| | Editorial Nucleic Acids Res. 2006 January 1; 34(Database issue): D1. Published online 2005 December 28. doi: 10.1093/nar/gkj150.PMCID: PMC1347512 Articles The Molecular Biology Database Collection: 2006 update Michael Y. Galperin PMCID: PMC1347524 DDBJ in preparation for overview of research activities behind data submissions Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, and Yoshio Tateno PMCID: PMC1347473 EMBL Nucleotide Sequence Database: developments in 2005 Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler PMCID: PMC1347492 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler PMCID: PMC1347519 ChimerDB—a knowledgebase for fusion sequences Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, and Sanghyuk Lee PMCID: PMC1347382 HUMHOT: a database of human meiotic recombination hot spots K. T. Nishant, Chetan Kumar, and M. R. S. Rao PMCID: PMC1347372 The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations Rivka L. Glaser, Joshua P. Ramsay, and Ian M. Morison PMCID: PMC1347463 ISfinder: the reference centre for bacterial insertion sequences P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, and M. Chandler PMCID: PMC1347377 Transterm—extended search facilities and improved integration with other databases Grant H. Jacobs, Peter A. Stockwell, Warren P. Tate, and Chris M. Brown PMCID: PMC1347521 ASAP: a resource for annotating, curating, comparing, and disseminating genomic data Jeremy D. Glasner, Michael Rusch, Paul Liss, Guy Plunkett, III, Eric L. Cabot, Aaron Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C. Gilson, and Nicole T. Perna PMCID: PMC1347526 ASD: a bioinformatics resource on alternative splicing Stefan Stamm, Jean-Jack Riethoven, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Yesheng Tang, Nuno L. Barbosa-Morais, and Thangavel Alphonse Thanaraj PMCID: PMC1347394 Hollywood: a comparative relational database of alternative splicing Dirk Holste, George Huo, Vivian Tung, and Christopher B. Burge PMCID: PMC1347411 ABS: a database of Annotated regulatory Binding Sites from orthologous promoters Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer, and Roderic Guigó PMCID: PMC1347478 cisRED: a database system for genome-scale computational discovery of regulatory elements G. Robertson, M. Bilenky, K. Lin, A. He, W. Yuen, M. Dagpinar, R. Varhol, K. Teague, O. L. Griffith, X. Zhang, Y. Pan, M. Hassel, M. C. Sleumer, W. Pan, E. D. Pleasance, M. Chuang, H. Hao, Y. Y. Li, N. Robertson, C. Fjell, B. Li, S. B. Montgomery, T. Astakhova, J. Zhou, J. Sander, A. S. Siddiqui, and S. J. M. Jones PMCID: PMC1347438 DBD: a transcription factor prediction database Sarah K. Kummerfeld and Sarah A. Teichmann PMCID: PMC1347493 EPD in its twentieth year: towards complete promoter coverage of selected model organisms Christoph D. Schmid, Rouaïda Perier, Viviane Praz, and Philipp Bucher PMCID: PMC1347508 DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, and Sumio Sugano PMCID: PMC1347491 HTPSELEX—a database of high-throughput SELEX libraries for transcription factor binding sites Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, and Philipp Bucher PMCID: PMC1347412 A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, and Boris Lenhard PMCID: PMC1347477 MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim H.-M. Huang, and Ramana V. Davuluri PMCID: PMC1347458 TiProD: the Tissue-specific Promoter Database Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander Kel, and Edgar Wingender PMCID: PMC1347475 TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes V. Matys, O. V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B. Lewicki-Potapov, H. Saxel, A. E. Kel, and E. Wingender PMCID: PMC1347505 ARED 3.0: the large and diverse AU-rich transcriptome Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar PMCID: PMC1347415 Argonaute—a database for gene regulation by mammalian microRNAs Priyanka Shahi, Serguei Loukianiouk, Andreas Bohne-Lang, Marc Kenzelmann, Stefan Küffer, Sabine Maertens, Roland Eils, Herrmann-Josef Gröne, Norbert Gretz, and Benedikt Brors PMCID: PMC1347455 GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences Rumen Kostadinov, Nishtha Malhotra, Manuel Viotti, Robert Shine, Lawrence D'Antonio, and Paramjeet Bagga PMCID: PMC1347436 IRESite: the database of experimentally verified IRES structures ( www.iresite.org) Martin Mokrejš, Václav Vopálenský, Ondřej Kolenatý, Tomáš Mašek, Zuzana Feketová, Petra Sekyrová, Barbora Škaloudová, Vítězslav Kříž, and Martin Pospíšek PMCID: PMC1347444 MeRNA: a database of metal ion binding sites in RNA structures Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, and Stephen R. Holbrook PMCID: PMC1347421 miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes Paul W.C. Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, and Ivo L. Hofacker PMCID: PMC1347497 miRBase: microRNA sequences, targets and gene nomenclature Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, and Anton J. Enright PMCID: PMC1347474 MODOMICS: a database of RNA modification pathways Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki PMCID: PMC1347447 NPInter: the noncoding RNAs and protein related biomacromolecules interaction database Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen PMCID: PMC1347388 RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs A. Olson, N. Sheth, J. S. Lee, G. Hannon, and R. Sachidanandam PMCID: PMC1347414 snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs Laurent Lestrade and Michel J. Weber PMCID: PMC1347365 The tmRDB and SRPDB resources Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, and Christian Zwieb PMCID: PMC1347504 MIPS: analysis and annotation of proteins from whole genomes in 2005 H. W. Mewes, D. Frishman, K. F. X. Mayer, M. Münsterkötter, O. Noubibou, P. Pagel, T. Rattei, M. Oesterheld, A. Ruepp, and V. Stümpflen PMCID: PMC1347510 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, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Stephen T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O. Suzek, Roman Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko PMCID: PMC1347520 TCDB: the Transporter Classification Database for membrane transport protein analyses and information Milton H. Saier, Jr, Can V. Tran, and Ravi D. Barabote PMCID: PMC1334385 The Universal Protein Resource (UniProt): an expanding universe of protein information Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, and Baris Suzek PMCID: PMC1347523 CyBase: a database of cyclic protein sequence and structure Jason P. Mulvenna, Conan Wang, and David J. Craik PMCID: PMC1347368 PINT: Protein–protein Interactions Thermodynamic Database M. D. Shaji Kumar and M. Michael Gromiha PMCID: PMC1347380 PPD v1.0—an integrated, web-accessible database of experimentally determined protein pKa values Christopher P. Toseland, Helen McSparron, Matthew N. Davies, and Darren R. Flower PMCID: PMC1347398 ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions M. D. Shaji Kumar, K. Abdulla Bava, M. Michael Gromiha, Ponraj Prabakaran, Koji Kitajima, Hatsuho Uedaira, and Akinori Sarai PMCID: PMC1347465 The REFOLD database: a tool for the optimization of protein expression and refolding Michelle K. M. Chow, Abdullah A. Amin, Kate F. Fulton, Thushan Fernando, Lawrence Kamau, Chris Batty, Michael Louca, Storm Ho, James C. Whisstock, Stephen P. Bottomley, and Ashley M. Buckle PMCID: PMC1347443 LOCATE: a mouse protein subcellular localization database J. Lynn Fink, Rajith N. Aturaliya, Melissa J. Davis, Fasheng Zhang, Kelly Hanson, Melvena S. Teasdale, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, and Rohan D. Teasdale PMCID: PMC1347432 NOPdb: Nucleolar Proteome Database Anthony Kar Lun Leung, Laura Trinkle-Mulcahy, Yun Wah Lam, Jens S. Andersen, Matthias Mann, and Angus I. Lamond PMCID: PMC1347367 Nuclear Receptor Signaling Atlas ( www.nursa.org): hyperlinking the nuclear receptor signaling community Rainer B. Lanz, Zeljko Jericevic, William J. Zuercher, Chris Watkins, David L. Steffen, Ronald Margolis, and Neil J. McKenna PMCID: PMC1347392 The PROSITE database Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, and Christian J. A. Sigrist PMCID: PMC1347426 SitesBase: a database for structure-based protein–ligand binding site comparisons Nicola D. Gold and Richard M. Jackson PMCID: PMC1347425 BIOZON: a hub of heterogeneous biological data Aaron Birkland and Golan Yona PMCID: PMC1347515 MulPSSM: a database of multiple position-specific scoring matrices of protein domain families V. S. Gowri, O. Krishnadev, C. S. Swamy, and N. Srinivasan PMCID: PMC1347406 Pfam: clans, web tools and services Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, and Alex Bateman PMCID: PMC1347511 SIMAP: the similarity matrix of proteins Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, and H. Werner Mewes PMCID: PMC1347468 SMART 5: domains in the context of genomes and networks Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, and Peer Bork PMCID: PMC1347442 The EROP-Moscow oligopeptide database Alexander A. Zamyatnin, Alexander S. Borchikov, Michail G. Vladimirov, and Olga L. Voronina PMCID: PMC1347371 LGICdb: a manually curated sequence database after the genomes Marco Donizelli, Marie-Ange Djite, and Nicolas Le Novère PMCID: PMC1347466 MEROPS: the peptidase database Neil D. Rawlings, Fraser R. Morton, and Alan J. Barrett PMCID: PMC1347452 DMAPS: a database of multiple alignments for protein structures Chittibabu Guda, Lipika R. Pal, and Ilya N. Shindyalov PMCID: PMC1347381 Flexible Structural Neighborhood—a database of protein structural similarities and alignments Zhanwen Li, Yuzhen Ye, and Adam Godzik PMCID: PMC1347486 Gene3D: modelling protein structure, function and evolution Corin Yeats, Michael Maibaum, Russell Marsden, Mark Dibley, David Lee, Sarah Addou, and Christine A. Orengo PMCID: PMC1347420 iMOTdb—a comprehensive collection of spatially interacting motifs in proteins Ganesan Pugalenthi, Anirban Bhaduri, and R. Sowdhamini PMCID: PMC1347487 E-MSD: improving data deposition and structure quality M. Tagari, J. Tate, G. J. Swaminathan, R. Newman, A. Naim, W. Vranken, A. Kapopoulou, A. Hussain, J. Fillon, K. Henrick, and S. Velankar PMCID: PMC1347525 MODBASE: a database of annotated comparative protein structure models and associated resources Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, M. S. Madhusudhan, Andrea Rossi, Marc Marti-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, and Andrej Sali PMCID: PMC1347422 The Database of Macromolecular Motions: new features added at the decade mark Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, and Mark Gerstein PMCID: PMC1347409 The RCSB PDB information portal for structural genomics Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John Westbrook, Philip E. Bourne, and Helen M. Berman PMCID: PMC1347482 The PMDB Protein Model Database Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto, Ivano Giuseppe Talamo, and Anna Tramontano PMCID: PMC1347467 SCOPPI: a structural classification of protein–protein interfaces Christof Winter, Andreas Henschel, Wan Kyu Kim, and Michael Schroeder PMCID: PMC1347461 The SWISS-MODEL Repository: new features and functionalities Jürgen Kopp and Torsten Schwede PMCID: PMC1347419 The HUGO Gene Nomenclature Database, 2006 updates Tina A. Eyre, Fabrice Ducluzeau, Tam P. Sneddon, Sue Povey, Elspeth A. Bruford, and Michael J. Lush PMCID: PMC1347509 The Gene Ontology (GO) project in 2006 Gene Ontology Consortium PMCID: PMC1347384 PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees Simon Whelan, Paul I. W. de Bakker, Emmanuel Quevillon, Nicolas Rodriguez, and Nick Goldman PMCID: PMC1347450 The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, and Nikos C. Kyrpides PMCID: PMC1347507 xBASE, a collection of online databases for bacterial comparative genomics Roy R. Chaudhuri and Mark J. Pallen PMCID: PMC1347502 ICDS database: interrupted CoDing sequences in prokaryotic genomes Emmanuel Perrodou, Caroline Deshayes, Jean Muller, Christine Schaeffer, Alain Van Dorsselaer, Raymond Ripp, Olivier Poch, Jean-Marc Reyrat, and Odile Lecompte PMCID: PMC1347423 The integrated microbial genomes (IMG) system Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia Ivanova, and Nikos C. Kyrpides PMCID: PMC1347387 INVHOGEN: a database of homologous invertebrate genes Ingo Paulsen and Arndt von Haeseler PMCID: PMC1347462 From genomics to chemical genomics: new developments in KEGG Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F. Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, and Mika Hirakawa PMCID: PMC1347464 ODB: a database of operons accumulating known operons across multiple genomes Shujiro Okuda, Toshiaki Katayama, Shuichi Kawashima, Susumu Goto, and Minoru Kanehisa PMCID: PMC1347400 OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups Feng Chen, Aaron J. Mackey, Christian J. Stoeckert, Jr, and David S. Roos PMCID: PMC1347485 PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza PMCID: PMC1347457 SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes Huiquan Wang, Miroslava Kaloper, and Craig J. Benham PMCID: PMC1347370 VMD: a community annotation database for oomycetes and microbial genomes Sucheta Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas, and Brett M. Tyler PMCID: PMC1347405 DPVweb: a comprehensive database of plant and fungal virus genes and genomes Michael J. Adams and John F. Antoniw PMCID: PMC1347386 VIPERdb: a relational database for structural virology Craig M. Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay Siddavanahalli, Chandrajit Bajaj, John E. Johnson, Charles L. Brooks, III, and Vijay S. Reddy PMCID: PMC1347395 Megx.net—database resources for marine ecological genomics Thierry Lombardot, Renzo Kottmann, Hauke Pfeffer, Michael Richter, Hanno Teeling, Christian Quast, and Frank Oliver Glöckner PMCID: PMC1347433 RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides PMCID: PMC1347518 ShiBASE: an integrated database for comparative genomics of Shigella Jian Yang, Lihong Chen, Jun Yu, Lilian Sun, and Qi Jin PMCID: PMC1347396 LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species Guido Dieterich, Uwe Kärst, Elmar Fischer, Jürgen Wehland, and Lothar Jänsch PMCID: PMC1347434 The UCSC Archaeal Genome Browser Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe PMCID: PMC1347496 Human protein reference database—2006 update Gopa R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, Raghunath Reddy, T. Madhan Raghavan, Shalini Menon, G. Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M. Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K. S. Arun, Salil Sharma, K. N. Chandrika, Nandan Deshpande, Kshitish Palvankar, R. Raghavnath, R. Krishnakanth, Hiren Karathia, B. Rekha, Rashmi Nayak, G. Vishnupriya, H. G. Mohan Kumar, M. Nagini, G. S. Sameer Kumar, Rojan Jose, P. Deepthi, S. Sujatha Mohan, T. K. B. Gandhi, H. C. Harsha, Krishna S. Deshpande, Malabika Sarker, T. S. Keshava Prasad, and Akhilesh Pandey PMCID: PMC1347503 The LIFEdb database in 2006 Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann PMCID: PMC1347501 CryptoDB: a Cryptosporidium bioinformatics resource update Mark Heiges, Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita Kaluskar, Philippa Rhodes, Sammy Wang, Cong-Zhou He, Yanqi Su, John Miller, Eileen Kraemer, and Jessica C. Kissinger PMCID: PMC1347441 dictyBase, the model organism database for Dictyostelium discoideum Rex L. Chisholm, Pascale Gaudet, Eric M. Just, Karen E. Pilcher, Petra Fey, Sohel N. Merchant, and Warren A. Kibbe PMCID: PMC1347453 TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi Fernán Agüero, Wenlong Zheng, D. Brent Weatherly, Pablo Mendes, and Jessica C. Kissinger PMCID: PMC1347470 Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts David Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet PMCID: PMC1347522 MPact: the MIPS protein interaction resource on yeast Ulrich Güldener, Martin Münsterkötter, Matthias Oesterheld, Philipp Pagel, Andreas Ruepp, Hans-Werner Mewes, and Volker Stümpflen PMCID: PMC1347366 Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert Nash, Julie Park, Rose Oughtred, Marek Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, and J. Michael Cherry PMCID: PMC1347479 The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Miguel C. Teixeira, Pedro Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira, and Isabel Sá-Correia PMCID: PMC1347376 Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser Kevin P. Byrne and Kenneth H. Wolfe PMCID: PMC1347404 FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes, and Gerhard Adam PMCID: PMC1347389 PHI-base: a new database for pathogen host interactions Rainer Winnenburg, Thomas K. Baldwin, Martin Urban, Chris Rawlings, Jacob Köhler, and Kim E. Hammond-Kosack PMCID: PMC1347410 Phytophthora functional genomics database (PFGD): functional genomics of phytophthora–plant interactions Kamal Gajendran, Michael D. Gonzales, Andrew Farmer, Eric Archuleta, Joe Win, Mark E. Waugh, and Sophien Kamoun PMCID: PMC1347481 SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans David H. Johnson, Jun Tsao, Ming Luo, and Mike Carson PMCID: PMC1347399 WormBase: better software, richer content Erich M. Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa Girard, Todd W. Harris, Eimear E. Kenny, Ranjana Kishore, Dan Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Phil Ozersky, Andrei Petcherski, Anthony Rogers, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin, John Spieth, Lincoln D. Stein, and Paul W. Sternberg PMCID: PMC1347424 FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets David Sims, Borisas Bursteinas, Qiong Gao, Marketa Zvelebil, and Buzz Baum PMCID: PMC1347401 FlyBase: anatomical data, images and queries Gary Grumbling, Victor Strelets, and The FlyBase Consortium PMCID: PMC1347431 FlyRNAi: the Drosophila RNAi screening center database Ian Flockhart, Matthew Booker, Amy Kiger, Michael Boutros, Susan Armknecht, Nadire Ramadan, Kris Richardson, Andrew Xu, Norbert Perrimon, and Bernard Mathey-Prevot PMCID: PMC1347476 StellaBase: The Nematostella vectensis Genomics Database James C. Sullivan, Joseph F. Ryan, James A. Watson, Jeramy Webb, James C. Mullikin, Daniel Rokhsar, and John R. Finnerty PMCID: PMC1347383 Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research Nicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert Nash, Anand Sethuraman, Shuai Weng, and J. Michael Cherry PMCID: PMC1347417 Pathguide: a Pathway Resource List Gary D. Bader, Michael P. Cary, and Chris Sander PMCID: PMC1347488 LMPD: LIPID MAPS proteome database Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, and Shankar Subramaniam PMCID: PMC1347484 MetaCyc: a multiorganism database of metabolic pathways and enzymes Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp PMCID: PMC1347490 The University of Minnesota Biocatalysis/Biodegradation Database: the first decade Lynda B. M. Ellis, Dave Roe, and Lawrence P. Wackett PMCID: PMC1347439 AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB Peter Block, Christoph A. Sotriffer, Ingo Dramburg, and Gerhard Klebe PMCID: PMC1347402 pSTIING: a ‘systems’ approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, and Marketa Zvelebil PMCID: PMC1347407 BioGRID: a general repository for interaction datasets Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers PMCID: PMC1347471 EndoNet: an information resource about endocrine networks Anatolij Potapov, Ines Liebich, Jürgen Dönitz, Knut Schwarzer, Nicole Sasse, Torsten Schoeps, Torsten Crass, and Edgar Wingender PMCID: PMC1347483 TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations Mathias Krull, Susanne Pistor, Nico Voss, Alexander Kel, Ingmar Reuter, Deborah Kronenberg, Holger Michael, Knut Schwarzer, Anatolij Potapov, Claudia Choi, Olga Kel-Margoulis, and Edgar Wingender PMCID: PMC1347469 DBTGR: a database of tunicate promoters and their regulatory elements Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, and Kenta Nakai PMCID: PMC1347427 Ensembl 2006 E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Gräf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kähäri, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and T. J. P. Hubbard PMCID: PMC1347495 The Mouse Genome Database (MGD): updates and enhancements Judith A. Blake, Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, and Mouse Genome Database Group PMCID: PMC1347448 The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context Andreas Ruepp, Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Christine Skornia, Steffi Wanka, Thomas Rattei, Philipp Pagel, Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen, and H. Werner Mewes PMCID: PMC1347437 TreeFam: a curated database of phylogenetic trees of animal gene families Heng Li, Avril Coghlan, Jue Ruan, Lachlan James Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Weimou Zheng, Paramvir Dehal, Jun Wang, and Richard Durbin PMCID: PMC1347480 The Zebrafish Information Network: the zebrafish model organism database Judy Sprague, Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Prita Mani, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Sierra Taylor, Ceri E. Van Slyke, and Monte Westerfield PMCID: PMC1347449 QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL Kremena V. Star, Quingbin Song, Andy Zhu, and Erwin P. Böttinger PMCID: PMC1347390 The UCSC Genome Browser Database: update 2006 A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, J. Hillman-Jackson, R. M. Kuhn, J. S. Pedersen, A. Pohl, B. J. Raney, K. R. Rosenbloom, A. Siepel, K. E. Smith, C. W. Sugnet, A. Sultan-Qurraie, D. J. Thomas, H. Trumbower, R. J. Weber, M. Weirauch, A. S. Zweig, D. Haussler, and W. J. Kent PMCID: PMC1347506 OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI Johann Lenffer, Frank W. Nicholas, Kao Castle, Arjun Rao, Stefan Gregory, Michael Poidinger, Matthew D. Mailman, and Shoba Ranganathan PMCID: PMC1347514 CTGA: the database for genetic disorders in Arab populations Ghazi O. Tadmouri, Mahmoud Taleb Al Ali, Sarah Al-Haj Ali, and Najib Al Khaja PMCID: PMC1347378 HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma Xiaosong Wang, Haitao Zhao, Qingwen Xu, Weibo Jin, Changning Liu, Huagang Zhang, Zhibin Huang, Xinyu Zhang, Yu Zhang, Dianqi Xin, Andrew J. G. Simpson, Lloyd J. Old, Yanqun Na, Yi Zhao, and Weifeng Chen PMCID: PMC1347445 ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, and Emmanuel Barillot PMCID: PMC1347385 SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes Bernice R. Packer, Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman, Liqun Qi, Hugues Sicotte, Brian Staats, Mekhala Acharya, Andrew Crenshaw, Andrew Eckert, Vinita Puri, Daniela S. Gerhard, and Stephen J. Chanock PMCID: PMC1347513 dbPTM: an information repository of protein post-translational modification Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, and Tzu-Hao Wang PMCID: PMC1347446 BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka, Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto, and Kousaku Okubo PMCID: PMC1347499 CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, and Yoshihide Hayashizaki PMCID: PMC1347397 EMAGE: a spatial database of gene expression patterns during mouse embryo development Jeffrey H. Christiansen, Yiya Yang, Shanmugasundaram Venkataraman, Lorna Richardson, Peter Stevenson, Nicholas Burton, Richard A. Baldock, and Duncan R. Davidson PMCID: PMC1347369 The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse Alex S. Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, and Thomas E. Ferrin PMCID: PMC1347459 PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns Thomas McLaughlin, Jennifer A. Siepen, Julian Selley, Jennifer A. Lynch, King Wai Lau, Hujun Yin, Simon J. Gaskell, and Simon J. Hubbard PMCID: PMC1347429 The PeptideAtlas project Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, and Ruedi Aebersold PMCID: PMC1347403 PRIDE: a public repository of protein and peptide identifications for the proteomics community Philip Jones, Richard G. Côté, Lennart Martens, Antony F. Quinn, Chris F. Taylor, William Derache, Henning Hermjakob, and Rolf Apweiler PMCID: PMC1347500 AOBase: a database for antisense oligonucleotides selection and design Xiaochen Bo, Shaoke Lou, Daochun Sun, Jing Yang, and Shengqi Wang PMCID: PMC1347428 DrugBank: a comprehensive resource for in silico drug discovery and exploration David S. Wishart, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, and Jennifer Woolsey PMCID: PMC1347430 GLIDA: GPCR-ligand database for chemical genomic drug discovery Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi, and Gozoh Tsujimoto PMCID: PMC1347391 SuperNatural: a searchable database of available natural compounds Mathias Dunkel, Melanie Fullbeck, Stefanie Neumann, and Robert Preissner PMCID: PMC1347494 RTPrimerDB: the real-time PCR primer and probe database, major update 2006 Filip Pattyn, Piet Robbrecht, Anne De Paepe, Frank Speleman, and Jo Vandesompele PMCID: PMC1347517 BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nicolas Le Novère, Benjamin Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert Sauro, Maria Schilstra, Bruce Shapiro, Jacky L. Snoep, and Michael Hucka PMCID: PMC1347454 ChloroplastDB: the Chloroplast Genome Database Liying Cui, Narayanan Veeraraghavan, Alexander Richter, Kerr Wall, Robert K. Jansen, Jim Leebens-Mack, Izabela Makalowska, and Claude W. dePamphilis PMCID: PMC1347418 GOBASE—a database of organelle and bacterial genome information Emmet A. O'Brien, Yue Zhang, LiuSong Yang, Eric Wang, Veronique Marie, B. Franz Lang, and Gertraud Burger PMCID: PMC1347460 HvrBase++: a phylogenetic database for primate species Jochen Kohl, Ingo Paulsen, Thomas Laubach, Achim Radtke, and Arndt von Haeseler PMCID: PMC1347393 MitoP2: the mitochondrial proteome database—now including mouse data H. Prokisch, C. Andreoli, U. Ahting, K. Heiss, A. Ruepp, C. Scharfe, and T. Meitinger PMCID: PMC1347489 DRASTIC—INSIGHTS: querying information in a plant gene expression database Davina K. Button, Kevan M. A. Gartland, Leslie D. Ball, Louis Natanson, Jill S. Gartland, and Gary D. Lyon PMCID: PMC1347498 Gramene: a bird's eye view of cereal genomes Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard, Shuly Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler, Lincoln Stein, and Susan McCouch PMCID: PMC1347516 Phytome: a platform for plant comparative genomics Stefanie Hartmann, Dihui Lu, Jason Phillips, and Todd J. Vision PMCID: PMC1347408 Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA Mayumi Nakano, Kan Nobuta, Kalyan Vemaraju, Shivakundan Singh Tej, Jeremy W. Skogen, and Blake C. Meyers PMCID: PMC1347440 OryGenesDB: a database for rice reverse genetics G. Droc, M. Ruiz, P. Larmande, A. Pereira, P. Piffanelli, J. B. Morel, A. Dievart, B. Courtois, E. Guiderdoni, and C. Périn PMCID: PMC1347375 The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, and Takuji Sasaki PMCID: PMC1347456 RMD: a rice mutant database for functional analysis of the rice genome Jianwei Zhang, Caishun Li, Changyin Wu, Lizhong Xiong, Guoxing Chen, Qifa Zhang, and Shiping Wang PMCID: PMC1347379 mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences Max Ingman and Ulf Gyllensten PMCID: PMC1347373 Panzea: a database and resource for molecular and functional diversity in the maize genome Wei Zhao, Payan Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward Buckler, John Doebley, Brandon Gaut, Major Goodman, Jim Holland, Stephen Kresovich, Michael McMullen, Lincoln Stein, and Doreen Ware PMCID: PMC1347374 The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max Jeffry L. Shultz, Deepak Kurunam, Kay Shopinski, M. Javed Iqbal, Samreen Kazi, Kimberley Zobrist, Rabia Bashir, Satsuki Yaegashi, Nagajyothi Lavu, Ahmed J. Afzal, Charles R. Yesudas, M. Abdelmajid Kassem, Chengcang Wu, Hong Bin Zhang, Christopher D. Town, Khalid Meksem, and David A. Lightfoot PMCID: PMC1347413 Tomato Expression Database (TED): a suite of data presentation and analysis tools Zhangjun Fei, Xuemei Tang, Rob Alba, and James Giovannoni PMCID: PMC1347472 The TIGR Maize Database Agnes P. Chan, Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C. Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, and Pablo D. Rabinowicz PMCID: PMC1347435 Epitome: database of structure-inferred antigenic epitopes Avner Schlessinger, Yanay Ofran, Guy Yachdav, and Burkhard Rost PMCID: PMC1347416 IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences Véronique Giudicelli, Patrice Duroux, Chantal Ginestoux, Géraldine Folch, Joumana Jabado-Michaloud, Denys Chaume, and Marie-Paule Lefranc PMCID: PMC1347451 |
