Open Access Research article

Annotating novel genes by integrating synthetic lethals and genomic information

Daniel Schöner15*, Markus Kalisch2, Christian Leisner3, Lukas Meier2, Marc Sohrmann35, Mahamadou Faty4, Yves Barral3, Matthias Peter35, Wilhelm Gruissem15 and Peter Bühlmann25

Author Affiliations

1 Institute of Plant Science, ETH Zurich, Universitaetsstr. 2, 8092 Zurich, Switzerland

2 Seminar for Statistics, ETH Zurich, Leonhardstr. 27, 8092 Zurich, Switzerland

3 Institute of Biochemistry, ETH Zurich, Schafmattstr. 18, 8093 Zurich, Switzerland

4 Friedrich Miescher Institute, Maulbeerstrasse 66, Basel, Switzerland

5 Competence Center for Systems Physiology and Metabolic Diseases (CC-SPMD), Zurich, Switzerland

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BMC Systems Biology 2008, 2:3  doi:10.1186/1752-0509-2-3

Published: 14 January 2008

Additional files

Additional File 1:

Synthetic lethality data for spindle migration genes. The xls-file contains the standard and systematic gene names for all synthetic lethality interactions found in a systematic screen performed with arp1 and jnm1 performed in the lab of Yves Barral.

Format: XLS Size: 55KB Download file

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Additional File 2:

Genes known to be involved in spindle migration. The xls-file contains all genes that were experimentally shown to be involved in the process of spindle migration. The list covers genes of the dynein-dependent pathway, the Kar9-dependent pathway and genes that showed defects in Kar9-localization.

Format: XLS Size: 20KB Download file

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Additional File 3:

Histogram of the posterior probabilities for the small group of the spindle migration mixture model. The pdf-file contains a figure showing the distribution of posterior probabilities for the small group of genetic interaction partners with arp1 and jnm1. High posteriors mean high likelihood for the respective genes of being involved in spindle migration.

Format: PDF Size: 17KB Download file

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Additional File 4:

List of genes ranked according to their probability for involvement in spindle migration. The xls-file contains all genes used in the mixture modeling approach in the order of their probability of being involved in spindle migration. The genes already known to be involved are marked in cyan. The top 6 and top 50 groups are marked with a black horizontal line.

Format: XLS Size: 33KB Download file

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Additional File 5:

Data matrix used for mixture modeling for spindle migration. The xls-file contains the data set that was used for mixture modeling for the arp1 and jnm1 targets. Due to missing data in the source data sets biological variables were only calculated for genetic interactions for which complete information was available.

Format: XLS Size: 93KB Download file

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Additional File 6:

Movie of Kar9-localization in WT cell. Avi-file showing WT cell in metaphase. The cell is expressing CFP-Tub1 (red) and Kar9-YFP (green). 10 images were captured every 10s showing Kar9 localizing on the SPB and astral MT on bud-directed pole only (asymmetric).

Format: AVI Size: 392KB Download file

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Additional File 7:

Movie of Kar9-localization in a tvp38Δ cell. Avi-file showing a tvp38Δ cell in metaphase. The cell is expressing CFP-Tub1 (red) and Kar9-YFP (green). 10 images were captured every 10s showing Kar9 localizing on the SPB and astral MT on both sides of the spindle (symmetric).

Format: AVI Size: 141KB Download file

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Additional File 8:

Quantification of Kar9-localization. Xls-file showing the quantified results for the experimental validation based on the Kar9-localization phenotypic screens. The results for each gene in the small group are shown for two separate clones and averaged over both clones.

Format: XLS Size: 29KB Download file

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Additional File 9:

Movie of Kar9-localization in a YHR127WΔ cell. Avi-file showing a YHR127WΔ cell in metaphase. The experiment was carried out as for tvp38Δ and revealed a similar phenotype.

Format: AVI Size: 233KB Download file

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Additional File 10:

Movie of Kar9-localization in a uba4Δ cell. Avi-file showing a uba4Δ cell in metaphase. The experiment was carried out as for tvp38Δ and revealed a similar phenotype.

Format: AVI Size: 146KB Download file

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Additional File 11:

Movie of Kar9-localization in a she1Δ cell. Avi-file showing a she1Δ cell in metaphase. The experiment was carried out as for tvp38Δ and revealed a similar phenotype.

Format: AVI Size: 96KB Download file

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Additional File 12:

Movie of spindle integrity and elongation in WT cell. Avi-file showing a WT cell in anaphase. The cell is expressing CFP-Tub1, which labels the elongated anaphase spindle. 10 images were captured every 10s revealing the relatively rigid structure of the spindle.

Format: AVI Size: 47KB Download file

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Additional File 13:

Movie of spindle integrity and elongation in mutant cell. Avi-file showing a she1Δ cell in anaphase. The cell is expressing CFP-Tub, which labels the elongated anaphase spindle. 10 images were captured every 10s showing the spindle breaking due to loss of spindle integrity in this mutant.

Format: AVI Size: 48KB Download file

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Additional File 14:

Synthetic lethality data for TOR2 signaling. The xls-file contains the standard and systematic gene names for all synthetic lethality interactions found in a systematic screen performed with tor2-21 performed in the lab of Charlie Boone. The screen was performed twice and only hits identified in both rounds are in the data set.

Format: XLS Size: 13KB Download file

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Additional File 15:

Data matrix used for mixture modeling for TOR2 signaling. The xls-file contains the data set that was used for mixture modeling for the tor2-21 targets. Due to missing data in the source data sets biological variables were only calculated for genetic interactions where complete information was available.

Format: XLS Size: 35KB Download file

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Additional File 16:

Histogram of the posterior probabilities for the small group of the TOR2 signaling mixture model. The pdf-file contains a figure showing the distribution of posterior probabilities for the small group of tor2 genetic interaction partners. High posteriors mean high likelihood for the respective genes of being involved in TOR2 signaling.

Format: PDF Size: 3KB Download file

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Additional File 17:

List of genes ranked according to the posterior probability for involvement in TOR2 signaling. The xls-file contains all genes used in the mixture modeling approach in the order of their probability of being involved in TOR2 signaling. The genes already known to be involved are marked in yellow and the literature reference is given in the file. The top 18 is marked with a black horizontal line.

Format: XLS Size: 16KB Download file

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Additional File 18:

Best subset of features for TOR2 signaling. The pdf-file shows the scatterplot for the best subset of features for the TOR2 signaling mixture model {aa, hughes, mnaimneh} with a cutoff of 0.29. Target genes belonging to the small group are marked by red triangles, the big group is marked in black. The members of the small group all share very high values for amino acid correlation (aa) and intermediate to high values of correlation in gene expression data with respect to tor2 (hughes and mnaimneh).

Format: PDF Size: 23KB Download file

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