Research article
Towards the identification of essential genes using targeted genome sequencing and comparative analysis
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* Corresponding authors: Adam M Gustafson gustafad@bu.edu - Evan S Snitkin esnitkin@bu.edu
- † Equal contributors
1 Bioinformatics Graduate Program, Boston University, Boston, MA 02215 USA
2 Department of Biomedical Engineering, Boston University, MA 02215 USA
3 Children's Hospital Informatics Program of the Harvard MIT Division in Health Sciences and Technology, Boston, MA, USA
BMC Genomics 2006, 7:265 doi:10.1186/1471-2164-7-265
Published: 19 October 2006Additional files
Additional File 5:
List of organisms used to calculate phyletic retention. A list of organisms used in the calculation of phyletic retention is shown. KEGG three letter codes are used to represent the organisms, unless otherwise noted.
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Additional File 3:
Feature matrices for S. cerevisiae. A raw data feature matrix, as well as an entropy discretized feature matrix are included.
Format: XLS Size: 4.5MB Download file
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Additional File 4:
Feature matrices for E. coli. A raw data feature matrix, as well as an entropy discretized feature matrix are included.
Format: XLS Size: 2.6MB Download file
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Additional File 1:
CMIM feature ranking. This excel file includes tables showing the CMIM feature ranking.
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Additional File 2:
Performance of naïve Bayes classifiers using subsets of features. For each set of features analyzed in this paper (e.g. SC_GenProt, EC_GenProt, etc...), CMIM was calculated such that features were ranked in order of most informative to least. PPV for the top 1, 5, 10 and 15% of predictions are shown when naïve Bayes classifier is constructed when using the top N features.
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Additional File 6:
Naïve Bayes classification results. For each of the feature sets used on E. coli and S. cerevisiae, the probability of a gene being essential, as reported by naïve Bayes, is provided.
Format: XLS Size: 1.5MB Download file
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