A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver

Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correlation that exists between them. On the other hand, some multivariate feature selection methods are proposed for biomarker discovery. Provided with various biomarker discovery methods, how to choose the most suitable method for a specific dataset becomes a problem. In this paper, we present a framework for comparison of potential biomarker discovery methods: three methods that stem from different theories are compared by how stable they are and how well they can improve the classification accuracy. The three methods we have considered are: Significance Analysis of Microarrays (SAM) which identifies the differentially expressed genes; minimum Redundancy Maximum Relevance (mRMR) based on information theory; and Characteristic Direction (GeoDE) inspired by a graphical perspective. Tested on the gene expression data from two experiments exposing the cod fish to two different toxicants (MeHg and PCB 153), different methods stand out in different cases, so a decision upon the most suitable method should be made based on the dataset under study and the research interest

A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver

Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individually, disregarding the correlation that exists between them. On the other hand, some multivariate feature selection methods are proposed for biomarker discovery. Provided with various biomarker discovery methods, how to choose the most suitable method for a specific dataset becomes a problem. In this paper, we present a framework for comparison of potential biomarker discovery methods: three methods that stem from different theories are compared by how stable they are and how well they can improve the classification accuracy. The three methods we have considered are: Significance Analysis of Microarrays (SAM) which identifies the differentially expressed genes; minimum Redundancy Maximum Relevance (mRMR) based on information theory; and Characteristic Direction (GeoDE) inspired by a graphical perspective. Tested on the gene expression data from two experiments exposing the cod fish to two different toxicants (MeHg and PCB 153), different methods stand out in different cases, so a decision upon the most suitable method should be made based on the dataset under study and the research interest

Inter-population variability and character description in the sponge-associated Haplosyllis spongicola complex (Polychaeta: Syllidae)

18 páginas, 17 figuras, 3 tablas.Haplosyllis spongicola is probably the most representative symbiotic syllid harboured by sponges and has been widely reported from tropical, subtropical and temperate seas. Its external morphology seems to be very well adapted for its life-style, with all chaetae being simple and having two small teeth and a large main fang. However, the species has been the subject of a long-lasting taxonomic controversy, which gave rise to more than 15 synonymies, with hundreds of records worldwide. The present paper is based on the study of more than 28 populations obtained from around the world. These populations have been carefully analysed using different approaches (morphometry, morphology and biology). As a consequence, the existence of a pseudo-sibling species-complex within the socalled cosmopolitan H. spongicola has been revealed. The most relevant characters (as well as their variability) that will allow a future identification of the species involved in the complex are fully described, illustrated and analysed.The study has been partly financed by a research contract between the CEAB (CSIC) and French company CREOCEAN and has been partly sponsored by TOTAL. This paper is a contribution to the research project INTAS–OPEN–97–0916.Peer reviewe