| | Editorial Nucleic Acids Res. 2008 January; 36(Database issue): D1. Published online 2008 January. doi: 10.1093/nar/gkm1139.PMCID: PMC2238861 Articles The Molecular Biology Database Collection: 2008 update Michael Y. Galperin PMCID: PMC2238887 Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim Hubbard, and Ewan Birney PMCID: PMC2238915 Database resources of the National Center for Biotechnology Information David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko PMCID: PMC2238880 DDBJ with new system and face H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori, and Y. Tateno PMCID: PMC2238829 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler PMCID: PMC2238942 GISSD: Group I Intron Sequence and Structure Database Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, and Yi Zhang PMCID: PMC2238919 The Gypsy Database (GyDB) of mobile genetic elements C. Lloréns, R. Futami, D. Bezemer, and A. Moya PMCID: PMC2238898 TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates Asaf Levy, Noa Sela, and Gil Ast PMCID: PMC2238949 UgMicroSatdb: database for mining microsatellites from unigenes Veenu Aishwarya and P. C. Sharma PMCID: PMC2238862 UTRome.org: a platform for 3′UTR biology in C. elegans Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, and Kristin C. Gunsalus PMCID: PMC2238901 ProSAS: a database for analyzing alternative splicing in the context of protein structures Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, and Ralf Zimmer PMCID: PMC2238869 CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, and Naren Ramakrishnan PMCID: PMC2238953 COXPRESdb: a database of coexpressed gene networks in mammals Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita PMCID: PMC2238883 CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators Lei Bao, Mi Zhou, and Yan Cui PMCID: PMC2238977 DBD––taxonomically broad transcription factor predictions: new content and functionality Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, and Sarah A. Teichmann PMCID: PMC2238844 DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information Nicolas Sierro, Yuko Makita, Michiel de Hoon, and Kenta Nakai PMCID: PMC2247474 DBTSS: database of transcription start sites, progress report 2008 Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, and Kenta Nakai PMCID: PMC2238895 JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, and Albin Sandelin PMCID: PMC2238834 ORegAnno: an open-access community-driven resource for regulatory annotation Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, and The Open Regulatory Annotation Consortium PMCID: PMC2239002 ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, and Huaiqiu Zhu PMCID: PMC2238952 RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spinola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez-Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, and Julio Collado-Vides PMCID: PMC2238961 TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors Barrett C. Foat, Ronald G. Tepper, and Harmen J. Bussemaker PMCID: PMC2238954 YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d’Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, and Ana T. Freitas PMCID: PMC2238916 ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse Anason S. Halees, Rashad El-Badrawi, and Khalid S. A. Khabar PMCID: PMC2238997 GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs Oleg Kikin, Zachary Zappala, Lawrence D’Antonio, and Paramjeet S. Bagga PMCID: PMC2238929 The microRNA.org resource: targets and expression Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, and Chris Sander PMCID: PMC2238905 miRBase: tools for microRNA genomics Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, and Anton J. Enright PMCID: PMC2238936 miRGator: an integrated system for functional annotation of microRNAs Seungyoon Nam, Bumjin Kim, Seokmin Shin, and Sanghyuk Lee PMCID: PMC2238850 miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, and Hsien-Da Huang PMCID: PMC2238982 NONCODE v2.0: decoding the non-coding Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, and Runsheng Chen PMCID: PMC2238973 piRNABank: a web resource on classified and clustered Piwi-interacting RNAs S. Sai Lakshmi and Shipra Agrawal PMCID: PMC2238943 The 3D rRNA modification maps database: with interactive tools for ribosome analysis Dorota Piekna-Przybylska, Wayne A. Decatur, and Maurille J. Fournier PMCID: PMC2238946 Vir-Mir db: prediction of viral microRNA candidate hairpins Sung-Chou Li, Cheng-Kai Shiau, and Wen-chang Lin PMCID: PMC2238904 The Universal Protein Resource (UniProt) The UniProt Consortium PMCID: PMC2238893 MIPS: analysis and annotation of genome information in 2007 H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Münsterkötter, A. Ruepp, M. Spannagl, V. Stümpflen, and T. Rattei PMCID: PMC2238900 AAindex: amino acid index database, progress report 2008 Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, and Minoru Kanehisa PMCID: PMC2238890 CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering Conan K. L. Wang, Quentin Kaas, Laurent Chiche, and David J. Craik PMCID: PMC2239000 MALISAM: a database of structurally analogous motifs in proteins Hua Cheng, Bong-Hyun Kim, and Nick V. Grishin PMCID: PMC2238938 MegaMotifBase: a database of structural motifs in protein families and superfamilies Ganesan Pugalenthi, P. N. Suganthan, R. Sowdhamini, and Saikat Chakrabarti PMCID: PMC2238926 PPT-DB: the protein property prediction and testing database David S. Wishart, David Arndt, Mark Berjanskii, An Chi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, and Guohui Lin PMCID: PMC2238980 LOCATE: a mammalian protein subcellular localization database Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, and Rohan D. Teasdale PMCID: PMC2238969 TOPDB: topology data bank of transmembrane proteins Gábor E. Tusnády, Lajos Kalmár, and István Simon PMCID: PMC2238857 Phospho.ELM: a database of phosphorylation sites—update 2008 Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, and Toby J. Gibson PMCID: PMC2238828 The 20 years of PROSITE Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard de Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, and Christian J. A. Sigrist PMCID: PMC2238851 eggNOG: automated construction and annotation of orthologous groups of genes Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, and Peer Bork PMCID: PMC2238944 EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, and Yixue Li PMCID: PMC2238967 InParanoid 6: eukaryotic ortholog clusters with inparalogs Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, and Erik L. L. Sonnhammer PMCID: PMC2238924 OPTIC: orthologous and paralogous transcripts in clades Andreas Heger and Chris P. Ponting PMCID: PMC2238935 OrthoDB: the hierarchical catalog of eukaryotic orthologs Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, and Evgeny M. Zdobnov PMCID: PMC2238902 PairsDB atlas of protein sequence space Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, and Liisa Holm PMCID: PMC2238971 The Pfam protein families database Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, and Alex Bateman PMCID: PMC2238907 SIMAP—structuring the network of protein similarities Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, and Werner Mewes PMCID: PMC2238827 ATDB: a uni-database platform for animal toxins Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, and Song-Ping Liang PMCID: PMC2238984 ChromDB: The Chromatin Database Karla Gendler, Tara Paulsen, and Carolyn Napoli PMCID: PMC2238968 DB-PABP: a database of polyanion-binding proteins Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, and C. Russell Middaugh PMCID: PMC2238912 Development of a heme protein structure–electrochemical function database Charles J. Reedy, Margaret M. Elvekrog, and Brian R. Gibney PMCID: PMC2238922 KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007 Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, and Laurent Chiche PMCID: PMC2238874 MEROPS: the peptidase database Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, and Alan J. Barrett PMCID: PMC2238837 NORINE: a database of nonribosomal peptides Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, and Gregory Kucherov PMCID: PMC2238963 SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, and Marla J. Berry PMCID: PMC2238826 The Telomerase Database Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, and Julian J.-L. Chen PMCID: PMC2238860 ChEBI: a database and ontology for chemical entities of biological interest Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner PMCID: PMC2238832 ChemBank: a small-molecule screening and cheminformatics resource database Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, *, and Paul A. Clemons PMCID: PMC2238881 R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, and Piotr Cieplak PMCID: PMC2238896 Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, and Shin-Ichiro Nishimura PMCID: PMC2238941 Greglist: a database listing potential G-quadruplex regulated genes Ren Zhang, Yan Lin, and Chun-Ting Zhang PMCID: PMC2238908 The ITS2 Database II: homology modelling RNA structure for molecular systematics Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, and Jörg Schultz PMCID: PMC2238964 QuadBase: genome-wide database of G4 DNA—occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, and Shantanu Chowdhury PMCID: PMC2238983 RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures Mariusz Popenda, Marek Błażewicz, Marta Szachniuk, and Ryszard W. Adamiak PMCID: PMC2238875 RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, and Bruce A. Shapiro PMCID: PMC2238914 AutoPSI: a database for automatic structural classification of protein sequences and structures Fabian Birzele, Jan E. Gewehr, and Ralf Zimmer PMCID: PMC2238976 BioMagResBank Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, and John L. Markley PMCID: PMC2238925 coliSNP database server mapping nsSNPs on protein structures Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, and Kei Yura PMCID: PMC2238833 Gene3D: comprehensive structural and functional annotation of genomes Corin Yeats, Jonathan Lees, Adam Reid, Paul Kellam, Nigel Martin, Xinhui Liu, and Christine Orengo PMCID: PMC2238970 Data growth and its impact on the SCOP database: new developments Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin PMCID: PMC2238974 Remediation of the protein data bank archive Kim Henrick, Zukang Feng, Wolfgang F. Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, and Helen M. Berman PMCID: PMC2238854 FunSimMat: a comprehensive functional similarity database Andreas Schlicker and Mario Albrecht PMCID: PMC2238903 The Gene Ontology project in 2008 The Gene Ontology Consortium PMCID: PMC2238979 The HGNC Database in 2008: a resource for the human genome Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, and Ewan Birney PMCID: PMC2238870 The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, and Doreen Ware PMCID: PMC2238838 IDBD: Infectious Disease Biomarker Database In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, and Kyung Hyun Kim PMCID: PMC2238845 SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis) Nicolas J. Tourasse and Anne-Brit Kolstø PMCID: PMC2238978 GenoList: an integrated environment for comparative analysis of microbial genomes Pierre Lechat, Laurence Hummel, Sandrine Rousseau, and Ivan Moszer PMCID: PMC2238853 The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, and Nikos C. Kyrpides PMCID: PMC2238992 KEGG for linking genomes to life and the environment Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, and Yoshihiro Yamanishi PMCID: PMC2238879 Narcisse: a mirror view of conserved syntenies Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, and Thomas Faraut PMCID: PMC2238891 PhylomeDB: a database for genome-wide collections of gene phylogenies Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, and Toni Gabaldón PMCID: PMC2238872 BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, and Richard H. Scheuermann PMCID: PMC2238987 CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, and Kwok-yung Yuen PMCID: PMC2238867 The hepatitis C sequence database in Los Alamos Carla Kuiken, Peter Hraber, James Thurmond, and Karina Yusim PMCID: PMC2238885 AlterORF: a database of alternate open reading frames Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, and David S. Holmes PMCID: PMC2238990 Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria Jeremy D. Glasner, Guy Plunkett, III, Bradley D. Anderson, David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, and Nicole T. Perna PMCID: PMC2238966 HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection Pere Puigbò, Antoni Romeu, and Santiago Garcia-Vallvé PMCID: PMC2238906 The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides PMCID: PMC2238897 IMG/M: a data management and analysis system for metagenomes Victor M. Markowitz, Natalia N. Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Philip Hugenholtz, and Nikos C. Kyrpides PMCID: PMC2238950 VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, and Qi Jin PMCID: PMC2238871 xBASE2: a comprehensive resource for comparative bacterial genomics Roy R. Chaudhuri, Nicholas J. Loman, Lori A.S. Snyder, Christopher M. Bailey, Dov J. Stekel, and Mark J. Pallen PMCID: PMC2238843 ProtozoaDB: dynamic visualization and exploration of protozoan genomes Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago Satake, Kary A. C. S. Ocaña, Omar Triana, Sérgio M. S. Cruz, Henrique C. L. Jucá, Juliano C. Cury, Fabricio N. Silva, Guilherme A. Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano P. Silva, Jr, Christian M. Probst, Edmundo C. Grisard, Marco A. Krieger, Samuel Goldenberg, Maria C. R. Cavalcanti, Milton O. Moraes, Maria L. M. Campos, and Marta Mattoso PMCID: PMC2238986 ToxoDB: an integrated Toxoplasma gondii database resource Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert, Jr, Haiming Wang, and Brian P. Brunk PMCID: PMC2238934 CandidaDB: a multi-genome database for Candida species and related Saccharomycotina Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, and Christophe d’Enfert PMCID: PMC2238939 CFGP: a web-based, comparative fungal genomics platform Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, and Yong-Hwan Lee PMCID: PMC2238957 PHI-base update: additions to the pathogen–host interaction database Rainer Winnenburg, Martin Urban, Andrew Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher Rawlings, Kim E. Hammond-Kosack, and Jacob Köhler PMCID: PMC2238852 Gene Ontology annotations at SGD: new data sources and annotation methods Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, and J. Michael Cherry PMCID: PMC2238894 ButterflyBase: a platform for lepidopteran genomics Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, and Chris D. Jiggins PMCID: PMC2238913 FlyBase: integration and improvements to query tools Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, and The FlyBase Consortium PMCID: PMC2238994 REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila Marc S. Halfon, Steven M. Gallo, and Casey M. Bergman PMCID: PMC2238825 SmedGD: the Schmidtea mediterranea genome database Sofia M.C. Robb, Eric Ross, and Alejandro Sánchez Alvarado PMCID: PMC2238899 Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis James C. Sullivan, Adam M. Reitzel, and John R. Finnerty PMCID: PMC2238866 WormBase 2007 Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis, Jolene Fernandes, Tristan J. Fiedler, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg PMCID: PMC2238927 PROCOGNATE: a cognate ligand domain mapping for enzymes Matthew Bashton, Irene Nobeli, and Janet M. Thornton PMCID: PMC2238937 The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne Paley, Seung Y. Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, and Peter D. Karp PMCID: PMC2238876 Bacteriome.org—an integrated protein interaction database for E. coli Chong Su, Jose M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, and John Parkinson PMCID: PMC2238847 The BioGRID Interaction Database: 2008 update Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, and Mike Tyers PMCID: PMC2238873 The cell cycle DB: a systems biology approach to cell cycle analysis Roberta Alfieri, Ivan Merelli, Ettore Mosca, and Luciano Milanesi PMCID: PMC2238882 CORUM: the comprehensive resource of mammalian protein complexes Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, and H. Werner Mewes PMCID: PMC2238909 DIMA 2.0—predicted and known domain interactions Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Norman Strack, Volker Stümpflen, and Dmitrij Frishman PMCID: PMC2238836 DOMINE: a database of protein domain interactions Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and Raja Jothi PMCID: PMC2238965 HotSprint: database of computational hot spots in protein interfaces Emre Guney, Nurcan Tuncbag, Ozlem Keskin, and Attila Gursoy PMCID: PMC2238999 LigASite—a database of biologically relevant binding sites in proteins with known apo-structures Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, and Shoshana J. Wodak PMCID: PMC2238865 Binding MOAD, a high-quality protein–ligand database Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, and Heather A. Carlson PMCID: PMC2238910 PepCyber:P~PEP: a database of human protein–protein interactions mediated by phosphoprotein-binding domains Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, and Tongbin Li PMCID: PMC2238930 STITCH: interaction networks of chemicals and proteins Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, and Peer Bork PMCID: PMC2238848 EndoNet: an information resource about regulatory networks of cell-to-cell communication Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, and Anatolij P. Potapov PMCID: PMC2238947 NetworKIN: a resource for exploring cellular phosphorylation networks Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, and Tony Pawson PMCID: PMC2238868 The Molecule Pages database Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, and Shankar Subramaniam PMCID: PMC2238911 Ensembl 2008 P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider, M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson, A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel, S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk, G. Proctor, J. Smith, A. Ureta-Vidal, and S. Searle PMCID: PMC2238821 EuroPhenome and EMPReSS: online mouse phenotyping resource Ann-Marie Mallon, Andrew Blake, and John M. Hancock PMCID: PMC2238991 Gallus GBrowse: a unified genomic database for the chicken Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine Mardis, and Lincoln D. Stein PMCID: PMC2238981 The Mouse Genome Database (MGD): mouse biology and model systems Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake, and the Mouse Genome Database Group PMCID: PMC2238849 PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice Ling V. Sun, Ke Jin, Yiming Liu, Wenwei Yang, Xing Xie, Lin Ye, Li Wang, Lin Zhu, Sheng Ding, Yi Su, Jie Zhou, Min Han, Yuan Zhuang, Tian Xu, Xiaohui Wu, Ning Gu, and Yang Zhong PMCID: PMC2238892 TreeFam: 2008 Update Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, and Richard Durbin PMCID: PMC2238856 The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones Guglielmo Roma, Marco Sardiello, Gilda Cobellis, Pedro Cruz, Giampiero Lago, Remo Sanges, and Elia Stupka PMCID: PMC2238955 UTGB/medaka: genomic resource database for medaka biology Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro L. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi Shimizu, Shin-ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-I, Hiroyuki Takeda, Yuji Kohara, and Shinichi Morishita PMCID: PMC2238888 The vertebrate genome annotation (Vega) database L. G. Wilming, J. G. R. Gilbert, K. Howe, S. Trevanion, T. Hubbard, and J. L. Harrow PMCID: PMC2238886 Xenbase: a Xenopus biology and genomics resource Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Ross Gibb, Chris Jarabek, Etienne Noumen, Nicolas Pollet, and Peter D. Vize PMCID: PMC2238855 The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes Judy Sprague, Leyla Bayraktaroglu, Yvonne Bradford, Tom Conlin, Nathan Dunn, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Jonathan Knight, Prita Mani, Sierra A.T. Moxon, Christian Pich, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Xiang Shao, Amy Singer, Peiran Song, Brock Sprunger, Ceri E. Van Slyke, and Monte Westerfield PMCID: PMC2238839 The UCSC Genome Browser Database: 2008 update D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney, B. Rhead, K. R. Rosenbloom, K. E. Smith, M. Stanke, A. Thakkapallayil, H. Trumbower, T. Wang, A. S. Zweig, D. Haussler, and W. J. Kent PMCID: PMC2238835 X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis Tim Yates, Michał J. Okoniewski, and Crispin J. Miller PMCID: PMC2238884 Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Kaori Yamaguchi, Toshinori Endo, Satoshi OOta, Wojciech Makalowski, Kazuho Ikeo, Yoshiyuki Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lihua Jin, Yayoi Kaneko, Masako Kanno, Katsuhiko Murakami, Akiko Ogura Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun-ichi Takeda, Masayuki Tanaka, Takashi Gojobori, Tadashi Imanishi, and Takeshi Itoh PMCID: PMC2238928 The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts Genome Information Integration Project And H-Invitational 2 PMCID: PMC2238988 Human PAML browser: a database of positive selection on human genes using phylogenetic methods Gabrielle C. Nickel, David Tefft, and Mark D. Adams PMCID: PMC2238824 MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome Julian Lange, Helen Skaletsky, George W. Bell, and David C. Page PMCID: PMC2238960 MutDB: update on development of tools for the biochemical analysis of genetic variation Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy Heiland, and Sean D. Mooney PMCID: PMC2238958 F-SNP: computationally predicted functional SNPs for disease association studies Phil Hyoun Lee and Hagit Shatkay PMCID: PMC2238878 Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases Joke Reumers, Lucia Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost Van Durme, Joaquin Dopazo, Frederic Rousseau, and Joost Schymkowitz PMCID: PMC2238831 CanGEM: mining gene copy number changes in cancer Ilari Scheinin, Samuel Myllykangas, Ioana Borze, Tom Böhling, Sakari Knuutila, and Juha Saharinen PMCID: PMC2238975 MethyCancer: the database of human DNA methylation and cancer Ximiao He, Suhua Chang, Jiajie Zhang, Qian Zhao, Haizhen Xiang, Kanthida Kusonmano, Liu Yang, Zhong Sheng Sun, Huanming Yang, and Jing Wang PMCID: PMC2238864 PubMeth: a cancer methylation database combining text-mining and expert annotation Maté Ongenaert, Leander Van Neste, Tim De Meyer, Gerben Menschaert, Sofie Bekaert, and Wim Van Criekinge PMCID: PMC2238841 4DXpress: a database for cross-species expression pattern comparisons Yannick Haudry, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, and Thorsten Henrich PMCID: PMC2238840 Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments Nicholas Paul Gauthier, Malene Erup Larsen, Rasmus Wernersson, Ulrik de Lichtenberg, Lars Juhl Jensen, Søren Brunak, and Thomas Skøt Jensen PMCID: PMC2238932 EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Lorna Richardson, Nicholas Burton, Thomas P. Perry, Paul Smith, Richard A. Baldock, Duncan R. Davidson, and Jeffrey H. Christiansen PMCID: PMC2238921 Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata Jeremiah J. Faith, Michael E. Driscoll, Vincent A. Fusaro, Elissa J. Cosgrove, Boris Hayete, Frank S. Juhn, Stephen J. Schneider, and Timothy S. Gardner PMCID: PMC2238822 The Stanford Tissue Microarray Database Robert J. Marinelli, Kelli Montgomery, Chih Long Liu, Nigam H. Shah, Wijan Prapong, Michael Nitzberg, Zachariah K. Zachariah, Gavin J. Sherlock, Yasodha Natkunam, Robert B. West, Matt van de Rijn, Patrick O. Brown, and Catherine A. Ball PMCID: PMC2238948 PRIDE: new developments and new datasets Philip Jones, Richard G. Côté, Sang Yun Cho, Sebastian Klie, Lennart Martens, Antony F. Quinn, David Thorneycroft, and Henning Hermjakob PMCID: PMC2238846 An emerging cyberinfrastructure for biodefense pathogen and pathogen–host data C. Zhang, O. Crasta, S. Cammer, R. Will, R. Kenyon, D. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, T. Xue, Y. Zhang, M. Moore, P. McGarvey, H. Huang, Y. Chen, J. Zhang, R. Mazumder, C. Wu, and B. Sobral PMCID: PMC2239001 CEBS—Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data Michael Waters, Stanley Stasiewicz, B. Alex Merrick, Kenneth Tomer, Pierre Bushel, Richard Paules, Nancy Stegman, Gerald Nehls, Kenneth J. Yost, C. Harris Johnson, Scott F. Gustafson, Sandhya Xirasagar, Nianqing Xiao, Cheng-Cheng Huang, Paul Boyer, Denny D. Chan, Qinyan Pan, Hui Gong, John Taylor, Danielle Choi, Asif Rashid, Ayazaddin Ahmed, Reese Howle, James Selkirk, Raymond Tennant, and Jennifer Fostel PMCID: PMC2238989 DrugBank: a knowledgebase for drugs, drug actions and drug targets David S. Wishart, Craig Knox, An Chi Guo, Dean Cheng, Savita Shrivastava, Dan Tzur, Bijaya Gautam, and Murtaza Hassanali PMCID: PMC2238889 GLIDA: GPCR—ligand database for chemical genomics drug discovery—database and tools update Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, and Chunlai Feng PMCID: PMC2238933 The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge Tina Hernandez-Boussard, Michelle Whirl-Carrillo, Joan M. Hebert, Li Gong, Ryan Owen, Mei Gong, Winston Gor, Feng Liu, Chuong Truong, Ryan Whaley, Mark Woon, Tina Zhou, Russ B. Altman, and Teri E. Klein PMCID: PMC2238877 SuperTarget and Matador: resources for exploring drug-target relationships Stefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, and Robert Preissner PMCID: PMC2238858 VIOLIN: vaccine investigation and online information network Zuoshuang Xiang, Thomas Todd, Kim P. Ku, Bethany L. Kovacic, Charles B. Larson, Fang Chen, Andrew P. Hodges, Yuying Tian, Elizabeth A. Olenzek, Boyang Zhao, Lesley A. Colby, Howard G. Rush, Janet R. Gilsdorf, George W. Jourdian, and Yongqun He PMCID: PMC2238972 The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research Shoji Mano, Tomoki Miwa, Shuh-ichi Nishikawa, Tetsuro Mimura, and Mikio Nishimura PMCID: PMC2238956 Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals Yong Seok Lee, Jeongsu Oh, Young Uk Kim, Namchul Kim, Sungjin Yang, and Ui Wook Hwang PMCID: PMC2238945 The Generation Challenge Programme comparative plant stress-responsive gene catalogue Samart Wanchana, Supat Thongjuea, Victor Jun Ulat, Mylah Anacleto, Ramil Mauleon, Matthieu Conte, Mathieu Rouard, Manuel Ruiz, Nandini Krishnamurthy, Kimmen Sjolander, Theo van Hintum, and Richard M. Bruskiewich PMCID: PMC2238985 Gramene: a growing plant comparative genomics resource Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens, Bonnie Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Tecle, Jim Thomason, Chih-wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, and Lincoln Stein PMCID: PMC2238951 MetaCrop: a detailed database of crop plant metabolism Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Uwe Scholz, Björn H. Junker, and Falk Schreiber PMCID: PMC2238923 PlantGDB: a resource for comparative plant genomics Jon Duvick, Ann Fu, Usha Muppirala, Mukul Sabharwal, Matthew D. Wilkerson, Carolyn J. Lawrence, Carol Lushbough, and Volker Brendel PMCID: PMC2238959 PlantTFDB: a comprehensive plant transcription factor database An-Yuan Guo, Xin Chen, Ge Gao, He Zhang, Qi-Hui Zhu, Xiao-Chuan Liu, Ying-Fu Zhong, Xiaocheng Gu, Kun He, and Jingchu Luo PMCID: PMC2238823 PlantTribes: a gene and gene family resource for comparative genomics in plants P. Kerr Wall, Jim Leebens-Mack, Kai F. Müller, Dawn Field, Naomi S. Altman, and Claude W. dePamphilis PMCID: PMC2238917 ppdb: a plant promoter database Yoshiharu Y. Yamamoto and Junichi Obokata PMCID: PMC2238996 Update of ASRP: the Arabidopsis Small RNA Project database Tyler W. H. Backman, Christopher M. Sullivan, Jason S. Cumbie, Zachary A. Miller, Elisabeth J. Chapman, Noah Fahlgren, Scott A. Givan, James C. Carrington, and Kristin D. Kasschau PMCID: PMC2238918 CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform Séverine Gagnot, Jean-Philippe Tamby, Marie-Laure Martin-Magniette, Frédérique Bitton, Ludivine Taconnat, Sandrine Balzergue, Sébastien Aubourg, Jean-Pierre Renou, Alain Lecharny, and Véronique Brunaud PMCID: PMC2238931 GreenPhylDB: a database for plant comparative genomics M. G. Conte, S. Gaillard, N. Lanau, M. Rouard, and C. Périn PMCID: PMC2238940 AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yixue Li, and Tieliu Shi PMCID: PMC2238993 The Arabidopsis Information Resource (TAIR): gene structure and function annotation David Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, and Eva Huala PMCID: PMC2238962 PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor Joshua L. Heazlewood, Pawel Durek, Jan Hummel, Joachim Selbig, Wolfram Weckwerth, Dirk Walther, and Waltraud X. Schulze PMCID: PMC2238998 Oryza Tag Line, a phenotypic mutant database for the Génoplante rice insertion line library Pierre Larmande, Céline Gay, Mathias Lorieux, Christophe Périn, Matthieu Bouniol, Gaëtan Droc, Christophe Sallaud, Pascual Perez, Isabelle Barnola, Corinne Biderre-Petit, Jérôme Martin, Jean Benoît Morel, Alexander A. T. Johnson, Fabienne Bourgis, Alain Ghesquière, Manuel Ruiz, Brigitte Courtois, and Emmanuel Guiderdoni PMCID: PMC2238859 The Rice Annotation Project Database (RAP-DB): 2008 update Rice Annotation Project PMCID: PMC2238920 GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, and Dorrie Main PMCID: PMC2238863 Panzea: an update on new content and features Payan Canaran, Edward S. Buckler, Jeffrey C. Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, and Doreen Ware PMCID: PMC2238995 Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica Guo-Zhang Wu, Qiu-Ming Shi, Ya Niu, Mei-Qing Xing, and Hong-Wei Xue PMCID: PMC2238842 MUGEN mouse database; Animal models of human immunological diseases V. Aidinis, C. Chandras, M. Manoloukos, A. Thanassopoulou, K. Kranidioti, M. Armaka, E. Douni, D. L. Kontoyiannis, M. Zouberakis, G. Kollias, and the Mugen NoE consortium PMCID: PMC2238830 |
