Data Mining in Bioinformatics

  • Xindong Wu
  • Lakhmi Jain
  • Jason T.L. Wang
  • Mohammed J. Zaki
  • Hannu T.T. Toivonen
  • Dennis Shasha

Part of the Advanced Information and Knowledge Processing book series (AI&KP)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Overview

    1. Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen, Dennis Shasha
      Pages 3-8
    2. Peter Bajcsy, Jiawei Han, Lei Liu, Jiong Yang
      Pages 9-39
  3. Sequence and Structure Alignment

    1. Cinzia Di Pietro, Alfredo Ferro, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa et al.
      Pages 43-57
    2. Kaizhong Zhang
      Pages 59-81
  4. Biological Data Mining

    1. Petteri Sevon, Hannu T. T. Toivonen, Päivi Onkamo
      Pages 105-126
    2. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff
      Pages 127-141
    3. Mukund Deshpande, Michihiro Kuramochi, George Karypis
      Pages 189-215
  5. Biological Data Management

    1. Roderic D. M. Page
      Pages 219-241
    2. Jignesh M. Patel, Donald P. Huddler, Laurie Hammel
      Pages 243-273
    3. Ambuj K. Singh
      Pages 275-296
  6. Back Matter
    Pages 297-340

About this book


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.


Alignment Markov chain XML bioinformatics biology calculus classification clustering computer data analysis data mining database microarray modeling protein

Editors and affiliations

  • Xindong Wu
  • Lakhmi Jain
  • Jason T.L. Wang
    • 1
  • Mohammed J. Zaki
    • 2
  • Hannu T.T. Toivonen
    • 3
  • Dennis Shasha
    • 4
  1. 1.New Jersey Institute of TechnologyUSA
  2. 2.Computer Science DepartmentRensselaer Polytechnic InstituteUSA
  3. 3.University of Helsinki and Nokia Research CenterHelsinki
  4. 4.New York UniversityUSA

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