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This article is part of the supplement: Ninth Annual MCBIOS Conference. Dealing with the Omics Data Deluge

Open Access Proceedings

Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses

Yixiang Zhang12, Sanmin Liu2, Susie Y Dai34* and Joshua S Yuan12*

Author Affiliations

1 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA

2 Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA

3 Office of Texas State Chemist, Texas A&M University, College Station, TX 77843, USA

4 Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA

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BMC Bioinformatics 2012, 13(Suppl 15):S8  doi:10.1186/1471-2105-13-S15-S8

Published: 11 September 2012

Additional files

Additional file 1:

Workflow of sample preparation and bioinformatics analysis. Additional file 1A shows the workflow of organelle enrichment, protein isolation and 2D LC/MS/MS. Additional file 1B illustrates the flow of protein classification package. Additional file1C shows workflow of traditional plant total protein isolation by TCA/acetone.

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Additional file 2:

Protein classification software for organelles enrichment analysis. The package was developed by Python. For usage, open the code in text editor and type the key word in Keywords function. Follow the instruction at the beginning of the package.

Format: PY Size: 5KB Download file

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Additional file 3:

All differentially expressed proteins in zeatin treated sample. The list was generated by PatternLab. The data from DTASelect were normalized by Row Sigma method and processed by TFold pairwise analysis. The minimum signal in all classes is 2. The cutoff of fold change, p-value and Benjamin-Hochberg (BH) theoretical false-positive rate are 2.0, 0.05 and 0.1, respectively.

Format: XLS Size: 227KB Download file

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Additional file 4:

All differentially expressed proteins in BR treated sample. The list was generated by PatternLab. The data from DTASelect were normalized by Row Sigma method and processed by TFold pairwise analysis. The minimum signal in all classes is 2. The cutoff of fold change, p-value and Benjamin-Hochberg (BH) theoretical false-positive rate are 2.0, 0.05 and 0.1, respectively.

Format: XLS Size: 191KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data