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Open Access Research article

Computational prediction of the osmoregulation network in Synechococcus sp. WH8102

Xizeng Mao1, Victor Olman1, Rhona Stuart4, Ian T Paulsen3, Brian Palenik4 and Ying Xu12*

Author Affiliations

1 Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA

2 College of Computer Science and Technology, Jilin University, Changchun, Jilin, China

3 The Institute for Genomic Research and the J. Craig Venter Institute, Rockville, MD 20850, USA

4 Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA

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BMC Genomics 2010, 11:291  doi:10.1186/1471-2164-11-291

Published: 10 May 2010

Additional files

Additional file 1:

Gene Mapping from A. halo to WH8102. This file contains genes mapped from the template organism A. halo to WH8102 in the initial osmoregulation network. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-fifth columns, operon information if applicable in the sixth column, and comparison of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Gene Mapping from C.glut to WH8102. This file contains genes mapped from the template organism C.glut to WH8102 in the initial osmoregulation network. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-fifth columns, operon information if applicable in the sixth column, and comparison of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Gene Mapping from E.coli to WH8102. This file contains genes mapped from the template organism E.coli to WH8102 in the initial osmoregulation network. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-fifth columns, operon information if applicable in the sixth column, and comparison of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 22KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Gene Mapping from P.mari to WH8102. This file contains genes mapped from the template organism P.mari to WH8102 in the initial osmoregulation network. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-fifth columns, operon information if applicable in the sixth column, and comparison of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Gene Mapping from PCC6803 to WH8102. This file contains genes mapped from the template organism PCC6803 to WH8102 in the initial osmoregulation network. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-fifth columns, operon information if applicable in the sixth column, and comparison of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 20KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Expanded Model of Osmoregulation in WH8102. This file contains an expanded model of osmoregulation network in WH8102, including basic gene information (gene synonym, symbol, GI number and annotation) in the first-second and tenth-eleventh columns, computational evidences about cross-organism mapping in the third column and network expanding by guilt-by-association with co-operon, co-interaction, co-regulon and co-evolution information in the four-seven columns, and microarray experimental evidences in the eighth-ninth columns. "X" in the third column means the gene is mapped from a template organism, and "X" in the seven column means that the gene is recruited by sigma 38 regulon.

Format: XLS Size: 42KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Sigma 38 Dependent Genes Mapping from E. coli to PCC6803. This file contains genes in sigma 38 regulon mapped from the template organism E. coli to PCC6803. The file has thirteen columns: basic gene information including synonym, GI number and symbol in the first-sixth columns, operon information if applicable in the sixth column, comparison information of protein domain architecture if applicable in the seventh-ninth columns, and microarray experimental data in the tenth-eleventh columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 27KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Microarray data of PCC6803 collected from the public domain. This file contains summary of microarray data of PCC6803 collected from the public domain including Pubmed ID, experimental condition, gene number and microarray platform.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Sigma 38 Dependent Genes Mapping from E. coli to WH8102. This file contains genes in sigma 38 regulon mapped from the template organism E. coli to WH8102. The file has nine columns: basic gene information including synonym, GI number and symbol in the first-sixth columns, operon information if applicable in the sixth column, comparison information of protein domain architecture if applicable in the seventh-ninth columns. The score in the seven column measures the similarity of protein domain architectures: 1 and 0 means completely identical and different, respectively, and values between them means partially identical.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

WH8102 Saltshock Genes With 1%FDR. This file contains genes with less than 1% false discovery rate under slat shock in WH8102, including basic gene information in the first column, statistical significance information in the second-forth columns, and gene expression values under different experimental treats in the fifth-thirteen columns

Format: XLS Size: 45KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Pathway Enrichment Analysis of Osmoregulation Network in WH8102. This file contains enriched KEGG pathways involved in the osmoregulation network. The P-value in the second column measures the statistical significance of each pathway populated by the genes in the osmoregulation network with respect to all the genes encoded in the whole genome as the background.

Format: XLS Size: 24KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

PCC6803 Genome-Wide Gene Expression Under Osmotic Stress. This file contains expression data of genes in PCC6803 under hyperosmotic stress, collected from published papers. Fold change > 2 means the gene is up-regulated by at least 2 fold, and fold change < 0.5 means the gene is down-regulated by at least 2 fold.

Format: XLS Size: 134KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data