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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Database [Publication Type]

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Disease relevance of Database [Publication Type]


Psychiatry related information on Database [Publication Type]

  • To this data base we have also added the number of syringes distributed through community associations, as well as methadone treatments prescribed in public drug dependence clinics [6].
  • This information provides a data base for designing smoking cessation strategies for critical care nurses and educational interventions aimed at increasing skills in helping patients cope with the abrupt withdrawal from nicotine imposed by an episode of acute illness [7].

High impact information on Database [Publication Type]

  • Here we report a coincidence in the positions of the first eight putative membrane-spanning domains found in the virus receptor and in two related proteins, the arginine and histidine permeases of Saccharomyces cerevisiae (Fig. 1), but not in any other proteins identified by computer-based sequence comparison of the GenBank data base [8].
  • We report the crystal structure of the ligand-binding domains (LBDs) of LXRalpha and RXRbeta complexed to the synthetic LXR agonist T-0901317 and the RXR agonist methoprene acid (Protein Data Base entry 1UHL) [9].
  • However, the smaller isoform has 114 residues at the NH2 terminus that are unique as compared to the current protein sequence data base [10].
  • The mutants were analyzed for binding to digoxin, digitoxin, digoxigenin, and ouabain resulting in the generation of a comprehensive data base of 456 relative affinity values [11].
  • Our cDNA analyses and data-base searches reveal that the predicted dodo protein has homologs in other eukaryotes and that it is made up of two different domains [12].

Chemical compound and disease context of Database [Publication Type]


Biological context of Database [Publication Type]


Anatomical context of Database [Publication Type]


Associations of Database [Publication Type] with chemical compounds

  • We have developed a data base of lymphoid proteins detectable by two-dimensional polyacrylamide gel electrophoresis [28].
  • The motif was present in all of the cysteine proteases in the data base with the exception of the cathepsin B-like proteins, which have shorter propeptides [29].
  • However, three of the data base proteins differed by having an extra methionine or by missing an acetyl or heme substitution [30].
  • To obtain a diverse hemodynamic data base, loading conditions were changed by infusions of volume and angiotensin II [31].
  • PATIENTS AND METHODS: We retrospectively reviewed all patients entered into the Memorial Sloan-Kettering Cancer Center clinical data base from 1985 through 1995 who had a diagnosis of IBD, had a gastrointestinal malignancy, and were treated with systemic 5FU-based chemotherapy [32].

Gene context of Database [Publication Type]

  • No other protein sequences similar to that of the predicted PTA1 gene product have been identified within the EMBL or GenBank data base [33].
  • Data base searching also indicates golgin-84 is similar in structure and sequence to giantin, a membrane protein that tethers coatamer complex I vesicles to the Golgi [34].
  • Analysis of the data base with both ERG25 and the human homologue resulted in the identification of a putative set of metal binding motifs with similarity to that seen in a family of membrane desaturases-hydroxylases [35].
  • Data base searches revealed that MP25 had significant similarity of structure only with MAGP, indicating that the two proteins form a new family of microfibrillar proteins [36].
  • A second ubiquitously expressed member of the GIT protein family, GIT2, has been identified in data base searches [37].

Analytical, diagnostic and therapeutic context of Database [Publication Type]


  1. Serum- and oncoprotein-mediated induction of a gene with sequence similarity to the gene encoding carcinoembryonic antigen. Klemenz, R., Hoffmann, S., Werenskiold, A.K. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  2. Pleiotropic functions of a Streptomyces pristinaespiralis autoregulator receptor in development, antibiotic biosynthesis, and expression of a superoxide dismutase. Folcher, M., Gaillard, H., Nguyen, L.T., Nguyen, K.T., Lacroix, P., Bamas-Jacques, N., Rinkel, M., Thompson, C.J. J. Biol. Chem. (2001) [Pubmed]
  3. An abundant, trans-spliced mRNA from Toxocara canis infective larvae encodes a 26-kDa protein with homology to phosphatidylethanolamine-binding proteins. Gems, D., Ferguson, C.J., Robertson, B.D., Nieves, R., Page, A.P., Blaxter, M.L., Maizels, R.M. J. Biol. Chem. (1995) [Pubmed]
  4. Biochemical characterization of 2-Cys peroxiredoxins from Schistosoma mansoni. Sayed, A.A., Williams, D.L. J. Biol. Chem. (2004) [Pubmed]
  5. Human cytomegalovirus open reading frame US28 encodes a functional beta chemokine receptor. Gao, J.L., Murphy, P.M. J. Biol. Chem. (1994) [Pubmed]
  6. Harm reduction interventions, behaviours and associated health outcomes in France, 1996-2003. Emmanuelli, J., Desenclos, J.C. Addiction (2005) [Pubmed]
  7. Smoking practices of critical care nurses. Haughey, B.P., Mathewson, M.K., Dittmar, S.S., Wu, Y.W. Heart & lung : the journal of critical care. (1989) [Pubmed]
  8. Transport of cationic amino acids by the mouse ecotropic retrovirus receptor. Kim, J.W., Closs, E.I., Albritton, L.M., Cunningham, J.M. Nature (1991) [Pubmed]
  9. Crystal structure of the heterodimeric complex of LXRalpha and RXRbeta ligand-binding domains in a fully agonistic conformation. Svensson, S., Ostberg, T., Jacobsson, M., Norström, C., Stefansson, K., Hallén, D., Johansson, I.C., Zachrisson, K., Ogg, D., Jendeberg, L. EMBO J. (2003) [Pubmed]
  10. Analysis of Drosophila paramyosin: identification of a novel isoform which is restricted to a subset of adult muscles. Becker, K.D., O'Donnell, P.T., Heitz, J.M., Vito, M., Bernstein, S.I. J. Cell Biol. (1992) [Pubmed]
  11. In vitro scanning saturation mutagenesis of an antibody binding pocket. Burks, E.A., Chen, G., Georgiou, G., Iverson, B.L. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  12. The Drosophila melanogaster dodo (dod) gene, conserved in humans, is functionally interchangeable with the ESS1 cell division gene of Saccharomyces cerevisiae. Maleszka, R., Hanes, S.D., Hackett, R.L., de Couet, H.G., Miklos, G.L. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  13. Nosocomial infection rate as a function of human immunodeficiency virus type 1 status in hemophiliacs. Weber, D.J., Becherer, P.R., Rutala, W.A., Samsa, G.P., Wilson, M.B., White, G.C. Am. J. Med. (1991) [Pubmed]
  14. Prognostic significance of nonfatal myocardial reinfarction. Multicenter Diltiazem Postinfarction Trial Research Group. Benhorin, J., Moss, A.J., Oakes, D. J. Am. Coll. Cardiol. (1990) [Pubmed]
  15. Characterization of a Flavobacterium glutathione S-transferase gene involved reductive dechlorination. Orser, C.S., Dutton, J., Lange, C., Jablonski, P., Xun, L., Hargis, M. J. Bacteriol. (1993) [Pubmed]
  16. Predictors of treatment after initial surveillance in men with prostate cancer: results from CaPSURE. Meng, M.V., Elkin, E.P., Harlan, S.R., Mehta, S.S., Lubeck, D.P., Carroll, P.R. J. Urol. (2003) [Pubmed]
  17. Suppression of severe retinopathy of prematurity with vitamin E supplementation. Ultrastructural mechanism of clinical efficacy. Hittner, H.M., Rudolph, A.J., Kretzer, F.L. Ophthalmology (1984) [Pubmed]
  18. Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library. Dynes, J.L., Firtel, R.A. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  19. Molecular cloning and characterization of a cDNA showing negative regulation in v-src-transformed 3Y1 rat fibroblasts. Ozaki, T., Sakiyama, S. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  20. Cloning and characterization of subunit genes of ribonucleotide reductase, a cell-cycle-regulated enzyme, from Plasmodium falciparum. Chakrabarti, D., Schuster, S.M., Chakrabarti, R. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  21. The thyroid hormone-induced tail resorption program during Xenopus laevis metamorphosis. Brown, D.D., Wang, Z., Furlow, J.D., Kanamori, A., Schwartzman, R.A., Remo, B.F., Pinder, A. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  22. HMG1-related DNA-binding protein isolated with V-(D)-J recombination signal probes. Shirakata, M., Hüppi, K., Usuda, S., Okazaki, K., Yoshida, K., Sakano, H. Mol. Cell. Biol. (1991) [Pubmed]
  23. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Bork, P., Sander, C., Valencia, A. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  24. The 220-kDa rim protein of retinal rod outer segments is a member of the ABC transporter superfamily. Illing, M., Molday, L.L., Molday, R.S. J. Biol. Chem. (1997) [Pubmed]
  25. Profile-based data base scanning for animal L-type lectins and characterization of VIPL, a novel VIP36-like endoplasmic reticulum protein. Nufer, O., Mitrovic, S., Hauri, H.P. J. Biol. Chem. (2003) [Pubmed]
  26. A novel and highly divergent homolog of human eosinophil granule major basic protein. Plager, D.A., Loegering, D.A., Weiler, D.A., Checkel, J.L., Wagner, J.M., Clarke, N.J., Naylor, S., Page, S.M., Thomas, L.L., Akerblom, I., Cocks, B., Stuart, S., Gleich, G.J. J. Biol. Chem. (1999) [Pubmed]
  27. Mouse LYVE-1 is an endocytic receptor for hyaluronan in lymphatic endothelium. Prevo, R., Banerji, S., Ferguson, D.J., Clasper, S., Jackson, D.G. J. Biol. Chem. (2001) [Pubmed]
  28. Data base analysis of protein expression patterns during T-cell ontogeny and activation. Hanash, S.M., Strahler, J.R., Chan, Y., Kuick, R., Teichroew, D., Neel, J.V., Hailat, N., Keim, D.R., Gratiot-Deans, J., Ungar, D. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  29. Two distinct gene subfamilies within the family of cysteine protease genes. Karrer, K.M., Peiffer, S.L., DiTomas, M.E. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  30. Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases. Mørtz, E., O'Connor, P.B., Roepstorff, P., Kelleher, N.L., Wood, T.D., McLafferty, F.W., Mann, M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  31. Left ventricular filling dynamics: influence of left ventricular relaxation and left atrial pressure. Ishida, Y., Meisner, J.S., Tsujioka, K., Gallo, J.I., Yoran, C., Frater, R.W., Yellin, E.L. Circulation (1986) [Pubmed]
  32. Influence of inflammatory bowel disease on the ability of patients to tolerate systemic fluorouracil-based chemotherapy. Tiersten, A., Saltz, L.B. J. Clin. Oncol. (1996) [Pubmed]
  33. PTA1, an essential gene of Saccharomyces cerevisiae affecting pre-tRNA processing. O'Connor, J.P., Peebles, C.L. Mol. Cell. Biol. (1992) [Pubmed]
  34. Identification and characterization of golgin-84, a novel Golgi integral membrane protein with a cytoplasmic coiled-coil domain. Bascom, R.A., Srinivasan, S., Nussbaum, R.L. J. Biol. Chem. (1999) [Pubmed]
  35. Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue. Li, L., Kaplan, J. J. Biol. Chem. (1996) [Pubmed]
  36. Further characterization of proteins associated with elastic fiber microfibrils including the molecular cloning of MAGP-2 (MP25). Gibson, M.A., Hatzinikolas, G., Kumaratilake, J.S., Sandberg, L.B., Nicholl, J.K., Sutherland, G.R., Cleary, E.G. J. Biol. Chem. (1996) [Pubmed]
  37. The GIT family of ADP-ribosylation factor GTPase-activating proteins. Functional diversity of GIT2 through alternative splicing. Premont, R.T., Claing, A., Vitale, N., Perry, S.J., Lefkowitz, R.J. J. Biol. Chem. (2000) [Pubmed]
  38. Fibroblast growth factor (FGF) homologous factors: new members of the FGF family implicated in nervous system development. Smallwood, P.M., Munoz-Sanjuan, I., Tong, P., Macke, J.P., Hendry, S.H., Gilbert, D.J., Copeland, N.G., Jenkins, N.A., Nathans, J. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  39. A novel candidate metastasis-associated gene, mta1, differentially expressed in highly metastatic mammary adenocarcinoma cell lines. cDNA cloning, expression, and protein analyses. Toh, Y., Pencil, S.D., Nicolson, G.L. J. Biol. Chem. (1994) [Pubmed]
  40. The granulin/epithelin precursor abrogates the requirement for the insulin-like growth factor 1 receptor for growth in vitro. Xu, S.Q., Tang, D., Chamberlain, S., Pronk, G., Masiarz, F.R., Kaur, S., Prisco, M., Zanocco-Marani, T., Baserga, R. J. Biol. Chem. (1998) [Pubmed]
  41. A newly identified member of the tumor necrosis factor receptor superfamily with a wide tissue distribution and involvement in lymphocyte activation. Kwon, B.S., Tan, K.B., Ni, J., Oh, K.O., Lee, Z.H., Kim, K.K., Kim, Y.J., Wang, S., Gentz, R., Yu, G.L., Harrop, J., Lyn, S.D., Silverman, C., Porter, T.G., Truneh, A., Young, P.R. J. Biol. Chem. (1997) [Pubmed]
  42. Estrogen and progesterone replacement therapy reduces glucocorticoid-induced bone loss. Lukert, B.P., Johnson, B.E., Robinson, R.G. J. Bone Miner. Res. (1992) [Pubmed]
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