Gene prioritization through genomic data fusion
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Kanehisa, M. & Bork, P. Bioinformatics in the post-sequence era. Nat. Genet. 33 Suppl. 305–310 (2003).
Ball, C.A., Sherlock, G. & Brazma, A. Funding high-throughput data sharing. Nat. Biotechnol. 22, 1179–1183 (2004).
Freudenberg, J. & Propping, P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 18 Suppl. 2, S110–S115 (2002).
Perez-Iratxeta, C., Bork, P. & Andrade, M.A. Association of genes to genetically inherited diseases using data mining. Nat. Genet. 31, 316–319 (2002).
Turner, F.S., Clutterbuck, D.R. & Semple, C.A. POCUS: mining genomic sequence annotation to predict disease genes. Genome Biol. 4, R75 (2003).
Tiffin, N. et al. Integration of text- and data-mining using ontologies successfully selects disease gene candidates. Nucleic Acids Res. 33, 1544–1552 (2005).
Adie, E.A., Adams, R.R., Evans, K.L., Porteous, D.J. & Pickard, B.S. Speeding disease gene discovery by sequence based candidate prioritization. BMC Bioinformatics 6, 55 (2005).
Lopez-Bigas, N. & Ouzounis, C.A. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res. 32, 3108–3114 (2004).
Kent, W.J. et al. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 15, 737–741 (2005).
Altermann, E. & Klaenhammer, T.R. PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. BMC Genomics 6, 60 (2005).
Aerts, S. et al. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res. 33, W393–W396 (2005).
Aerts, S., Van Loo, P., Thijs, G., Moreau, Y. & De Moor, B. Computational detection of cis-regulatory modules. Bioinformatics 19 (Suppl 2), II5–II14 (2003).
Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96, 2907–2912 (1999).
Stegmaier, K. et al. Gene expression-based high-throughput screening (GE-HTS) and application to leukemia differentiation. Nat. Genet. 36, 257–263 (2004).
Pixley, F.J. et al. BCL6 suppresses RhoA activity to alter macrophage morphology and motility. J. Cell Sci. 118, 1873–1883 (2005).
Galimi, F. et al. Hepatocyte growth factor is a regulator of monocyte-macrophage function. J. Immunol. 166, 1241–1247 (2001).
Brown, N.J. et al. Fas death receptor signaling represses monocyte numbers and macrophage activation in vivo. J. Immunol. 173, 7584–7593 (2004).
Jerome, L.A. & Papaioannou, V.E. DiGeorge syndrome phenotype in mice mutant for the T-box gene, Tbx1. Nat. Genet. 27, 286–291 (2001).
Merscher, S. et al. TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome. Cell 104, 619–629 (2001).
Lindsay, E.A. et al. Tbx1 haploinsufficieny in the DiGeorge syndrome region causes aortic arch defects in mice. Nature 410, 97–101 (2001).
Piotrowski, T. et al. The zebrafish van gogh mutation disrupts tbx1, which is involved in the DiGeorge deletion syndrome in humans. Development 130, 5043–5052 (2003).
Rauch, A. et al. A novel 22q11.2 microdeletion in DiGeorge syndrome. Am. J. Hum. Genet. 64, 659–666 (1999).
Stalmans, I. et al. VEGF: a modifier of the del22q11 (DiGeorge) syndrome? Nat. Med. 9, 173–182 (2003).
Glenisson, P. et al. TXTGate: profiling gene groups with text-based information. Genome Biol. 5, R43 (2004).
Bader, G.D., Betel, D. & Hogue, C.W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250 (2003).
Aerts, S., Van Loo, P., Moreau, Y. & De Moor, B. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics 20, 1974–1976 (2004).
Stuart, J.M., Segal, E., Koller, D. & Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249–255 (2003).
Westerfield, M. The Zebrafish Book. A Guide for the Laboratory Use of Zebrafish, (University of Oregon Press, Eugene, Oregon, 1994).
Kimmel, C.B. et al. The shaping of pharyngeal cartilages during early development of the zebrafish. Dev. Biol. 203, 245–263 (1998).
Splawski, I. et al. Ca(V)1.2 calcium channel dysfunction causes a multisystem disorder including arrhythmia and autism. Cell 119, 19–31 (2004).
Robinson, S.W. et al. Missense mutations in CRELD1 are associated with cardiac atrioventricular septal defects. Am. J. Hum. Genet. 72, 1047–1052 (2003).
Hayashi, T. et al. Identification and functional analysis of a caveolin-3 mutation associated with familial hypertrophic cardiomyopathy. Biochem. Biophys. Res. Commun. 313, 178–184 (2004).
Zimprich, A. et al. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 44, 601–607 (2004).
Zuchner, S. et al. Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease. Nat. Genet. 37, 289–294 (2005).
Munch, C. et al. Point mutations of the p150 subunit of dynactin (DCTN1) gene in ALS. Neurology 63, 724–726 (2004).
Tian, X.L. et al. Identification of an angiogenic factor that when mutated causes susceptibility to Klippel-Trenaunay syndrome. Nature 427, 640–645 (2004).
Bienengraeber, M. et al. ABCC9 mutations identified in human dilated cardiomyopathy disrupt catalytic KATP channel gating. Nat. Genet. 36, 382–387 (2004).
Windpassinger, C. et al. Heterozygous missense mutations in BSCL2 are associated with distal hereditary motor neuropathy and Silver syndrome. Nat. Genet. 36, 271–276 (2004).
Tonkin, E.T., Wang, T.J., Lisgo, S., Bamshad, M.J. & Strachan, T. NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome. Nat. Genet. 36, 636–641 (2004).
Krantz, I.D. et al. Exclusion of linkage to the CDL1 gene region on chromosome 3q26.3 in some familial cases of Cornelia de Lange syndrome. Am. J. Med. Genet. 101, 120–129 (2001).
Wang, X. et al. Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility. Nat. Genet. 37, 365–372 (2005).
Peltekova, V.D. et al. Functional variants of OCTN cation transporter genes are associated with Crohn disease. Nat. Genet. 36, 471–475 (2004).
Aharon-Peretz, J., Rosenbaum, H. & Gershoni-Baruch, R. Mutations in the glucocerebrosidase gene and Parkinson's disease in Ashkenazi Jews. N. Engl. J. Med. 351, 1972–1977 (2004).
Begovich, A.B. et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am. J. Hum. Genet. 75, 330–337 (2004).
Helgadottir, A. et al. The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke. Nat. Genet. 36, 233–239 (2004).