Open Access Highly Accessed Research article

Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

Osbaldo Resendis-Antonio*, Magdalena Hernández, Emmanuel Salazar, Sandra Contreras, Gabriel Martínez Batallar, Yolanda Mora and Sergio Encarnación*

Author Affiliations

Programa de Genomica Funcional de Procariotes. Centro de Ciencias Genómicas-UNAM. Av. Universidad s/n, Col. Chamilpa, Cuernavaca Morelos, C.P. 62210. Mexico

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BMC Systems Biology 2011, 5:120  doi:10.1186/1752-0509-5-120

Published: 29 July 2011

Additional files

Additional file 1:

Microarray Data Analysis. This table shows those genes that were over expressed during bacteroid activity in nitrogen fixation.

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Additional file 2:

Proteome Data. By using mass spectrometry, we identified a set of proteins during bacterial nitrogen fixation for R. etli. In each row, we named the protein and presented some of the parameter utilized for concluding the protein identify.

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Additional file 3:

Intersect between proteome and transcriptome. Genes that were simultaneously identified by proteome and transcriptome technologies.

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Additional file 4:

This file contains an extended descriptive analysis deduced from the genes identified by proteome and transcriptome data.

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Additional file 5:

(A) MA plot and representation of Metabolic activity. In this figure we show the MA-plot obtained from microarray data and a selected representation of the metabolic activity predicted by FBA in some metabolic pathways: (B) TCA cycle, (C) purine and pyrimidine metabolism.

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Additional file 6:

Abbreviations. This file enlists the main abbreviations used along the paper.

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Additional file 7:

Metabolic Reconstruction for Rhizobium etli. This table depicts the gene-protein-reaction association for Rhizobium etli metabolic reconstruction, iOR450. Overall the reconstruction contains 450 genes codifying for a set of enzymes participating in 405 metabolic reactions and 377 metabolites.

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