README

The present directory contains the datasets used for the co-inertia analysis described by Thioulouse and Lobry (1995). 1. LIST OF FILES WITH SHORT DESCRIPTION --------------------------------------- File Name Number of rows Number of columns Content AANames 20 1 Amino-acid 3-letter code ProtNames 999 1 Proteins names IndiceNames 402 1 Indices names IndiceVals 402 20 Indices values ProtComp 999 20 Proteins composition 2. THE FILE AANames ------------------- This file contains the names of the 20 amino-acids using the 3-letter code, for instance gly for glycine. The amino-acids are sorted in alphabetic-order. 3. THE FILE ProtNames --------------------- This file contains the names of the 999 proteins. The name is in two parts, for instance XYLEECOM.MALM. The prefix XYLEECOM refers to the DNA contig from wich the coding sequence was obtained in ECOSEQ6 collection (Rudd, 1993). The suffix MALM is the standard name for the protein (Bachmann, 1990). 4. THE FILE IndiceNames ----------------------- This file contains the names of the 402 physico-chemical properties of amino-acids using the accession number of the AA-index collection (Nakai et al., 1988) which is available and described at the URL: ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex. 5. THE FILE IndiceVals ---------------------- This file contains in row the physico-chemical properties in the same order than in the file IndiceNames and in columns the amino- acids in the same order than in the file AANames. If i stands for the row number and j for the column number, then the element (i,j) of this table is the value of the index i for the amino-acid j. These values are from the AA-index collection (Nakai et al., 1988) described at the URL:ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex. 6. THE FILE ProtComp -------------------- This file contains in row the proteins in the same order than in the file ProtNames and in column the amino-acids in the same order than in the file AANames. If i is the row number and j the column number, then the element (i,j) in this table is the number of amino-acids j in the protein i. These values were obtained from a subset of ECOSEQ6 collection (Rudd, 1993). The criteria used for the construction of this subset are described in Lobry and Gautier (1994). 7. REFERENCES ------------- Please quote Rudd (1993) if you use the protein composition dataset and Nikai et al. (1988) if you use the amino-acid indices dataset. Bachmann, B.J. (1990) Linkage map of Escherichia coli K-12, Edition 8. Microbiological Reviews, 54 : 130-197. Lobry, J.R. and Gautier, C. (1994) Hydrophobicity, expressivity and araomaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Research, 22 : 3174-3180. Nakai, K., Kidera, A., Kanehisa, M. (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Engineering, 2 : 93-100. Rudd, K.E. (1993) Maps, genes, sequences, and computers: an Escherichia coli case study. ASM news, 7 : 335-341. Thioulouse, J. and Lobry, J.R. (1995) Co-inertia analysis of amino-acid physico-chemical properties and protein composition with ADE package. Computer Applications in Biosciences, 11 : 321-329. 7b. FORWARD BIBLIOGRAPHY ------------------------ The paper by Thioulouse & Lobry (1995) just above was cited by the following papers: Picard N, Gueguen K, Abdoulaye HA, Diarisso D, Karembe M, Birnbaum P, Nasi R (2005) Tree formations in relation with soil and grasses in a dry savanna in Mali, West Africa. African Journal of Ecology, 43:201-207. Culhane, A.C., Perriere G., Higgins, D.G. (2003) Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. BMC Bioinformatics, 4:59. Perriere, G., Thioulouse, J. (2003) Use of correspondence discriminant analysis to predict the subcellular location of bacterial proteins. Comput. Meth. Prog. Bio., 70:99-105. Lekve, K., Stenseth, N.C., Gjosaeter, J., et al. (2002) Species richness and environmental conditions of fish along the Norwegian Skagerrak coast. ICES J. Mar. Sci, 59:757-769. Da Costa, K.S., Gourene, G., De Morais, L.T., et al. (2000) Fish populations in two West-African coastal rivers facing different agricultural and hydroelectric schemes. Vie Milieu, 50:65-77. Reynaud, P.A., Thioulouse, J. (2000) Identification of birds as biological markers along a neotropical urban-rural gradient (Cayenne, French Guiana), using co-inertia analysis. J. Environ. Manage., 59:121-140. Doledec, S., Statzner, B., Bournard, M. (1999) Species traits for future biomonitoring across ecoregions: patterns along a human-impacted river. Freshwater Biol., 42:737-758. Truu, J., Talpsep, E., Heinaru, E., et al. (1999) Comparison of API 20NE and Biolog GN identification systems assessed by techniques of multivariate analyses. J. Microbiol. Meth., 36:193-201. Townsend, C.R., Scarsbrook, M.R., Doledec, S. (1997) Quantifying disturbance in streams: alternative measures of disturbance in relation to macroinvertebrate species traits and species richness. J. N. Am. Benthol. Soc., 16:531-544. Statzner, B., Hoppenhaus, K., Arens, M.F., et al. (1997) Reproductive traits, habitat use and templet theory: a synthesis of world-wide data on aquatic insects. Freashwater Biol., 38:109-135. Damborsky, J. (1997) Quantitative structure-function relationships of the single-point mutants of haloalkane dehalogenase: A multivariate approach. Quant. Struct.-Act. Rel., 16:126-135. Thioulouse, J., Chessel, D., Doledec, S., et al. (1997) ADE-4: A multivariate analysis and graphical display software. Stat. Comput., 7:75-83. Bournaud, M., Cellot, B., Richoux, P., et al. (1996) Macroinvertebrate community structure and environmental characteristics along a large river: Congruity of patterns for identification to species or family. J. N. Am. Benthol. Soc., 15:232-253. Thioulouse, J. (1996) Towards better graphics for multivariate analysis: The interactive factor map. Computation Stat., 11:11-21. Perriere, G., Thioulouse, J. (1996) On-line tools for sequence retrieval and multivariate statistics in molecular biology. Comput. Appl. Biosci., 12::63-69. 8. ADRESSES ----------- For ECOSEQ6 collection : rudd@jorma.nlm.nih.gov For AA-index collection : tomii@kuicr.kyoto-u.ac.jp For Co-inertia analysis : Jean.Thioulouse@biomserv.univ-lyon1.fr lobry@biomserv.univ-lyon1.fr 9. UPDATES ---------- 15-JUL-2006 : the last (extra) tabulations in file IndiceVals were deleted. 14-JUL-2006 : Switch to the html site. Some minor typos in this README file fixed. Forward bibliography (section 7b) updated. 19-JUN-2004 : Thanks to Daniel Chessel, a bug in the file ProtComp was found: the columns were not in the lexical order of the amino-acids, but in the same order as in the file ftp://pbil.univ-lyon1.fr/pub/datasets/NAR94/data.txt This is now fixed, and the file ProtComp in the present directory is consistent with the file AANames. Forward bibliography (section 7b in the README file) added. 25-SEP-1996 : Update bibliographical references 14-DEC-1994 : files put at the URL: ftp://biom3.univ-lyon1.fr/pub/datasets/CABIOS95

If you have any problems or comments, please contact Jean Lobry.