Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework

doi:10.1186/1471-2105-8-403

BMC Bioinformatics

Volume 8

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Methodology article

Modeling SAGE tag formation and its effects on data interpretation within a Bayesian framework

Michael A Gilchrist¹ , Hong Qin¹^,3 and Russell Zaretzki²

¹Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA

²Department of Statistics, University of Tennessee, Knoxville, TN 37996, USA

³Dept of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:403doi:10.1186/1471-2105-8-403


Published:	18 October 2007

Additional files

Additional file 1:

Marginal posterior percentiles for S experiments. Table of percentile values for the marginal posterior distribution of mRNA frequencies of S. cerevisiae during stationary phase.

Format: TSV Size: 12.9MB Download file

Additional file 2:

Marginal posterior percentiles for L experiments. Table of percentile values for the marginal posterior distribution of mRNA frequencies of S. cerevisiae during log growth phase.

Format: TSV Size: 12.9MB Download file

Additional file 3:

Marginal posterior percentiles for G2M experiments. Table of percentile values for the marginal posterior distribution of mRNA frequencies of S. cerevisiae during G2M phase.

Format: TSV Size: 12.9MB Download file

Additional file 4:

Summary statistics of posterior distributions for S experiments. Table of posterior joint modes and marginal modes, median, variance and 95%PI of mRNA frequencies of S. cerevisiae during stationary phase.

Format: TSV Size: 709KB Download file

Additional file 5:

Summary statistics of posterior distributions for L experiments. Table of posterior joint modes and marginal modes, median, variance and 95%PI of mRNA frequencies of S. cerevisiae during log growth phase.

Format: TSV Size: 712KB Download file

Additional file 6:

Summary statistics of posterior distributions for G2M experiments. Table of posterior joint modes and marginal modes, median, variance and 95%PI of mRNA frequencies of S. cerevisiae during G2M phase.

Format: TSV Size: 706KB Download file

Additional file 7:

Tag information for S experiment. Table of total AE sites, unique AE sites, tag counts, φ and joint mode values for stationary phase experimental data in [9].

Format: TSV Size: 246KB Download file

Additional file 8:

Tag information for L experiment. Table of total AE sites, unique AE sites, tag counts, φ and joint mode values for log growth experimental data in [9].

Format: TSV Size: 255KB Download file

Additional file 9:

Tag information for G2M experiment. Table of total AE sites, unique AE sites, tag counts, φ and joint mode values for G2M growth experimental data in [9].

Format: TSV Size: 235KB Download file

Additional file 10:

Computer code. Tar archive of PERL scripts, R routines, and Mathematica routines used in this work. All code is released under GPL V2 and without warranty.

Format: GZ Size: 3.8MB Download file