Library of molecular associations: curating the complex molecular basis of liver diseases

详细信息    查看全文

• 作者：Stefan Buchkremer (1)
  Jasmin Hendel (1)
  Markus Krupp (1)
  Arndt Weinmann (1)
  Kai Schlamp (1)
  Thorsten Maass (1)
  Frank Staib (1)
  Peter R Galle (1)
  Andreas Teufel (1)
  
• 刊名：BMC Genomics
• 出版年：2010
• 出版时间：December 2010
• 年：2010
• 卷：11
• 期：1
• 全文大小：1140KB
• 参考文献：1. Hocquette JF: Where are we in genomics? / J Physiol Pharmacol 2005, 56 (Suppl 3) : 37鈥?0.
  2. Marinelli RJ, Montgomery K, Liu CL, Shah NH, Prapong W, Nitzberg M, Zachariah ZK, Sherlock GJ, Natkunam Y, West RB, Rijn M, Brown PO, Ball CA: The Stanford Tissue Microarray Database. / Nucleic Acids Res 2008, (36 Database) : D871鈥?.
  3. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A: ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. / Nucleic Acids Res 2009, (37 Database) : D868鈥?2.
  4. Conrotto P, Souchelnytskyi S: Proteomic approaches in biological and medical sciences: principles and applications. / Exp Oncol 2008, 30: 171鈥?0.
  5. Nugent C, Younossi ZM: Evaluation and management of obesity-related nonalcoholic fatty liver disease. / Nat Clin Pract Gastroenterol Hepatol 2007, 4: 432鈥?1. CrossRef
  6. Rockey DC: Antifibrotic therapy in chronic liver disease. / Clin Gastroenterol Hepatol 2005, 3 (2) : 95鈥?07. CrossRef
  7. Teufel A, Staib F, Kanzler S, Weinmann A, Schulze-Bergkamen H, Galle PR: Genetics of hepatocellular carcinoma. / World J Gastroenterol 2007, 13: 2271鈥?2.
  8. Yau T, Chan P, Epstein R, Poon RT: Evolution of systemic therapy of advanced hepatocellular carcinoma. / World J Gastroenterol 2008, 14: 6437鈥?1. CrossRef
  9. Teufel A, Galle PR, Kanzler S: Update on autoimmune hepatitis. / World J Gastroenterol 2009, 15: 1035鈥?1. CrossRef
  10. Muratori P, Granito A, Pappas G, Muratori L, Lenzi M, Bianchi FB: Autoimmune liver disease 2007. / Mol Aspects Med 2008, 29: 96鈥?02. CrossRef
  11. Kaneko S, Kobayashi K: Clinical application of a DNA chipin the field of liver diseases. / J Gastroenterol 2003, 38 (Suppl 15) : 85鈥?.
  12. Swanson KS: Using genomic biology to study liver metabolism. / J Anim Physiol Anim Nutr (Berl) 2008, 92: 246鈥?2. CrossRef
  13. Lee JS, Thorgeirsson SS: Comparative and integrative functional genomics of HCC. / Oncogene 2006, 25: 3801鈥?. CrossRef
  14. Thorgeirsson SS, Lee JS, Grisham JW: Functional genomics of hepatocellular carcinoma. / Hepatology 2006, 43 (2 Suppl 1) : S145鈥?0. CrossRef
  15. Lee JS, Heo J, Libbrecht L, Chu IS, Kaposi-Novak P, Calvisi DF, Mikaelyan A, Roberts LR, Demetris AJ, Sun Z, Nevens F, Roskams T, Thorgeirsson SS: A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells. / Nat Med 2006, 12: 410鈥?. CrossRef
  16. Tuomela M, Stanescu I, Krohn K: Validation overview of bio-analytical methods. / Gene Ther 2005, 12 (Suppl 1) : S131鈥?. CrossRef
  17. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J: Database resources of the National Center for Biotechnology Information. / Nucleic Acids Res 2009, (37 Database) : D5鈥?5.
  18. Spudich G, Fernandez-Suarez XM, Birney E: Genome browsing with Ensembl: a practical overview. / Brief Funct Genomic Proteomic 2007, 6: 202鈥?9. CrossRef
  19. Aoki KF, Kanehisa M: Using the KEGG database resource. / Curr Protoc Bioinformatics 2005, Chapter 1 (Unit 1) : 12.
  20. Wang C, Maass T, Krupp M, Thieringer F, Strand S, W枚rns MA, Barreiros AP, Galle PR, Teufel A: A systems biology perspective on CCC development. Focus on MAPK-Singnaling and extracellular environment. / Journal of Hepatology 2009, 50: 1122鈥?1. CrossRef
  21. Osterreicher CH, Stickel F, Brenner DA: Genomics of liver fibrosis and cirrhosis. / Semin Liver Dis 2007, 27: 28鈥?3. CrossRef
  22. Weber S, Gressner OA, Hall R, Gr眉nhage F, Lammert F: Genetic determinants in hepatic fibrosis: from experimental models to fibrogenic gene signatures in humans. / Clin Liver Dis 2008, 12: 747鈥?7. CrossRef
  23. Becker KG, Barnes KC, Bright TJ, Wang SA: The genetic association database. / Nat Genet 2004, 36: 431鈥?. CrossRef
  24. Blake JA, Richardson JE, Davisson MT, Eppig JT: The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group. / Nucleic Acids Res 1997, 25: 85鈥?1.
  25. Gene ontology [http://www.geneontology.org]
  26. Meng F, Wehbe-Janek H, Henson R, Smith H, Patel T: Epigenetic regulation of microRNA-370 by interleukin-6 in malignant human cholangiocytes. / Oncogene 2008, 27: 378鈥?6. CrossRef
  
• 作者单位：Stefan Buchkremer (1)
  Jasmin Hendel (1)
  Markus Krupp (1)
  Arndt Weinmann (1)
  Kai Schlamp (1)
  Thorsten Maass (1)
  Frank Staib (1)
  Peter R Galle (1)
  Andreas Teufel (1)
  
  1. Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
  

文摘

Background Systems biology approaches offer novel insights into the development of chronic liver diseases. Current genomic databases supporting systems biology analyses are mostly based on microarray data. Although these data often cover genome wide expression, the validity of single microarray experiments remains questionable. However, for systems biology approaches addressing the interactions of molecular networks comprehensive but also highly validated data are necessary. Results We have therefore generated the first comprehensive database for published molecular associations in human liver diseases. It is based on PubMed published abstracts and aimed to close the gap between genome wide coverage of low validity from microarray data and individual highly validated data from PubMed. After an initial text mining process, the extracted abstracts were all manually validated to confirm content and potential genetic associations and may therefore be highly trusted. All data were stored in a publicly available database, Library of Molecular Associations http://www.medicalgenomics.org/databases/loma/news, currently holding approximately 1260 confirmed molecular associations for chronic liver diseases such as HCC, CCC, liver fibrosis, NASH/fatty liver disease, AIH, PBC, and PSC. We furthermore transformed these data into a powerful resource for molecular liver research by connecting them to multiple biomedical information resources. Conclusion Together, this database is the first available database providing a comprehensive view and analysis options for published molecular associations on multiple liver diseases.