Preface... Table of Contents... Contributing Authors...1. Ensembl Plants: Integrating Tools for Visualizing, Mining and Analyzing Plant Genomics DataDan 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 DataManuel 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 GenomesJean Philippe Tamby and Véronique Brunaud 5. Mining Plant Genomic and Genetic Data Using the GnpIS Information SystemA-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 BiologyJamie 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 CropsManuel Ruiz, Guilhem Sempere, and Chantal Hamelin 9. Species-Specific Genome Sequence Databases: A Practical ReviewA.D.J. van Dijk 10. A Guide to the PLAZA 3.0 Plant Comparative Genomics DatabaseKlaas Vandepoele 11. Exploring Plant Co-Expression and Gene-Gene Interactions with CORNET 3.0Michiel Van Bel and Frederik Coppens12. PlaNet: Comparative Co-Expression Network Analyses for PlantsSebastian 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 SpeciesToru 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 StudySushma Naithani and Pankaj Jaiswal 15. CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae GrassesDong Zhang and Andrew H. Paterson 16. Plant Genome Duplication DatabaseTae-Ho Lee, Junah Kim, Jon S. Robertson, and Andrew H. Paterson 17. Variant Effect Prediction Analysis using Resources Available at Gramene DatabaseSushma Naithani, Matt Geniza, and Pankaj Jaiswal 18. Plant Promoter DatabaseKazutaka Kusunoki and Yoshiharu Y. Yamamoto 19. Construction of the Leaf Senescence Database and Functional Assessment of Senescence-Associated GenesZhonghai Li, Yi Zhao, Xiaochuan Liu, Zhiqiang Jiang, Jinying Peng, Jinpu Jin, Hongwei Guo, and Jingchu Luo