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Volume 32(Database issue);  January 1, 2004
Articles
EDITORIAL
Nucleic Acids Res. 2004 January 1; 32(Database issue): D1. doi: 10.1093/nar/gkh142.
PMCID: PMC308876
The Molecular Biology Database Collection: 2004 update
Michael Y. Galperin
Nucleic Acids Res. 2004 January 1; 32(Database issue): D3–D22. doi: 10.1093/nar/gkh143.
PMCID: PMC308877
GenBank: update
Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D23–D26. doi: 10.1093/nar/gkh045.
PMCID: PMC308779
The EMBL Nucleotide Sequence Database
Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D27–D30. doi: 10.1093/nar/gkh120.
PMCID: PMC308854
DDBJ in the stream of various biological data
S. Miyazaki, H. Sugawara, K. Ikeo, T. Gojobori, and Y. Tateno
Nucleic Acids Res. 2004 January 1; 32(Database issue): D31–D34. doi: 10.1093/nar/gkh127.
PMCID: PMC308861
Database resources of the National Center for Biotechnology Information: update
David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, and Lukas Wagner
Nucleic Acids Res. 2004 January 1; 32(Database issue): D35–D40. doi: 10.1093/nar/gkh073.
PMCID: PMC308807
MIPS: analysis and annotation of proteins from whole genomes
H. W. Mewes, C. Amid, R. Arnold, D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, and A. Ruepp
Nucleic Acids Res. 2004 January 1; 32(Database issue): D41–D44. doi: 10.1093/nar/gkh092.
PMCID: PMC308826
ACLAME: A CLAssification of Mobile genetic Elements
Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak, and Ariane Toussaint
Nucleic Acids Res. 2004 January 1; 32(Database issue): D45–D49. doi: 10.1093/nar/gkh084.
PMCID: PMC308818
HERVd: the Human Endogenous RetroViruses Database: update
Jan Pačes, Adam Pavlíček, Radek Zika, Vladimir V. Kapitonov, Jerzy Jurka, and Václav Pačes
Nucleic Acids Res. 2004 January 1; 32(Database issue): D50. doi: 10.1093/nar/gkh075.
PMCID: PMC308809
IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
Thierry-Pascal Baum, Nicolas Pasqual, Florence Thuderoz, Vivien Hierle, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, and Jacques Demongeot
Nucleic Acids Res. 2004 January 1; 32(Database issue): D51–D54. doi: 10.1093/nar/gkh041.
PMCID: PMC308775
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
Yogita Mantri and Kelly P. Williams
Nucleic Acids Res. 2004 January 1; 32(Database issue): D55–D58. doi: 10.1093/nar/gkh059.
PMCID: PMC308793
Xpro: database of eukaryotic protein-encoding genes
Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, and Shoba Ranganathan
Nucleic Acids Res. 2004 January 1; 32(Database issue): D59–D63. doi: 10.1093/nar/gkh051.
PMCID: PMC308785
ASD: the Alternative Splicing Database
T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack Riethoven, Vincent Le Texier, and Juha Muilu
Nucleic Acids Res. 2004 January 1; 32(Database issue): D64–D69. doi: 10.1093/nar/gkh030.
PMCID: PMC308764
EASED: Extended Alternatively Spliced EST Database
Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt, and Jens G. Reich
Nucleic Acids Res. 2004 January 1; 32(Database issue): D70–D74. doi: 10.1093/nar/gkh136.
PMCID: PMC308870
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, and Kenta Nakai
Nucleic Acids Res. 2004 January 1; 32(Database issue): D75–D77. doi: 10.1093/nar/gkh074.
PMCID: PMC308808
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Yutaka Suzuki, Riu Yamashita, Sumio Sugano, and Kenta Nakai
Nucleic Acids Res. 2004 January 1; 32(Database issue): D78–D81. doi: 10.1093/nar/gkh076.
PMCID: PMC308810
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, and Philipp Bucher
Nucleic Acids Res. 2004 January 1; 32(Database issue): D82–D85. doi: 10.1093/nar/gkh122.
PMCID: PMC308856
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
Twyla T. Pohar, Hao Sun, and Ramana V. Davuluri
Nucleic Acids Res. 2004 January 1; 32(Database issue): D86–D90. doi: 10.1093/nar/gkh056.
PMCID: PMC308790
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Albin Sandelin, Wynand Alkema, Pär Engström, Wyeth W. Wasserman, and Boris Lenhard
Nucleic Acids Res. 2004 January 1; 32(Database issue): D91–D94. doi: 10.1093/nar/gkh012.
PMCID: PMC308747
Aptamer Database
Jennifer F. Lee, Jay R. Hesselberth, Lauren Ancel Meyers, and Andrew D. Ellington
Nucleic Acids Res. 2004 January 1; 32(Database issue): D95–D100. doi: 10.1093/nar/gkh094.
PMCID: PMC308828
The European ribosomal RNA database
Jan Wuyts, Guy Perrière, and Yves Van de Peer
Nucleic Acids Res. 2004 January 1; 32(Database issue): D101–D103. doi: 10.1093/nar/gkh065.
PMCID: PMC308799
The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
Pulcherie Gueneau de Novoa and Kelly P. Williams
Nucleic Acids Res. 2004 January 1; 32(Database issue): D104–D108. doi: 10.1093/nar/gkh102.
PMCID: PMC308836
The microRNA Registry
Sam Griffiths-Jones
Nucleic Acids Res. 2004 January 1; 32(Database issue): D109–D111. doi: 10.1093/nar/gkh023.
PMCID: PMC308757
PIRSF: family classification system at the Protein Information Resource
Cathy H. Wu, Anastasia Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, C. R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, and Winona C. Barker
Nucleic Acids Res. 2004 January 1; 32(Database issue): D112–D114. doi: 10.1093/nar/gkh097.
PMCID: PMC308831
UniProt: the Universal Protein knowledgebase
Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale, Claire O’Donovan, Nicole Redaschi, and Lai-Su L. Yeh
Nucleic Acids Res. 2004 January 1; 32(Database issue): D115–D119. doi: 10.1093/nar/gkh131.
PMCID: PMC308865
ProTherm, version 4.0: thermodynamic database for proteins and mutants
K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, and Akinori Sarai
Nucleic Acids Res. 2004 January 1; 32(Database issue): D120–D121. doi: 10.1093/nar/gkh082.
PMCID: PMC308816
DBSubLoc: database of protein subcellular localization
Tao Guo, Sujun Hua, Xinglai Ji, and Zhirong Sun
Nucleic Acids Res. 2004 January 1; 32(Database issue): D122–D124. doi: 10.1093/nar/gkh109.
PMCID: PMC308843
THGS: a web-based database of Transmembrane Helices in Genome Sequences
S. A. Fernando, P. Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar, and K. Sekar
Nucleic Acids Res. 2004 January 1; 32(Database issue): D125–D128. doi: 10.1093/nar/gkh130.
PMCID: PMC308864
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton
Nucleic Acids Res. 2004 January 1; 32(Database issue): D129–D133. doi: 10.1093/nar/gkh028.
PMCID: PMC308762
Recent improvements to the PROSITE database
Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, and Amos Bairoch
Nucleic Acids Res. 2004 January 1; 32(Database issue): D134–D137. doi: 10.1093/nar/gkh044.
PMCID: PMC308778
The Pfam protein families database
Alex Bateman, Lachlan Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, and Sean R. Eddy
Nucleic Acids Res. 2004 January 1; 32(Database issue): D138–D141. doi: 10.1093/nar/gkh121.
PMCID: PMC308855
SMART 4.0: towards genomic data integration
Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, and Peer Bork
Nucleic Acids Res. 2004 January 1; 32(Database issue): D142–D144. doi: 10.1093/nar/gkh088.
PMCID: PMC308822
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins
Thierry Hotelier, Ludovic Renault, Xavier Cousin, Vincent Negre, Pascale Marchot, and Arnaud Chatonnet
Nucleic Acids Res. 2004 January 1; 32(Database issue): D145–D147. doi: 10.1093/nar/gkh141.
PMCID: PMC308875
EyeSite: a semi-automated database of protein families in the eye
David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, and Christine Slingsby
Nucleic Acids Res. 2004 January 1; 32(Database issue): D148–D152. doi: 10.1093/nar/gkh090.
PMCID: PMC308824
KinG: a database of protein kinases in genomes
A. Krupa, K. R. Abhinandan, and N. Srinivasan
Nucleic Acids Res. 2004 January 1; 32(Database issue): D153–D155. doi: 10.1093/nar/gkh019.
PMCID: PMC308754
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold
Jean-Christophe Gelly, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, and Laurent Chiche
Nucleic Acids Res. 2004 January 1; 32(Database issue): D156–D159. doi: 10.1093/nar/gkh015.
PMCID: PMC308750
MEROPS: the peptidase database
Neil D. Rawlings, Dominic P. Tolle, and Alan J. Barrett
Nucleic Acids Res. 2004 January 1; 32(Database issue): D160–D164. doi: 10.1093/nar/gkh071.
PMCID: PMC308805
Update of NUREBASE: nuclear hormone receptor functional genomics
David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi
Nucleic Acids Res. 2004 January 1; 32(Database issue): D165–D167. doi: 10.1093/nar/gkh062.
PMCID: PMC308796
RPG: the Ribosomal Protein Gene database
Akihiro Nakao, Maki Yoshihama, and Naoya Kenmochi
Nucleic Acids Res. 2004 January 1; 32(Database issue): D168–D170. doi: 10.1093/nar/gkh004.
PMCID: PMC308739
TrSDB: a proteome database of transcription factors
Antoni Hermoso, Daniel Aguilar, Francesc X. Aviles, and Enrique Querol
Nucleic Acids Res. 2004 January 1; 32(Database issue): D171–D173. doi: 10.1093/nar/gkh101.
PMCID: PMC308835
AANT: the Amino Acid–Nucleotide Interaction Database
Michael M. Hoffman, Maksim A. Khrapov, J. Colin Cox, Jianchao Yao, Lingnan Tong, and Andrew D. Ellington
Nucleic Acids Res. 2004 January 1; 32(Database issue): D174–D181. doi: 10.1093/nar/gkh128.
PMCID: PMC308862
SCOR: Structural Classification of RNA, version 2.0
Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, and Stephen R. Holbrook
Nucleic Acids Res. 2004 January 1; 32(Database issue): D182–D184. doi: 10.1093/nar/gkh080.
PMCID: PMC308814
ArchDB: automated protein loop classification as a tool for structural genomics
Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, and Baldomero Oliva
Nucleic Acids Res. 2004 January 1; 32(Database issue): D185–D188. doi: 10.1093/nar/gkh002.
PMCID: PMC308737
The ASTRAL Compendium in 2004
John-Marc Chandonia, Gary Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner
Nucleic Acids Res. 2004 January 1; 32(Database issue): D189–D192. doi: 10.1093/nar/gkh034.
PMCID: PMC308768
DomIns: a web resource for domain insertions in known protein structures
R. Aroul Selvam and Rajkumar Sasidharan
Nucleic Acids Res. 2004 January 1; 32(Database issue): D193–D195. doi: 10.1093/nar/gkh047.
PMCID: PMC308781
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
Liam J. McGuffin, Stefano A. Street, Kevin Bryson, Søren-Aksel Sørensen, and David T. Jones
Nucleic Acids Res. 2004 January 1; 32(Database issue): D196–D199. doi: 10.1093/nar/gkh043.
PMCID: PMC308777
DSDBASE: a consortium of native and modelled disulphide bonds in proteins
A. Vinayagam, G. Pugalenthi, R. Rajesh, and R. Sowdhamini
Nucleic Acids Res. 2004 January 1; 32(Database issue): D200–D202. doi: 10.1093/nar/gkh026.
PMCID: PMC308760
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
Lucy A. Stebbings and Kenji Mizuguchi
Nucleic Acids Res. 2004 January 1; 32(Database issue): D203–D207. doi: 10.1093/nar/gkh027.
PMCID: PMC308761
IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
Quentin Kaas, Manuel Ruiz, and Marie-Paule Lefranc
Nucleic Acids Res. 2004 January 1; 32(Database issue): D208–D210. doi: 10.1093/nar/gkh042.
PMCID: PMC308776
E-MSD: an integrated data resource for bioinformatics
A. Golovin, T. J. Oldfield, J. G. Tate, S. Velankar, G. J. Barton, H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Hussain, J. M. C. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, A. Pajon, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, G. J. Swaminathan, M. Tagari, S. Tromm, W. Vranken, and K. Henrick
Nucleic Acids Res. 2004 January 1; 32(Database issue): D211–D216. doi: 10.1093/nar/gkh078.
PMCID: PMC308812
MODBASE, a database of annotated comparative protein structure models, and associated resources
Ursula Pieper, Narayanan Eswar, Hannes Braberg, M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, and Andrej Sali
Nucleic Acids Res. 2004 January 1; 32(Database issue): D217–D222. doi: 10.1093/nar/gkh095.
PMCID: PMC308829
The distribution and query systems of the RCSB Protein Data Bank
Philip E. Bourne, Kenneth J. Addess, Wolfgang F. Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John Westbrook, and Helen M. Berman
Nucleic Acids Res. 2004 January 1; 32(Database issue): D223–D225. doi: 10.1093/nar/gkh096.
PMCID: PMC308830
SCOP database in 2004: refinements integrate structure and sequence family data
Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin
Nucleic Acids Res. 2004 January 1; 32(Database issue): D226–D229. doi: 10.1093/nar/gkh039.
PMCID: PMC308773
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
Jürgen Kopp and Torsten Schwede
Nucleic Acids Res. 2004 January 1; 32(Database issue): D230–D234. doi: 10.1093/nar/gkh008.
PMCID: PMC308743
The SUPERFAMILY database in 2004: additions and improvements
Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough
Nucleic Acids Res. 2004 January 1; 32(Database issue): D235–D239. doi: 10.1093/nar/gkh117.
PMCID: PMC308851
SURFACE: a database of protein surface regions for functional annotation
Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, and Manuela Helmer-Citterich
Nucleic Acids Res. 2004 January 1; 32(Database issue): D240–D244. doi: 10.1093/nar/gkh054.
PMCID: PMC308788
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Keiran Fleming, Arne Müller, Robert M. MacCallum, and Michael J. E. Sternberg
Nucleic Acids Res. 2004 January 1; 32(Database issue): D245–D250. doi: 10.1093/nar/gkh064.
PMCID: PMC308798
TOPS: an enhanced database of protein structural topology
Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, and David R. Westhead
Nucleic Acids Res. 2004 January 1; 32(Database issue): D251–D254. doi: 10.1093/nar/gkh060.
PMCID: PMC308794
Genew: the Human Gene Nomenclature Database, 2004 updates
Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Varsha K. Khodiyar, and Sue Povey
Nucleic Acids Res. 2004 January 1; 32(Database issue): D255–D257. doi: 10.1093/nar/gkh072.
PMCID: PMC308806
The Gene Ontology (GO) database and informatics resource
Nucleic Acids Res. 2004 January 1; 32(Database issue): D258–D261. doi: 10.1093/nar/gkh036.
PMCID: PMC308770
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D262–D266. doi: 10.1093/nar/gkh021.
PMCID: PMC308756
The Unified Medical Language System (UMLS): integrating biomedical terminology
Olivier Bodenreider
Nucleic Acids Res. 2004 January 1; 32(Database issue): D267–D270. doi: 10.1093/nar/gkh061.
PMCID: PMC308795
DEG: a database of essential genes
Ren Zhang, Hong-Yu Ou, and Chun-Ting Zhang
Nucleic Acids Res. 2004 January 1; 32(Database issue): D271–D272. doi: 10.1093/nar/gkh024.
PMCID: PMC308758
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
Karsten Suhre and Jean-Michel Claverie
Nucleic Acids Res. 2004 January 1; 32(Database issue): D273–D276. doi: 10.1093/nar/gkh053.
PMCID: PMC308787
The KEGG resource for deciphering the genome
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, and Masahiro Hattori
Nucleic Acids Res. 2004 January 1; 32(Database issue): D277–D280. doi: 10.1093/nar/gkh063.
PMCID: PMC308797
The ORFanage: an ORFan database
Naomi Siew, Yaniv Azaria, and Daniel Fischer
Nucleic Acids Res. 2004 January 1; 32(Database issue): D281–D283. doi: 10.1093/nar/gkh116.
PMCID: PMC308850
TransportDB: a relational database of cellular membrane transport systems
Qinghu Ren, Katherine H. Kang, and Ian T. Paulsen
Nucleic Acids Res. 2004 January 1; 32(Database issue): D284–D288. doi: 10.1093/nar/gkh016.
PMCID: PMC308751
VirGen: a comprehensive viral genome resource
Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, and A. S. Kolaskar
Nucleic Acids Res. 2004 January 1; 32(Database issue): D289–D292. doi: 10.1093/nar/gkh098.
PMCID: PMC308832
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, and David S. Wishart
Nucleic Acids Res. 2004 January 1; 32(Database issue): D293–D295. doi: 10.1093/nar/gkh108.
PMCID: PMC308842
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
Roy R. Chaudhuri, Arshad M. Khan, and Mark J. Pallen
Nucleic Acids Res. 2004 January 1; 32(Database issue): D296–D299. doi: 10.1093/nar/gkh031.
PMCID: PMC308765
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
Margrethe H. Serres, Sulip Goswami, and Monica Riley
Nucleic Acids Res. 2004 January 1; 32(Database issue): D300–D302. doi: 10.1093/nar/gkh087.
PMCID: PMC308821
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, and Julio Collado-Vides
Nucleic Acids Res. 2004 January 1; 32(Database issue): D303–D306. doi: 10.1093/nar/gkh140.
PMCID: PMC308874
MolliGen, a database dedicated to the comparative genomics of Mollicutes
Aurélien Barré, Antoine de Daruvar, and Alain Blanchard
Nucleic Acids Res. 2004 January 1; 32(Database issue): D307–D310. doi: 10.1093/nar/gkh114.
PMCID: PMC308848
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry
Nucleic Acids Res. 2004 January 1; 32(Database issue): D311–D314. doi: 10.1093/nar/gkh033.
PMCID: PMC308767
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet
Nucleic Acids Res. 2004 January 1; 32(Database issue): D315–D318. doi: 10.1093/nar/gkh091.
PMCID: PMC308825
SCMD: Saccharomyces cerevisiae Morphological Database
Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita
Nucleic Acids Res. 2004 January 1; 32(Database issue): D319–D322. doi: 10.1093/nar/gkh113.
PMCID: PMC308847
yMGV: a cross-species expression data mining tool
Gaëlle Lelandais, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, Claude Jacq, and Philippe Marc
Nucleic Acids Res. 2004 January 1; 32(Database issue): D323–D325. doi: 10.1093/nar/gkh135.
PMCID: PMC308869
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, Jr, L. David Sibley, and David S. Roos
Nucleic Acids Res. 2004 January 1; 32(Database issue): D326–D328. doi: 10.1093/nar/gkh112.
PMCID: PMC308846
CryptoDB: the Cryptosporidium genome resource
Daniela Puiu, Shinichiro Enomoto, Gregory A. Buck, Mitchell S. Abrahamsen, and Jessica C. Kissinger
Nucleic Acids Res. 2004 January 1; 32(Database issue): D329–D331. doi: 10.1093/nar/gkh050.
PMCID: PMC308784
dictyBase: a new Dictyostelium discoideum genome database
Lisa Kreppel, Petra Fey, Pascale Gaudet, Eric Just, Warren A. Kibbe, Rex L. Chisholm, and Alan R. Kimmel
Nucleic Acids Res. 2004 January 1; 32(Database issue): D332–D333. doi: 10.1093/nar/gkh138.
PMCID: PMC308872
Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
Junichi Watanabe, Yutaka Suzuki, Masahide Sasaki, and Sumio Sugano
Nucleic Acids Res. 2004 January 1; 32(Database issue): D334–D338. doi: 10.1093/nar/gkh115.
PMCID: PMC308849
GeneDB: a resource for prokaryotic and eukaryotic organisms
Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream, and Bart Barrell
Nucleic Acids Res. 2004 January 1; 32(Database issue): D339–D343. doi: 10.1093/nar/gkh007.
PMCID: PMC308742
TcruziDB: an integrated Trypanosoma cruzi genome resource
Michael Luchtan, Chetna Warade, D. Brent Weatherly, Wim M. Degrave, Rick L. Tarleton, and Jessica C. Kissinger
Nucleic Acids Res. 2004 January 1; 32(Database issue): D344–D346. doi: 10.1093/nar/gkh049.
PMCID: PMC308783
FLAGdb++: a database for the functional analysis of the Arabidopsis genome
Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick De Oliveira, Michel Caboche, Alain Lecharny, and Sébastien Aubourg
Nucleic Acids Res. 2004 January 1; 32(Database issue): D347–D350. doi: 10.1093/nar/gkh134.
PMCID: PMC308868
PHYTOPROT: a database of clusters of plant proteins
S. Mohseni-Zadeh, A. Louis, P. Brézellec, and J.-L. Risler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D351–D353. doi: 10.1093/nar/gkh040.
PMCID: PMC308774
PlantGDB, plant genome database and analysis tools
Qunfeng Dong, Shannon D. Schlueter, and Volker Brendel
Nucleic Acids Res. 2004 January 1; 32(Database issue): D354–D359. doi: 10.1093/nar/gkh046.
PMCID: PMC308780
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
Shu Ouyang and C. Robin Buell
Nucleic Acids Res. 2004 January 1; 32(Database issue): D360–D363. doi: 10.1093/nar/gkh099.
PMCID: PMC308833
TropGENE-DB, a multi-tropical crop information system
Manuel Ruiz, Mathieu Rouard, Louis Marie Raboin, Marc Lartaud, Pierre Lagoda, and Brigitte Courtois
Nucleic Acids Res. 2004 January 1; 32(Database issue): D364–D367. doi: 10.1093/nar/gkh105.
PMCID: PMC308839
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl
Nucleic Acids Res. 2004 January 1; 32(Database issue): D368–D372. doi: 10.1093/nar/gkh017.
PMCID: PMC308752
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-Werner Mewes, and Klaus F. X. Mayer
Nucleic Acids Res. 2004 January 1; 32(Database issue): D373–D376. doi: 10.1093/nar/gkh068.
PMCID: PMC308802
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang
Nucleic Acids Res. 2004 January 1; 32(Database issue): D377–D382. doi: 10.1093/nar/gkh085.
PMCID: PMC308819
The Rice PIPELINE: a unification tool for plant functional genomics
Junshi Yazaki, Keiichi Kojima, Kouji Suzuki, Naoki Kishimoto, and Shoshi Kikuchi
Nucleic Acids Res. 2004 January 1; 32(Database issue): D383–D387. doi: 10.1093/nar/gkh001.
PMCID: PMC308736
Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
Setsuko Komatsu, Keiichi Kojima, Kouji Suzuki, Kazuo Ozaki, and Kenichi Higo
Nucleic Acids Res. 2004 January 1; 32(Database issue): D388–D392. doi: 10.1093/nar/gkh020.
PMCID: PMC308755
MaizeGDB, the community database for maize genetics and genomics
Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, and Volker Brendel
Nucleic Acids Res. 2004 January 1; 32(Database issue): D393–D397. doi: 10.1093/nar/gkh011.
PMCID: PMC308746
SGMD: the Soybean Genomics and Microarray Database
Nadim W. Alkharouf and Benjamin F. Matthews
Nucleic Acids Res. 2004 January 1; 32(Database issue): D398–D400. doi: 10.1093/nar/gkh126.
PMCID: PMC308860
CADRE: the Central Aspergillus Data REpository
J. E. Mabey, M. J. Anderson, P. F. Giles, C. J. Miller, T. K. Attwood, N. W. Paton, E. Bornberg-Bauer, G. D. Robson, S. G. Oliver, and D. W. Denning
Nucleic Acids Res. 2004 January 1; 32(Database issue): D401–D405. doi: 10.1093/nar/gkh009.
PMCID: PMC308744
RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
Kristin C. Gunsalus, Wan-Chen Yueh, Philip MacMenamin, and Fabio Piano
Nucleic Acids Res. 2004 January 1; 32(Database issue): D406–D410. doi: 10.1093/nar/gkh110.
PMCID: PMC308844
WormBase: a multi-species resource for nematode biology and genomics
Todd W. Harris, Nansheng Chen, Fiona Cunningham, Marcela Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, and Lincoln D. Stein
Nucleic Acids Res. 2004 January 1; 32(Database issue): D411–D417. doi: 10.1093/nar/gkh066.
PMCID: PMC308800
Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
Reed J. Kelso, Michael Buszczak, Ana T. Quiñones, Claudia Castiblanco, Stacy Mazzalupo, and Lynn Cooley
Nucleic Acids Res. 2004 January 1; 32(Database issue): D418–D420. doi: 10.1093/nar/gkh014.
PMCID: PMC308749
AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
Jagan Srinivasan, Georg W. Otto, Ulrich Kahlow, Robert Geisler, and Ralf J. Sommer
Nucleic Acids Res. 2004 January 1; 32(Database issue): D421–D422. doi: 10.1093/nar/gkh057.
PMCID: PMC308791
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Todd Wylie, John C. Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W. Clifton, Asif Chinwalla, Robert H. Waterston, Richard K. Wilson, and James P. McCarter
Nucleic Acids Res. 2004 January 1; 32(Database issue): D423–D426. doi: 10.1093/nar/gkh010.
PMCID: PMC308745
NEMBASE: a resource for parasitic nematode ESTs
John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson, and Mark Blaxter
Nucleic Acids Res. 2004 January 1; 32(Database issue): D427–D430. doi: 10.1093/nar/gkh018.
PMCID: PMC308753
BRENDA, the enzyme database: updates and major new developments
Ida Schomburg, Antje Chang, Christian Ebeling, Marion Gremse, Christian Heldt, Gregor Huhn, and Dietmar Schomburg
Nucleic Acids Res. 2004 January 1; 32(Database issue): D431–D433. doi: 10.1093/nar/gkh081.
PMCID: PMC308815
IntEnz, the integrated relational enzyme database
Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, and Rolf Apweiler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D434–D437. doi: 10.1093/nar/gkh119.
PMCID: PMC308853
MetaCyc: a multiorganism database of metabolic pathways and enzymes
Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee, and Peter D. Karp
Nucleic Acids Res. 2004 January 1; 32(Database issue): D438–D442. doi: 10.1093/nar/gkh100.
PMCID: PMC308834
The aMAZE LightBench: a web interface to a relational database of cellular processes
Christian Lemer, Erick Antezana, Fabian Couche, Frédéric Fays, Xavier Santolaria, Rekin’s Janky, Yves Deville, Jean Richelle, and Shoshana J. Wodak
Nucleic Acids Res. 2004 January 1; 32(Database issue): D443–D448. doi: 10.1093/nar/gkh139.
PMCID: PMC308873
The Database of Interacting Proteins: 2004 update
Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, and David Eisenberg
Nucleic Acids Res. 2004 January 1; 32(Database issue): D449–D451. doi: 10.1093/nar/gkh086.
PMCID: PMC308820
IntAct: an open source molecular interaction database
Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David Sherman, and Rolf Apweiler
Nucleic Acids Res. 2004 January 1; 32(Database issue): D452–D455. doi: 10.1093/nar/gkh052.
PMCID: PMC308786
STCDB: Signal Transduction Classification Database
Ming Chen, Susana Lin, and Ralf Hofestaedt
Nucleic Acids Res. 2004 January 1; 32(Database issue): D456–D458. doi: 10.1093/nar/gkh079.
PMCID: PMC308813
MitoP2, an integrated database on mitochondrial proteins in yeast and man
C. Andreoli, H. Prokisch, K. Hörtnagel, J. C. Mueller, M. Münsterkötter, C. Scharfe, and T. Meitinger
Nucleic Acids Res. 2004 January 1; 32(Database issue): D459–D462. doi: 10.1093/nar/gkh137.
PMCID: PMC308871
MitoProteome: mitochondrial protein sequence database and annotation system
Dawn Cotter, Purnima Guda, Eoin Fahy, and Shankar Subramaniam
Nucleic Acids Res. 2004 January 1; 32(Database issue): D463–D467. doi: 10.1093/nar/gkh048.
PMCID: PMC308782
Ensembl 2004
E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp, and T. Hubbard
Nucleic Acids Res. 2004 January 1; 32(Database issue): D468–D470. doi: 10.1093/nar/gkh038.
PMCID: PMC308772
FREP: a database of functional repeats in mouse cDNAs
Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, , , Akihiko Konagaya, and Christian Schönbach
Nucleic Acids Res. 2004 January 1; 32(Database issue): D471–D475. doi: 10.1093/nar/gkh123.
PMCID: PMC308857
The Mouse Genome Database (MGD): integrating biology with the genome
Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig, and
Nucleic Acids Res. 2004 January 1; 32(Database issue): D476–D481. doi: 10.1093/nar/gkh125.
PMCID: PMC308859
The Mouse SAGE Site: database of public mouse SAGE libraries
Petr Divina and Jiří Forejt
Nucleic Acids Res. 2004 January 1; 32(Database issue): D482–D483. doi: 10.1093/nar/gkh058.
PMCID: PMC308792
PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries
Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, and Takashi Awata
Nucleic Acids Res. 2004 January 1; 32(Database issue): D484–D488. doi: 10.1093/nar/gkh037.
PMCID: PMC308771
AluGene: a database of Alu elements incorporated within protein-coding genes
Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, and Dan Graur
Nucleic Acids Res. 2004 January 1; 32(Database issue): D489–D492. doi: 10.1093/nar/gkh132.
PMCID: PMC308866
The UCSC Table Browser data retrieval tool
Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, and W. James Kent
Nucleic Acids Res. 2004 January 1; 32(Database issue): D493–D496. doi: 10.1093/nar/gkh103.
PMCID: PMC308837
Human protein reference database as a discovery resource for proteomics
Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T. K. B. Gandhi, K. N. Chandrika, Nandan Deshpande, Shubha Suresh, B. P. Rashmi, K. Shanker, N. Padma, Vidya Niranjan, H. C. Harsha, Naveen Talreja, B. M. Vrushabendra, M. A. Ramya, A. J. Yatish, Mary Joy, H. N. Shivashankar, M. P. Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R. Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C. K. Prasad, Chandan Kumar-Sinha, Krishna S. Deshpande, and Akhilesh Pandey
Nucleic Acids Res. 2004 January 1; 32(Database issue): D497–D501. doi: 10.1093/nar/gkh070.
PMCID: PMC308804
HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
Reiko Kikuno, Takahiro Nagase, Manabu Nakayama, Hisashi Koga, Noriko Okazaki, Daisuke Nakajima, and Osamu Ohara
Nucleic Acids Res. 2004 January 1; 32(Database issue): D502–D504. doi: 10.1093/nar/gkh035.
PMCID: PMC308769
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann
Nucleic Acids Res. 2004 January 1; 32(Database issue): D505–D508. doi: 10.1093/nar/gkh022.
PMCID: PMC314201
trome, trEST and trGEN: databases of predicted protein sequences
Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, and C. Victor Jongeneel
Nucleic Acids Res. 2004 January 1; 32(Database issue): D509–D511. doi: 10.1093/nar/gkh067.
PMCID: PMC308801
Pathbase: a database of mutant mouse pathology
Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Bjorn Rozell, Hannu Sariola, John P. Sundberg, and Andrew Ward
Nucleic Acids Res. 2004 January 1; 32(Database issue): D512–D515. doi: 10.1093/nar/gkh124.
PMCID: PMC308858
HGVbase: a curated resource describing human DNA variation and phenotype relationships
D. Fredman, G. Munns, D. Rios, F. Sjöholm, M. Siegfried, B. Lenhard, H. Lehväslaiho, and A. J. Brookes
Nucleic Acids Res. 2004 January 1; 32(Database issue): D516–D519. doi: 10.1093/nar/gkh111.
PMCID: PMC308845
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, and Jie Liang
Nucleic Acids Res. 2004 January 1; 32(Database issue): D520–D522. doi: 10.1093/nar/gkh104.
PMCID: PMC308838
RTCGD: retroviral tagged cancer gene database
Keiko Akagi, Takeshi Suzuki, Robert M. Stephens, Nancy A. Jenkins, and Neal G. Copeland
Nucleic Acids Res. 2004 January 1; 32(Database issue): D523–D527. doi: 10.1093/nar/gkh013.
PMCID: PMC308748
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
Bernice R. Packer, Meredith Yeager, Brian Staats, Robert Welch, Andrew Crenshaw, Maureen Kiley, Andrew Eckert, Michael Beerman, Edward Miller, Andrew Bergen, Nathaniel Rothman, Robert Strausberg, and Stephen J. Chanock
Nucleic Acids Res. 2004 January 1; 32(Database issue): D528–D532. doi: 10.1093/nar/gkh005.
PMCID: PMC308740
ERGDB: Estrogen Responsive Genes Database
Suisheng Tang, Hao Han, and Vladimir B. Bajic
Nucleic Acids Res. 2004 January 1; 32(Database issue): D533–D536. doi: 10.1093/nar/gkh083.
PMCID: PMC308817
Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, and Ross C. Hardison
Nucleic Acids Res. 2004 January 1; 32(Database issue): D537–D541. doi: 10.1093/nar/gkh006.
PMCID: PMC308741
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
Viviane Praz, Vidhya Jagannathan, and Philipp Bucher
Nucleic Acids Res. 2004 January 1; 32(Database issue): D542–D547. doi: 10.1093/nar/gkh107.
PMCID: PMC308841
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, and Yasushi Okazaki
Nucleic Acids Res. 2004 January 1; 32(Database issue): D548–D551. doi: 10.1093/nar/gkh093.
PMCID: PMC308827
GenePaint.org: an atlas of gene expression patterns in the mouse embryo
Axel Visel, Christina Thaller, and Gregor Eichele
Nucleic Acids Res. 2004 January 1; 32(Database issue): D552–D556. doi: 10.1093/nar/gkh029.
PMCID: PMC308763
The Centre for Modeling Human Disease Gene Trap resource
Christine To, Trevor Epp, Tammy Reid, Qing Lan, Mei Yu, Carol Y. J. Li, Minako Ohishi, Paula Hant, Nora Tsao, Guillermo Casallo, Janet Rossant, Lucy R. Osborne, and William L. Stanford
Nucleic Acids Res. 2004 January 1; 32(Database issue): D557–D559. doi: 10.1093/nar/gkh106.
PMCID: PMC308840
GermOnline, a cross-species community knowledgebase on germ cell differentiation
C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthière, L. Hermida, R. Koch, U. Schlecht, A. Amon, S. Brachat, M. Breitenbach, P. Briza, S. Caburet, M. Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. A. Grootegoed, R. Hawley, R. Ishii, B. Jégou, R. J. Kaufman, F. Klein, N. Lamb, B. Maro, K. Nasmyth, A. Nicolas, T. Orr-Weaver, P. Philippsen, C. Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, T. Schedl, M. Siep, A. Villeneuve, D. J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, and M. Primig
Nucleic Acids Res. 2004 January 1; 32(Database issue): D560–D567. doi: 10.1093/nar/gkh055.
PMCID: PMC308789
The mouse Gene Expression Database (GXD): updates and enhancements
David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and Martin Ringwald
Nucleic Acids Res. 2004 January 1; 32(Database issue): D568–D571. doi: 10.1093/nar/gkh069.
PMCID: PMC308803
Hembase: browser and genome portal for hematology and erythroid biology
Sung-Ho Goh, Y. Terry Lee, Gerard G. Bouffard, and Jeffery L. Miller
Nucleic Acids Res. 2004 January 1; 32(Database issue): D572–D574. doi: 10.1093/nar/gkh129.
PMCID: PMC308863
NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service
David J. Craigon, Nick James, John Okyere, Janet Higgins, Joan Jotham, and Sean May
Nucleic Acids Res. 2004 January 1; 32(Database issue): D575–D577. doi: 10.1093/nar/gkh133.
PMCID: PMC308867
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, and Eric P. Hoffman
Nucleic Acids Res. 2004 January 1; 32(Database issue): D578–D581. doi: 10.1093/nar/gkh003.
PMCID: PMC308738
GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
György Babnigg and Carol S. Giometti
Nucleic Acids Res. 2004 January 1; 32(Database issue): D582–D585. doi: 10.1093/nar/gkh089.
PMCID: PMC308823
ANTIMIC: a database of antimicrobial sequences
M. Brahmachary, S. P. T. Krishnan, J. L. Y. Koh, A. M. Khan, S. H. Seah, T. W. Tan, V. Brusic, and V. B. Bajic
Nucleic Acids Res. 2004 January 1; 32(Database issue): D586–D589. doi: 10.1093/nar/gkh032.
PMCID: PMC308766
APD: the Antimicrobial Peptide Database
Zhe Wang and Guangshun Wang
Nucleic Acids Res. 2004 January 1; 32(Database issue): D590–D592. doi: 10.1093/nar/gkh025.
PMCID: PMC308759
The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
Lee Whitmore and B. A. Wallace
Nucleic Acids Res. 2004 January 1; 32(Database issue): D593–D594. doi: 10.1093/nar/gkh077.
PMCID: PMC308811
Commercial Database Article
ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection
Feng Liang, Udayakumar Matrubutham, Babak Parvizi, Jessica Yen, Daniel Duan, Jyotika Mirchandani, Sandra Hashima, Uyen Nguyen, Eric Ubil, Jake Loewenheim, Xin Yu, Sara Sipes, Wendy Williams, Ling Wang, Robert Bennett, and John Carrino
Nucleic Acids Res. 2004 January 1; 32(Database issue): D595–D599. doi: 10.1093/nar/gkh118.
PMCID: PMC314203
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