GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing

J. Lin, Jiang Qian, Q. D. Greenbaum, P. Bertone, R. Das, N. Echols, A. Senes, B. Stenger, M. Gerstein

Research output: Contribution to journalArticle

Abstract

We present a prototype of a new database tool, GeneCensus, which focuses on comparing genomes globally, in terms of the collective properties of many genes, rather than in terms of the attributes of a single gene (e.g. sequence similarity for a particular ortholog). The comparisons are presented in a visual fashion over the web at GeneCensus.org. The system concentrates on two types of comparisons: (i) trees based on the sharing of generalized protein families between genomes, and (ii) whole pathway analysis in terms of activity levels. For the trees, we have developed a module (TreeViewer) that clusters genomes in terms of the folds, superfamilies or orthologs-all can be considered as generalized 'families' or 'protein parts'-they share, and compares the resulting trees side-by-side with those built from sequence similarity of individual genes (e.g. a traditional tree built on ribosomal similarity). We also include comparisons to trees built on whole-genome dinucleotide or codon composition. For pathway comparisons, we have implemented a module (PathwayPainter) that graphically depicts, in selected metabolic pathways, the fluxes or expression levels of the associated enzymes (i.e. generalized 'activities'). One can, consequently, compare organisms (and organism states) in terms of representations of these systemic quantities. Development of this module involved compiling, calculating and standardizing flux and expression information from many different sources. We illustrate pathway analysis for enzymes involved in central metabolism. We are able to show that, to some degree, flux and expression fluctuations have characteristic values in different sections of the central metabolism and that control points in this system (e.g. hexokinase, pyruvate kinase, phosphofructokinase, isocitrate dehydrogenase and citric synthase) tend to be especially variable in flux and expression. Both the TreeViewer and PathwayPainter modules connect to other information sources related to individual-gene or organism properties (e.g. a single-gene structural annotation viewer).

Original languageEnglish (US)
Pages (from-to)4574-4582
Number of pages9
JournalNucleic Acids Research
Volume30
Issue number20
StatePublished - Oct 15 2002
Externally publishedYes

Fingerprint

Metabolic Networks and Pathways
Genome
Genes
Proteins
Molecular Sequence Annotation
Isocitrate Dehydrogenase
Phosphofructokinases
Hexokinase
Pyruvate Kinase
Enzymes
Codon
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

Lin, J., Qian, J., Greenbaum, Q. D., Bertone, P., Das, R., Echols, N., ... Gerstein, M. (2002). GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Research, 30(20), 4574-4582.

GeneCensus : Genome comparisons in terms of metabolic pathway activity and protein family sharing. / Lin, J.; Qian, Jiang; Greenbaum, Q. D.; Bertone, P.; Das, R.; Echols, N.; Senes, A.; Stenger, B.; Gerstein, M.

In: Nucleic Acids Research, Vol. 30, No. 20, 15.10.2002, p. 4574-4582.

Research output: Contribution to journalArticle

Lin, J, Qian, J, Greenbaum, QD, Bertone, P, Das, R, Echols, N, Senes, A, Stenger, B & Gerstein, M 2002, 'GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing', Nucleic Acids Research, vol. 30, no. 20, pp. 4574-4582.
Lin J, Qian J, Greenbaum QD, Bertone P, Das R, Echols N et al. GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Research. 2002 Oct 15;30(20):4574-4582.
Lin, J. ; Qian, Jiang ; Greenbaum, Q. D. ; Bertone, P. ; Das, R. ; Echols, N. ; Senes, A. ; Stenger, B. ; Gerstein, M. / GeneCensus : Genome comparisons in terms of metabolic pathway activity and protein family sharing. In: Nucleic Acids Research. 2002 ; Vol. 30, No. 20. pp. 4574-4582.
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