiments: data acquisition and analysis. Methods in molecular biology (Clifton, N.J.). 546:197-226.
Abstract
In expression microarray experiments, post-hybridization procedures involving data acquisition and analysis are mainly computational and hence are described as "dry-lab procedures." The aim of these procedures is to acquire the fluorescent signals representing the relative abundance of tens of thousands of RNA species in samples with biological interest, and transform them into meaningful data with biological significance. These procedures begin with image and data acquisition followed by data normalization and processing, and thereafter primary and secondary data analyses. Although the actual data analysis is carried out after the wet-lab procedures, the strategy for data analysis should be planned prior to wet lab procedures when designing the experiment, to ensure effective downstream data handling and interpretation. Principal steps and advisory notes for acquiring, processing, and analyzing data that are commonly associated with various zebrafish expression profiling experiments are described in this chapter.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping