Methods for Large-Scale Mining of Networks of Human Genes

Abstract

In molecular biology there is much interest in various types of relationships between genes. Due to the complexity and rapid development of this field, much of this knowledge exists only in free-text form. A database of relationships between genes may allow background knowledge to be used in computerised analyses. As far as we know, no comprehensive manually cured database of this kind exists, and constructing and maintaining such a database manually would be very labour-intensive. Efficient automated methods for extraction and structuring of relationships between genes from free-text would be valuable. A database named PubGene has previously been created and it contains a comprehensive network of human genes created by automated extraction of co-occurrence of gene terms in over 10 million MEDLINE records. Co-occurring genes were linked together under the hypothesis that two genes will co-occur only if they have some biological relationship. In this paper, we show that for the subset of human genes encoding enzymes, pairs of co-occurring enzyme genes are significantly more closely related biologically than when these genes are compared randomly. Manual inspection, however, shows that some of the links in PubGene are not correct and it also indicates how the noise can be reduced. We propose a complementary method for automated extraction of relationships between genes by use of information from the Science Citation Index (SCI) database. We relate two genes if they have been co-referred, that is, having reference articles being co-cited in a third article. The alternative approach confirms relationships found in PubGene, and it also finds other relevant relationships.

Bioinformatics

“…These topics were also addressed at the Data Mining for Bioinformatics-Towards in Silico Biology conference supported by the EBI-Wellcome Trust (http:llindustry.ebi.ac.uWdatamining99). Jenssen, Oberg, Andersson, and Komorowski (2001) explore methods for mining networks of human genes.…”

“…Swanson's valuable literature investigations and Swanson and Smalheiser's (1997) work in finding complementary literatures are credited with stimulating the type of biological datditerature integration called for by Altman (2000) and others. Such work includes Cory (1997); Davies (1988); Lu, Janssen, Milios, and Japkowicz (2001) ;Jenssen, Oberg, Andersson, and Komorowski (2001); Valdes-Perez (1999); and many others. Swanson and collaborators continue to further research in literature-based discovery of scientific knowledge; see, for example: Gordon and Lindsay (1996);Weeber (2001) ;Weeber, Vos, Klein, and de Jong-van den Berg (2001); Swanson, Smalheiser, and Bookstein (2001); and expressly in biology (Gardy & Brinkman, 2003).…”

Finding Functionally Related Genes by Local and Global Analysis of MEDLINE Abstracts

“…Later, the method was utilized in a comprehensive manner by Jenssen et. al [5,6], who developed a genome-wide network of human genes. The co-occurrence method is very efficient for its purpose; to detect gene relations.…”

“…As shown in various experiments [5,6], the co-occurrence method has proved to be an efficient as well as valid approach of detecting meaningful biological relationships between genes. The methodology is simplistic; if two genes co-occur in an abstract, they are assumed to have a relationship of some kind.…”

Literature-Based Generation of Hypotheses on Chemical Composition Using Database Co-occurrence of Chemical Compounds

“…[5][6][7][8][9][10][11][12] Coword networks are also used for the generation of advanced hypotheses and the discovery of new relationships between phenomena in biomedicine. [13][14][15][16] Some words may be names of chemical compounds depicting research specialties [9][10][11] or having biological activity. [13][14][15] In our previous work, 2,4 the occurrence/co-occurrence behavior of constituents of three samples in 1987 and 1997 was studied and discussed.…”