Louis A. Chiapello H. Fabry C. Ollivier E. Henaut A. "Deciphering Arabidopsis thaliana gene neighborhoods through bibliographic co-citations" Computers and Chemistry 26(5):511-519 Sp.Iss. SI Jul 2002

Eugene Garfield garfield at CODEX.CIS.UPENN.EDU
Wed Dec 3 15:20:43 EST 2003

A. Louis : louis at genopole.cnrs.fr

TITLE     Deciphering Arabidopsis thaliana gene neighborhoods
          through bibliographic co-citations

AUTHOR    Louis A, Chiapello H, Fabry C, Ollivier E, Henaut A

JOURNAL   COMPUTERS & CHEMISTRY  26 (5): 511-519 Sp. Iss. SI JUL 2002

 Document type: Article   Language: English
 Cited References: 24     Times Cited: 0

In the framework of genome annotation, scientific literature is obviously
the major source of biological knowledge. The aim of the work described in
this paper is to exploit this source of data for the model plant Arabidopsis
thaliana. The first step has consisted in constituting a relevant
bibliographic references dataset for plant genomic research. Genes
co-citations have then been systematically annotated in this reference
dataset, starting from the simple idea that if genes are cited in the same
publication, they must probably share some related functional properties. In
order to deal with the synonymous gene name problem; a gene name reference
list has been constituted starting from A. thaliana SwissProt entries. This
list was used to build clusters of co-cited genes by a single linkage
procedure such that any gene in a given cluster possesses at least one
co-cited partner in the same cluster. Analysis of the clusters demonstrate
the biological consistency of this approach, with only very few
fortuitous links. As an example, a cluster including genes related to
flowering time is more deeply described in the paper. Finally, a graphical
representation of each cluster was performed, which provides a convenient
way to retrieve the genes (the nodes of the graphs) and the references in
which they were co-cited (the edges of the graphs). All the results can be
accessed at the URL http://chlora.Igi.infobiogen.fr:1234/bib_arath/. (C)
2002 Elsevier Science Ltd. All rights reserved.

Author Keywords:
information retrieval, gene names, single linkage procedure, representation
of knowledge

KeyWords Plus:

Louis A, Lab Genome & Informat, Tour Evry 2,523 Pl Terrases, F-91034 Evry,
Lab Genome & Informat, F-91034 Evry, France
INRA, Lab MIG, F-78026 Versailles, France
Inst Pasteur, Unite Genet Genomes Bacteriens, F-75724 Paris, France


IDS Number:


 Cited Author            Cited Work                Volume      Page   Year

 *AR GEN IN            NATURE                       408       796      2000
 BLASCHEK C            AUTOMATIC EXTRACTION                    60      1999
 FROHLICH M            594 U BREM DEP COMP                             1994
 FUKUDA K              PAC S BIOC                             707      1998
 GELBART WM            NUCLEIC ACIDS RES             27        85      1999
 GUO HW                SCIENCE                      279      1360      1998
 LEU WM                PLANT CELL                     7      2187      1995
 LOUIS A               GENOME RES                    11      1296      2001
 MEINKE D              PLANT J                       12       247      1997
 NITSCHKE P            FEMS MICROBIOL REV            22       207      1998
 ONO T                 BIOINFORMATICS                17       155      2001
 PILLET V              THESIS AIX MARSEILLE                   111      2000
 PRICE CA              NUCLEIC ACIDS RES             29       118      2001
 PROUX D               GENOME INFORM SER WO           9        72      1998
 PUTTERILL J           MOL GEN GENET                239       145      1993
 SCHULER GD            METHOD ENZYMOL               266       141      1996
 SEKIMIZU T            GENOME INFROM SER WO           9        62      1998
 SILBERZTEIN M         DICT ELECT ANAL AUTO                            1993
 SIMON R               NATURE                       384        59      1996
 STAPLEY BJ            PAC S BIOC                             529      2000
 SUAREZLOPEZ P         NATURE                       410      1116      2001
 THOMAS J              PAC S BIOC                             541      2000
 WHEELER DL            NUCLEIC ACIDS RES             29        11      2001
 WILBUR WJ             INFORM PROCESS MANAG          30       253      1994

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