Plant Genomics Databases: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

1. Ensembl Plants: Integrating Tools for Visualizing, Mining and Analyzing Plant Genomics Data
Dan M. Bolser, Daniel M. Staines, Emily Perry, and Paul J. Kersey

2. PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data
Manuel Spannagl, Thomas Nussbaumer, Kai Bader, Heidrun Gundlach, and Klaus FX Mayer

3. Plant Genome DataBase Japan (PGDBj)
Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Sachiko Shirasawa, Yasukazu Makamura, Satoshi Tabata, and Hideki Hirakawa

4. FLAGdb++: A Bioinformatic Environment to Study and Compare Plant Genomes
Jean Philippe Tamby and V?ronique Brunaud

5. Mining Plant Genomic and Genetic Data Using the GnpIS Information System
A-F Adam-Blondon, M. Alaux, S. Durand, T. Letellier, G. Merceron, N. Mohellibi, C. Pommier, D. Steinbach, F. Alfama, J. Amselem, D. Charruaud, N. Choisne, R. Flores, C. Guerche, V. Jamilloux, E. Kimmel, N. Lapalu, M. Loaec, C. Michotey, H. Quesneville

6. The Bio-Analytic Resource for Plant Biology
Jamie Waese and Nicholas J. Provart

7. The Evolution of Soybean Knowledge Base (SoyKB)
Trupti Joshi, Jiaojiao Wang, Hongxin Zhang, Shiyuan Chen, Shuai Zeng, Bowei Xu, and Dong Xu

8. Using TropGeneDB: a Database Containing Data on Molecular Markers, QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops
Manuel Ruiz, Guilhem Sempere, and Chantal Hamelin

9. Species-Specific Genome Sequence Databases: A Practical Review
A.D.J. van Dijk

10. A Guide to the PLAZA 3.0 Plant Comparative Genomics Database
Klaas Vandepoele

11. Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0
Michiel Van Bel and Frederik Coppens
12. PlaNet: Comparative Co-Expression Network Analyses for Plants
Sebastian Proost and Marek Mutwil

13. Practical Utilization of OryzaExpress and Plant Omics Data Center Databases to Explore Gene Expression Networks in Oryza sativa and Other Plant Species
Toru Kudo, Shin Terashima, Yuno Takaki, Yukino Nakamura, Masaaki Kobayashi, and Kentaro Yano

14. Pathway Analysis and Omics Data Visualization using Pathway Genome Databases: FragariaCyc, A Case Study
Sushma Naithani and Pankaj Jaiswal

15. CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses
Dong Zhang and Andrew H. Paterson

16. Plant Genome Duplication Database
Tae-Ho Lee, Junah Kim, Jon S. Robertson, and Andrew H. Paterson

17. Variant Effect Prediction Analysis using Resources Available at Gramene Database
Sushma Naithani, Matt Geniza, and Pankaj Jaiswal

18. Plant Promoter Database
Kazutaka Kusunoki and Yoshiharu Y. Yamamoto

19. Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated Genes
Zhonghai Li, Yi Zhao, Xiaochuan Liu, Zhiqiang Jiang, Jinying Peng, Jinpu Jin, Hongwei Guo, and Jingchu Luo