Data Mining in Bioinformatics

✍ Scribed by Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen, Dennis Shasha (auth.), Xindong Wu, Lakhmi Jain, Jason T.L. Wang PhD, Mohammed J. Zaki PhD, Hannu T.T. Toivonen PhD, Dennis Shasha PhD (eds.)

Publisher: Springer-Verlag London
Year: 2005
Tongue: English
Leaves: 336
Series: Advanced Information and Knowledge Processing
Edition: 1
Category: Library

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✦ Synopsis

8. 1. 1 Protein Subcellular Location The life sciences have entered the post-genome era where the focus of biologicalresearchhasshiftedfromgenomesequencestoproteinfunctionality. Withwhole-genomedraftsofmouseandhumaninhand,scientistsareputting more and more e?ort into obtaining information about the entire proteome in a given cell type. The properties of a protein include its amino acid sequences, its expression levels under various developmental stages and in di?erenttissues,its3Dstructureandactivesites,itsfunctionalandstructural binding partners, and its subcellular location. Protein subcellular location is important for understanding protein function inside the cell. For example, the observation that the product of a gene is localized in mitochondria will support the hypothesis that this protein or gene is involved in energy metabolism. Proteins localized in the cytoskeleton are probably involved in intracellular tra?cking and support. The context of protein functionality is well represented by protein subcellular location. Proteins have various subcellular location patterns [250]. One major category of proteins is synthesized on free ribosomes in the cytoplasm. Soluble proteins remain in the cytoplasm after their synthesis and function as small factories catalyzing cellular metabolites. Other proteins that have a target signal in their sequences are directed to their target organelle (such as mitochondria) via posttranslational transport through the organelle membrane. Nuclear proteins are transferred through pores on the nuclear envelope to the nucleus and mostly function as regulators. The second major category of proteins is synthesized on endoplasmic reticulum(ER)-associated ribosomes and passes through the reticuloendothelial system, consisting of the ER and the Golgi apparatus.

✦ Table of Contents

Introduction to Data Mining in Bioinformatics....Pages 3-8
Survey of Biodata Analysis from a Data Mining Perspective....Pages 9-39
AntiClustAl: Multiple Sequence Alignment by Antipole Clustering....Pages 43-57
RNA Structure Comparison and Alignment....Pages 59-81
Piecewise Constant Modeling of Sequential Data Using Reversible Jump Markov Chain Monte Carlo....Pages 85-103
Gene Mapping by Pattern Discovery....Pages 105-126
Predicting Protein Folding Pathways....Pages 127-141
Data Mining Methods for a Systematics of Protein Subcellular Location....Pages 143-187
Mining Chemical Compounds....Pages 189-215
Phyloinformatics: Toward a Phylogenetic Database....Pages 219-241
Declarative and Efficient Querying on Protein Secondary Structures....Pages 243-273
Scalable Index Structures for Biological Data....Pages 275-296

✦ Subjects

Database Management; Programming Techniques; Information Systems Applications (incl.Internet); Data Structures; Data Storage Representation; Bioinformatics

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