Interval based fuzzy systems for identification of important genes from microarray gene expression data: Application to carcinogenic development.
In the present article, we develop two interval based fuzzy systems for identification of some possible genes mediating the carcinogenic development in various tissues. The methodology involves dimensionality reduction, classifying the genes through incorporation of the notion of linguistic fuzzy sets low, medium and high, and finally selection of some possible genes mediating a particular disease, obtained by a rule generation/grouping technique. The effectiveness of the proposed methodology, is demonstrated using five microarray gene expression datasets dealing with human lung, colon, sarcoma, breast cancer and leukemia. Moreover, the superior capability of the methodology in selecting important genes, over five other existing gene selection methods, viz., Significance Analysis of Microarrays (SAM), Signal-to-Noise Ratio (SNR), Neighborhood analysis (NA), Bayesian Regularization (BR) and Data-adaptive (DA) is demonstrated, in terms of the enrichment of each GO category of the important genes based on P-values. The results are appropriately validated by earlier investigations, gene expression profiles and t-test. The proposed methodology has been able to select genes that are more biologically significant in mediating the development of a disease than those obtained by the others.
De
Rajat K
RK
Indian Statistical Institute, Kolkata, West Bengal, India. rajat@isical.ac.in
Ghosh
Anupam
A
D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D017143:Fuzzy Logic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results