Open Access Highly Accessed Research article

Comparative genomics and transcriptomics of trait-gene association

Sebastián Aguilar Pierlé1*, Michael J Dark23, Dani Dahmen1, Guy H Palmer1 and Kelly A Brayton1*

Author Affiliations

1 Program in Genomics, Department of Veterinary Microbiology and Pathology, Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164-7040, USA

2 Department of Infectious Diseases and Pathobiology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA

3 Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32611-0880, USA

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BMC Genomics 2012, 13:669  doi:10.1186/1471-2164-13-669

Published: 26 November 2012

Additional files

Additional file 1:

Nucleotide polymorphisms between the St. Maries and Florida strains. SNPs between the St. Maries and Florida strains are listed here together with the nucleotides reported for all the additional reported nucleotides.

Format: XLSX Size: 984KB Download file

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Additional file 2:

Absolute expression values of candidate genes. Gene identifications are provided on the x axis and the copy number per ml of blood on the y axis. The black bars represent the numbers obtained for the Florida strain and the white bars the numbers for the St. Maries strain. Transcription of all candidate genes is shown together with the calibrator MSP5.

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Open Data

Additional file 3:

Mapping of putative TSS and 5 UTRs length in the St. Maries strain. The location and length of 5 UTRs in the St. Maries strain are reported.

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Additional file 4:

Mapping of putative TSS and 5 UTRs length in the Florida strain. The location and length of 5 UTRs in the Florida strain are reported.

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Additional file 5:

Operon strucutres found through transcriptome sequencing in the St. Maries strain. Genes involved in the different operon structures are reported.

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Additional file 6:

Distribution of the normalized expression values of all replicates analyzed in this study with RNA-seq. The distribution of the normalized RPKM values for all replicates is plotted in a box plot. RNA-SeqFL1 and RNA-SeqFL2 designate distributions for Florida strain replicates 1 and 2 respectively. RNA-Seq STM 1 and RNA-Seq STM 2 designate RPKM distributions for St. Maries replicates 1 and 2 respectively. The distributions allow for comparisons.

Format: PPTX Size: 75KB Download file

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Additional file 7:

A. marginale genes arranged along dimensions of biological and statistical significance. A volcano plot shows the relationship between the p-values of a statistical test and the magnitude of the difference in expression values. On the y axis the negative log10 p-values are plotted. On the x-axis the log 2 values of the fold changes seen in whole transcriptome comparison. The red lines highlight the cutoffs for genes that were analyzed further. Only genes populating the upper right and left quadrants of the plot under two different statistical tests (Kal’s and Baggerly’s) were chosen. This plot shows results obtained for Kal’s test.

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Additional file 8:

Candidate non-synonymous changes predicted to be deleterious by the SIFT algorithm. Non-synonymous changes predicted to be deleterious by the SIFT algorithm found between the St. Maries and Florida strains are reported.

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