Integration of genomic data for pharmacology and toxicology using Internet resourcesFootnote¶

¶Presented at CMTPI 2005: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Shanghai, China, October 29–November 1, 2005).

References

• Kim , SK , Lund , J , Kiraly , M , Duke , K , Jiang , M , Stuart , JM , Eizinger , A , Wylie , BN and Davidson , GS . 2001 . Science , 293 : 2087
   PubMed Web of Science ®Google Scholar
• Bergmann , S , Ihmels , J and Barkai , N . 2004 . PLoS Biol. , 2 : 9
   Google Scholar
• McCarroll , SA , Murphy , CT , Zou , S , Pletcher , SD , Chin , CS , Jan , YN , Kenyon , C , Bargmann , CI and Li , H . 2004 . Nat. Genet. , 36 : 197
   PubMed Web of Science ®Google Scholar
• Harris , MA , Clark , J , Ireland , A , Lomax , J , Ashburner , M , Foulger , R , Eilbeck , K , Lewis , S , Marshall , B , Mungall , C , Richter , J , Rubin , GM , Blake , JA , Bult , C , Dolan , M , Drabkin , H , Eppig , JT , Hill , DP , Ni , L , Ringwald , M , Balakrishnan , R , Cherry , JM , Christie , KR , Costanzo , MC , Dwight , SS , Engel , S , Fisk , DG , Hirschman , JE , Hong , EL , Nash , RS , Sethuraman , A , Theesfeld , CL , Botstein , D , Dolinski , K , Feierbach , B , Berardini , T , Mundodi , S , Rhee , SY , Apweiler , R , Barrell , D , Camon , E , Dimmer , E , Lee , V , Chisholm , R , Gaudet , P , Kibbe , W , Kishore , R , Schwarz , EM , Sternberg , P , Gwinn , M , Hannick , L , Wortman , J , Berriman , M , Wood , V , de la Cruz , N , Tonellato , P , Jaiswal , P , Seigfried , T and White , R . 2004 . Nucleic Acids Res. , 32 : 258 Available online at: http://www.geneontology.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Microarray Gene Expression Data Society (MGED) website. (accessed 1 December 2005) http://www.mged.org (http://www.mged.org)
   Google Scholar
• Brazma , A , Hingamp , P , Quackenbush , J , Sherlock , G , Spellman , P , Stoeckert , C , Aach , J , Ansorge , W , Ball , CA , Causton , HC , Gaasterland , T , Glenisson , P , Holstege , FC , Kim , IF , Markowitz , V , Matese , JC , Parkinson , H , Robinson , A , Sarkans , U , Schulze-Kremer , S , Stewart , J , Taylor , R , Vilo , J and Vingron , M . 2001 . Nat. Genet , 29 : 365 Available online at: http://www.mged.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Spellman , PT , Miller , M , Stewart , J , Troup , C , Sarkans , U , Chervitz , S , Bernhart , D , Sherlock , G , Ball , C , Lepage , M , Swiatek , M , Marks , WL , Goncalves , J , Markel , S , Iordan , D , Shojatalab , M , Pizarro , A , White , J , Hubley , R , Deutsch , E , Senger , M , Aronow , BJ , Robinson , A , Bassett , D , Stoeckert , CJ Jr. and Brazma , A . 2002 . Genome Biol. , 3 Available online at: http://www.mged.org (accessed 1 December 2005)
   PubMedGoogle Scholar
• Hubbard , T , Andrews , D , Caccamo , M , Cameron , G , Chen , Y , Clamp , M , Clarke , L , Coates , G , Cox , T , Cunningham , F , Curwen , V , Cutts , T , Down , T , Durbin , R , Fernandez-Suarez , XM , Gilbert , J , Hammond , M , Herrero , J , Hotz , H , Howe , K , Iyer , V , Jekosch , K , Kahari , A , Kasprzyk , A , Keefe , D , Keenan , S , Kokocinsci , F , London , D , Longden , I , McVicker , G , Melsopp , C , Meidl , P , Potter , S , Proctor , G , Rae , M , Rios , D , Schuster , M , Searle , S , Severin , J , Slater , G , Smedley , D , Smith , J , Spooner , W , Stabenau , A , Stalker , J , Storey , R , Trevanion , S , Ureta-Vidal , A , Vogel , J , White , S , Woodwark , C and Birney , E . 2005 . Nucleic Acids Res. , 33 : 447 Available online at: http://www.ensembl.org (accessed 1 December 2005)
   Google Scholar
• de la Cruz , N , Bromberg , S , Pasko , D , Shimoyama , M , Twigger , S , Chen , J , Chen , CF , Fan , C , Foote , C , Gopinath , GR , Harris , G , Hughes , A , Ji , Y , Jin , W , Li , D , Mathis , J , Nenasheva , N , Nie , J , Nigam , R , Petri , V , Reilly , D , Wang , W , Wu , W , Zuniga-Meyer , A , Zhao , L , Kwitek , A , Tonellato , P and Jacob , H . 2005 . Nucleic Acids Res. , 33 : 485 Available online at: http://rgd.mcw.edu/ (accessed 1 December 2005)
   Google Scholar
• Drysdale , RA and Crosby , MA . 2005 . Nucleic Acids Res. , 33 : 390 Available online at: http://www.flybase.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Chen , N , Harris , TW , Antoshechkin , I , Bastiani , C , Bieri , T , Blasiar , D , Bradnam , K , Canaran , P , Chan , J , Chen , CK , Chen , WJ , Cunningham , F , Davis , P , Kenny , E , Kishore , R , Lawson , D , Lee , R , Muller , HM , Nakamura , C , Pai , S , Ozersky , P , Petcherski , A , Rogers , A , Sabo , A , Schwarz , EM , Van Auken , K , Wang , Q , Durbin , R , Spieth , J , Sternberg , PW and Stein , LD . 2005 . Nucleic Acids Res. , 33 : 383 Available online at: http://www.wormbase.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Christie , KR , Weng , S , Balakrishnan , R , Costanzo , MC , Dolinski , K , Dwight , SS , Engel , SR , Feierbach , B , Fisk , DG , Hirschman , JE , Hong , EL , Issel-Tarver , L , Nash , R , Sethuraman , A , Starr , B , Theesfeld , CL , Andrada , R , Binkley , G , Dong , Q , Lane , C , Schroeder , M , Botstein , D and Cherry , JM . 2004 . Nucleic Acids Res. , 32 : 311 Available online at: http://www.yeastgenome.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Culhane , AC , Perriere , G and Higgins , DG . 2003 . BMC Bioinformatics , 4 : 59
   PubMed Web of Science ®Google Scholar
• Hu , P , Greenwood , CM and Beyene , J . 2005 . BMC Bioinformatics , 6 : 128
   PubMed Web of Science ®Google Scholar
• Warnat , P , Eils , R and Brors , B . 2005 . BMC Bioinformatics , 6 : 265
   PubMed Web of Science ®Google Scholar
• Kanz , C , Aldebert , P , Althorpe , N , Baker , W , Baldwin , A , Bates , K , Browne , P , van den Broek , A , Castro , M , Cochrane , G , Duggan , K , Eberhardt , R , Faruque , N , Gamble , J , Diez , FG , Harte , N , Kulikova , T , Lin , Q , Lombard , V , Lopez , R , Mancuso , R , McHale , M , Nardone , F , Silventoinen , V , Sobhany , S , Stoehr , P , Tuli , MA , Tzouvara , K , Vaughan , R , Wu , D , Zhu , W and Apweiler , R . 2005 . Nucleic Acids Res. , 33 : 29 Available online at: http://www.ebi.ac.uk/embl/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Bairoch , A , Apweiler , R , Wu , CH , Barker , WC , Boeckmann , B , Ferro , S , Gasteiger , E , Huang , H , Lopez , R , Magrane , M , Martin , MJ , Natale , DA , O’Donovan , C , Redaschi , N and Yeh , LS . 2005 . Nucleic Acids Res. , 33 : 154 Available online at: http://www.ebi.ac.uk/swissprot/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Wheeler , DL , Barrett , T , Benson , DA , Bryant , SH , Canese , K , Church , DM , DiCuccio , M , Edgar , R , Federhen , S , Helmberg , W , Kenton , DL , Khovayko , O , Lipman , DJ , Madden , TL , Maglott , DR , Ostell , J , Pontius , JU , Pruitt , KD , Schuler , GD , Schriml , LM , Sequeira , E , Sherry , ST , Sirotkin , K , Starchenko , G , Suzek , TO , Tatusov , R , Tatusova , TA , Wagner , L and Yaschenko , E . 2005 . Nucleic Acids Res. , 33 : 39 Available online at: http://www.ncbi.nlm.nih.gov (accessed 1 December 2005)
   Web of Science ®Google Scholar
• Maglott , D , Ostell , J , Pruitt , KD and Tatusova , T . 2005 . Nucleic Acids Res. , 33 : 54 Available online at: http://www.ncbi.nlm.nih.gov (accessed 1 December 2005). Available online at: http://www.ncbi.nlm.nih.gov(accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Pruitt , KD , Tatusova , T and Maglott , DR . 2005 . Nucleic Acids Res. , 33 : 501 Available online at: http://www.ncbi.nlm.nih.gov (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Veldhoven , A , de Lange , D , Smid , M , de Jager , V , Kors , JA and Jenster , G . 2005 . BMC Bioinformatics , 6 : 192
   PubMed Web of Science ®Google Scholar
• Kulkarni , AV , Williams , NS , Lian , Y , Wren , JD , Mittelman , D , Pertsemlidis , A and Garner , HR . 2002 . Bioinformatics , 18 : 1410
   PubMed Web of Science ®Google Scholar
• Svensson , BA , Kreeft , AJ , van Ommen , GJ , den Dunnen , JT and Boer , JM . 2003 . Genome Biol. , 4 : 35
   Google Scholar
• Dennis , G , Jr. , Sherman , BT , Hosack , DA , Yang , J , Gao , W , Lane , HC and Lempicki , RA . 2003 . Genome Biol. , 4 : 3
   PubMed Web of Science ®Google Scholar
• Liu , G , Loraine , AE , Shigeta , R , Cline , M , Cheng , J , Valmeekam , V , Sun , S , Kulp , D and Siani-Rose. , MA . 2003 . Nucleic Acids Res. , 31 : 82 Available online at: http://www.affymetrix.com/analysis/netaffx/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Kasprzyk , A , Keefe , D , Smedley , D , London , D , Spooner , W , Melsopp , C , Hammond , M , Rocca-Serra , P , Cox , T and Birney. , E . 2004 . Genome Res. , 14 : 160 Available online at: http://www.ensembl.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Durinck , S , Moreau , Y , Kasprzyk , A , Davis , S , De Moor , B , Brazma , A and Huber , W . 2005 . Bioinformatics , 21 : 3439
   PubMed Web of Science ®Google Scholar
• Stabenau , A , McVicker , G , Melsopp , C , Proctor , G , Clamp , M and Birney , E . 2004 . Genome Res. , 14 : 929
   PubMed Web of Science ®Google Scholar
• Liefeld , T , Reich , M , Gould , J , Zhang , P , Tamayo , P and Mesirov , JP . 2005 . Bioinformatics , 21 : 3681
   PubMed Web of Science ®Google Scholar
• Lee , Y , Tsai , J , Sunkara , S , Karamycheva , S , Pertea , G , Sultana , R , Antonescu , V , Chan , A , Cheung , F and Quackenbush , J . 2005 . Nucleic Acids Res. , 33 : 71 Available online at: http://www.tigr.org/tdb/tgi/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Hsu , F , Pringle , TH , Kuhn , RM , Karolchik , D , Diekhans , M , Haussler , D and Kent , WJ . 2005 . Nucleic Acids Res. , 33 : 454 Available online at: http://genome.ucsc.edu/ (accessed 1 December 2005)
   Google Scholar
• Safran , M , Solomon , I , Shmueli , O , Lapidot , M , Shen-Orr , S , Adato , A , Ben-Dor , U , Esterman , N , Rosen , N , Peter , I , Olender , T , Chalifa-Caspi , V and Lancet , D . 2002 . Bioinformatics , 18 : 1542 Available online at: http://www.genecards.org (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Edgar , R , Domrachev , M and Lash , AE . 2002 . Nucleic Acids Res. , 30 : 207 Available online at: http://www.ncbi.nlm.nih.gov/geo/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Clark , T , Martin , S and Liefeld , T . 2004 . Brief Bioinform. , 5 : 59
   PubMed Web of Science ®Google Scholar
• Cheung , KH , Hager , J , Pan , D , Srivastava , R , Mane , S , Li , Y , Miller , P and Williams , KR . 2004 . Nucleic Acids Res. , 32 : 441
   PubMed Web of Science ®Google Scholar
• Bussey , KJ , Kane , D , Sunshine , M , Narasimhan , S , Nishizuka , S , Reinhold , WC , Zeeberg , B , Ajay , W and Weinstein , JN . 2003 . Genome Biol. , 4 : 27
   PubMedGoogle Scholar
• Wang , P , Ding , F , Chiang , H , Thompson , RC , Watson , SJ and Meng , F . 2002 . Bioinformatics , 18 : 488
   PubMed Web of Science ®Google Scholar
• Tsai , J , Sultana , R , Lee , Y , Pertea , G , Karamycheva , S , Antonescu , V , Cho , J , Parvizi , B , Cheung , F and Quackenbush , J . 2001 . Genome Biol. , 2
   PubMedGoogle Scholar
• Lee , Y , Sultana , R , Pertea , G , Cho , J , Karamycheva , S , Tsai , J , Parvizi , B , Cheung , F , Antonescu , V , White , J , Holt , I , Liang , F and Quackenbush , J . 2002 . Genome Res. , 12 : 493 Available online at: http://www.tigr.org/tdb/tgi/ego/ (accessed 1 December 2005)
   PubMed Web of Science ®Google Scholar
• Diehn , M , Sherlock , G , Binkley , G , Jin , H , Matese , JC , Hernandez-Boussard , T , Rees , CA , Cherry , JM , Botstein , D , Brown , PO and Alizadeh , AA . 2003 . Nucleic Acids Res. , 31 : 219
   PubMed Web of Science ®Google Scholar
• Finney , A and Hucka , M . 2003 . Biochem. Soc. Trans. , 31 : 1472
   PubMed Web of Science ®Google Scholar
• 2005 . J.J. Berman . Hum. Pathol. , 36 : 139
   PubMed Web of Science ®Google Scholar
• Guo , J , Takada , A , Tanaka , K , Sato , J , Suzuki , M , Suzuki , T , Nakashima , Y , Araki , K and Yoshihara , H . 2004 . J. Med. Syst. , 28 : 523
   PubMedGoogle Scholar
• Wang , H , Azuaje , F , Jung , B and Black , N . 2003 . BMC Med. Inform. Decis. Mak. , 3 : 4
   PubMedGoogle Scholar
• Sugimori , H , Yoshida , K , Hara , S , Furumi , K , Tofukuji , I , Kubodera , T , Yoda , T and Kawai , M . 2002 . Meth. Inf. Med. , 41 : 220
   PubMed Web of Science ®Google Scholar
• Hanisch , D , Zimmer , R and Lengauer , T . 2002 . In Silico Biol. , 2 : 313
   PubMedGoogle Scholar
• Liao , YM and Ghanadan , H . 2002 . Anal. Chem. , 74 : 389
   Google Scholar
• Kikuchi , N , Kameyama , A , Nakaya , S , Ito , H , Sato , T , Shikanai , T , Takahashi , Y and Narimatsu , H . 2005 . Bioinformatics , 21 : 1717
   PubMed Web of Science ®Google Scholar
• Achard , F , Vaysseix , G and Barillot , E . 2001 . Bioinformatics , 17 : 115
   PubMed Web of Science ®Google Scholar