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This article is part of the supplement: Proceedings of the 2009 International Conference on Bioinformatics & Computational Biology (BioComp 2009)

Open Access Research

Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana

Feng Xu16, Guang Li16, Chen Zhao2, Yuhua Li16*, Peng Li16, Jian Cui2, Youping Deng45 and Tieliu Shi23*

Author Affiliations

1 College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China

2 The Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China

3 Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai, China, 200031

4 Rush Cancer Center, Rush University Medical Center, Chicago, IL 60612, USA

5 Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS-39406, USA

6 Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, China

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BMC Genomics 2010, 11(Suppl 2):S2  doi:10.1186/1471-2164-11-S2-S2

Published: 2 November 2010

Additional files

Additional file 1:

The annotation result of unknown proteins with annealing simulation algorithm on the basis of our interactome.

Format: XLS Size: KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

The conservative PPI are listed. Moreover, further information about the PPI pairs such as their ID, GO annotation, species , the experiment that validate the PPI, the related literature etc. are listed under the conservative PPI pairs.

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Open Data

Additional file 3:

The pathway related interactions are stored in additional file 5. The interactive pairs pertaining to the pathways are listed under each pathway name.

Format: XLS Size: 26KB Download file

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Open Data

Additional file 4:

The first line of each part is the GO term that enriched in the tissue specific protein list. The information below the first line is the GO terms that enriched in the interactions partner of the first line listed GO term. All of the GO enrichment analysis related information including GO-ID, p-value, corr, total Description Genes in test set are listed.

Format: XLS Size: 508KB Download file

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Open Data

Additional file 5:

This file contains the result of new published validated protein interaction pairs in our predictive interactome.

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Open Data

Additional file 6:

The tables in the file contains the information about the predictive result of the seven methods applied in our study.

Format: XLS Size: 394KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data