Aliasing in gene feature detection by projective methods.
Because of measurements obtained under limited experimental conditions or time points compared to the presence of many genes, also known as the "large dimension, small sample size" problem, dimensionality reduction techniques are a common practice in statistical bioinformatics involving microarray analysis. However, in order to improve the performance of reverse engineering and statistical inference procedures aimed to estimate gene-gene connectivity links, some kind of regularization is usually needed to reduce the overall data complexities, together with ad hoc feature selection to uncover biologically relevant gene associations. The paper deals with feature selection by projective methods; in particular, it addresses some issues: Can the impact of noise on the data be limited by shrinkage or de-noising? How can complexity from convoluted dynamics associated with microarray measurements be discounted? In modeling such data, how to deal with over-parametrization, and control it? The problem of aliasing is then discussed and classified into two categories according to the trade-off between biological relevance and noise, and finally reported in analytical form via subspace analysis.
Capobianco
Enrico
E
CRS4 Bioinformatics Laboratory, Technology Park of Sardinia, Localita' Piscinamanna Bldg. 3, 09010 Pula (Cagliari), Italy. ecapob@crs4.it
D000465:Algorithms; D016477:Artifacts; D016000:Cluster Analysis; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
D020543:Proteome