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Computational Text Analysisfor functional genomics and bioinformatics$
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Soumya Raychaudhuri

Print publication date: 2006

Print ISBN-13: 9780198567400

Published to Oxford Scholarship Online: November 2020

DOI: 10.1093/oso/9780198567400.001.0001

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PRINTED FROM OXFORD SCHOLARSHIP ONLINE (oxford.universitypressscholarship.com). (c) Copyright Oxford University Press, 2021. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in OSO for personal use. date: 16 June 2021

Protein Interaction Networks

Protein Interaction Networks

10 (p.245) Protein Interaction Networks
Computational Text Analysis

Soumya Raychaudhuri

Oxford University Press

Genes and proteins interact with each other in many complicated ways. For example, proteins can interact directly with each other to form complexes or to modify each other so that their function is altered. Gene expression can be repressed or induced by transcription factor proteins. In addition there are countless other types of interactions. They constitute the key physiological steps in regulating or initiating biological responses. For example the binding of transcription factors to DNA triggers the assembly of the RNA assembly machinery that transcribes the mRNA that then is used as the template for protein production. Interactions such as these have been carefully elucidated and have been described in great detail in the scientific literature. Modern assays such as yeast-2-hybrid screens offer rapid means to ascertain many of the potential protein–protein interactions in an organism in a large-scale approach. In addition, other experimental modalities such as gene-expression array assays offer indirect clues about possible genetic interactions. One area that has been greatly explored in the bioinformatics literature is the possibility of learning genetic or protein networks, both from the scientific literature and from large-scale experimental data. Indeed, as we get to know more and more genes, it will become increasingly important to appreciate their interactions with each other. An understanding of the interactions between genes and proteins in a network allows for a meaningful global view of the organism and its physiology and is necessary to better understand biology. In this chapter we will explore methods to either (1) mine the scientific literature to identify documented genetic interactions and build networks of genes or (2) to confirm protein interactions that have been proposed experimentally. Our focus here is on direct physical protein–protein interactions, though the techniques described could be extended to any type of biological interaction between genes or proteins. There are multiple steps that must be addressed in identifying genetic interaction information contained within the text. After compiling the necessary documents and text, the first step is to identify gene and protein names in the text.

Keywords:   abstract co-occurrences, bait proteins, co-occurring gene names, gene networks, interaction verbs, mass spectroscopy, networks, genetic, parsing sentences, reporter genes, sentence co-occurrences

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