Database Issue 2006 @ NAR
http://nar.oxfordjournals.org/content/vol34/suppl_1/index.dtl
いつの間にか、2006年度号が出てますね。さて、注目を:
Rivka L. Glaser, Joshua P. Ramsay, and Ian M. Morison The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations Nucl. Acids Res. 2006 34: D29-D31; doi:10.1093/nar/gkj101 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D29 imprinting。つながらん... Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer, and Roderic Guigó ABS: a database of Annotated regulatory Binding Sites from orthologous promoters Nucl. Acids Res. 2006 34: D63-D67; doi:10.1093/nar/gkj116 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D63 Annotated、ってトコが魅かれる。どんな具合かな。 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 cisRED: a database system for genome-scale computational discovery of regulatory elements Nucl. Acids Res. 2006 34: D68-D73; doi:10.1093/nar/gkj075 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D68 EnsEMBL/UCSCとかでも見れるヤツ。 Sarah K. Kummerfeld and Sarah A. Teichmann DBD: a transcription factor prediction database Nucl. Acids Res. 2006 34: D74-D81; doi:10.1093/nar/gkj131 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D74 DBアクセスのクラスかと思ってしまうではないか。 Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, and Sumio Sugano DBTSS: DataBase of Human Transcription Start Sites, progress report 2006 Nucl. Acids Res. 2006 34: D86-D89; doi:10.1093/nar/gkj129 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D86 いわずもがな。DBTSS。 Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, and Philipp Bucher HTPSELEX―a database of high-throughput SELEX libraries for transcription factor binding sites Nucl. Acids Res. 2006 34: D90-D94; doi:10.1093/nar/gkj049 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D90 hyperselex、ステキな響きだ...と思ったら読み違えてた :-) Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, and Boris Lenhard A new generation of JASPAR, the open-access repository for transcription factor binding site profiles Nucl. Acids Res. 2006 34: D95-D97; doi:10.1093/nar/gkj115 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D95 いわずもがな。Jaspar。 Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim H.-M. Huang, and Ramana V. Davuluri MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data Nucl. Acids Res. 2006 34: D98-D103; doi:10.1093/nar/gkj096 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D98 ChIP/ChipのデータcentralなDB。ちょっと期待。 Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander Kel, and Edgar Wingender TiProD: the Tissue-specific Promoter Database Nucl. Acids Res. 2006 34: D104-D107; doi:10.1093/nar/gkj113 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D104 何のデータを使うのかな？ まさかchipじゃあるまいね。 Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar ARED 3.0: the large and diverse AU-rich transcriptome Nucl. Acids Res. 2006 34: D111-D114; doi:10.1093/nar/gkj052 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D111 そんな観点があるんだ。未知の世界。 Functional RNAなDBもいっぱいあるけど、疲れたので割愛。 Jason P. Mulvenna, Conan Wang, and David J. Craik CyBase: a database of cyclic protein sequence and structure Nucl. Acids Res. 2006 34: D192-D194; doi:10.1093/nar/gkj005 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D192 名前でびびったので一応。sybaseではナイ。 Rainer B. Lanz, Zeljko Jericevic, William J. Zuercher, Chris Watkins, David L. Steffen, Ronald Margolis, and Neil J. McKenna Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community Nucl. Acids Res. 2006 34: D221-D226; doi:10.1093/nar/gkj029 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D221 核レセプター。hyperlinkのデータベース、と開き直ってみる。 Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, and Christian J. A. Sigrist The PROSITE database Nucl. Acids Res. 2006 34: D227-D230; doi:10.1093/nar/gkj063 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D227 まだ更新するのね。すごい。 Shujiro Okuda, Toshiaki Katayama, Shuichi Kawashima, Susumu Goto, and Minoru Kanehisa ODB: a database of operons accumulating known operons across multiple genomes Nucl. Acids Res. 2006 34: D358-D362; doi:10.1093/nar/gkj037 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D358 こないだ話をしてくれたモノ、かな？ Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, and Mike Tyers BioGRID: a general repository for interaction datasets Nucl. Acids Res. 2006 34: D535-D539; doi:10.1093/nar/gkj109 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D535 うわっ。なんて名前を付けるんだ... Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, and Emmanuel Barillot ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis Nucl. Acids Res. 2006 34: D613-D616; doi:10.1093/nar/gkj022 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D613 中身によっては、非常に重要なリソースになり得る。 Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, and Yoshihide Hayashizaki CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis Nucl. Acids Res. 2006 34: D632-D636; doi:10.1093/nar/gkj034 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D632 プロモータDBまわりじゃなく、ここに位置している理由が謎。 Mathias Dunkel, Melanie Fullbeck, Stefanie Neumann, and Robert Preissner SuperNatural: a searchable database of available natural compounds Nucl. Acids Res. 2006 34: D678-D683; doi:10.1093/nar/gkj132 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D678 まるで歌のタイトルじゃん。かっけー。 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 BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucl. Acids Res. 2006 34: D689-D691; doi:10.1093/nar/gkj092 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D689 BioModels Gary D. Bader, Michael P. Cary, and Chris Sander Pathguide: a Pathway Resource List Nucl. Acids Res. 2006 34: D504-D506; doi:10.1093/nar/gkj126 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D504 データベースじゃなくてList、という開き直りが楽しい。BioPAXの惹き文句の一つ「いっぱいのnetwork/pathway DBを統合」の根拠はこのリスト、ということでしょう。 Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, and Marketa Zvelebil pSTIING: a ‘systems’ approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer Nucl. Acids Res. 2006 34: D527-D534; doi:10.1093/nar/gkj044 http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_1/D527 わかんないけど、要check (懐かしい言い回しだなぁ)
