Open Access Research

Conserved rules govern genetic interaction degree across species

Elizabeth N Koch1, Michael Costanzo23, Jeremy Bellay14, Raamesh Deshpande1, Kate Chatfield-Reed5, Gordon Chua5, Gennaro D'Urso6, Brenda J Andrews23, Charles Boone23 and Chad L Myers1*

Author Affiliations

1 Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455, USA

2 Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

3 Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada

4 Institute for Advanced Computer Studies, University of Maryland College Park, 3115 Biolmolecular Sciences Bldg #296, College Park, MD 20742, USA

5 Institute of Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4 Canada

6 Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, PO Box 016189, Miami, FL 33101, USA

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Genome Biology 2012, 13:R57  doi:10.1186/gb-2012-13-7-r57

Published: 2 July 2012

Additional files

Additional file 1:

Supplemental figures. Supplemental figures and legends are given.

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Additional file 2:

Gene features of S. pombe genes. Gene features and observed genetic interaction degrees are given for all S. pombe genes.

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Additional file 3:

Gene features of S. cerevisiae genes. Gene features and observed genetic interaction degrees are given for all S. cerevisiae genes.

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Additional file 4:

Orthology mapping from S. pombe genes to S. cerevisiae genes. Orthologs obtained from InParanoid and GeneDB for each S. pombe gene are given.

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Additional file 5:

Orthology mapping from S. cerevisiae genes to S. pombe genes. Orthologs obtained from InParanoid and GeneDB for each S. cerevisiae gene are given.

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Open Data

Additional file 6:

Regression trees. Regression trees trained on bootstrap samples of S. cerevisiae gene features and negative genetic interaction degree are pictured.

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Additional file 7:

Negative genetic interaction degree predictions for S. cerevisiae genes. Predictions of negative genetic interaction degree produced by each of the 100 regression trees that were trained on S. cerevisiae data are given for each S. cerevisiae gene. For a gene, a predicted degree is given from each tree for which the gene was held out from training; otherwise, NaN indicates that the gene was used for training. Columns correspond to trees pictured and ordered in Additional file 6.

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Open Data

Additional file 8:

Negative genetic interaction degree predictions for S. pombe genes. Predictions of negative genetic interaction degree produced by each of the 100 regression trees that were trained on S. cerevisiae data are given for each S. pombe gene. Columns correspond to trees pictured and ordered in Additional file 5.

Format: XLSX Size: 2.8MB Download file

Open Data

Additional file 9:

Genetic interaction degrees of non-essential S. pombe genes. The number of genes that interact with each non-essential S. pombe gene are given. The eight queries that were screened for genetic interactions with non-essential genes are SPCC1682.08c, SPBC21D10.12, SPBC13E7.09, SPAC4G8.13c, SPAC3A11.13, SPAC27D7.13c, SPAC22F3.09c, and SPAC16A10.07c.

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Open Data

Additional file 10:

Cross-species degree comparisons of protein complexes. Orthologous sets of genes, the predicted and observed average degrees of the sets, and the results of our cross-species comparison are given.

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Additional file 11:

Cross-species degree comparisons of genes annotated by GO terms. Orthologous sets of genes, the predicted and observed average degrees of the set, and the results of our cross-species comparison are given. GO terms are prefixed by a '(p)' or '(c)' to indicate that the term originated from S. pombe or S. cerevisiae annotations, respectively.

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Additional file 12:

The S. pombe co-expression network. The co-expression network is symmetric and is represented as a comma-delimited lower triangle of a matrix.

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Additional file 13:

S. pombe GEO co-expression studies. The listed co-expression studies were used to construct a co-expression network. Citations are for original publications.

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