Data Resource

1. Core Gene Set

    Core gene set has been manually collected to include genes that have been commonly considered as candidate genes in expert review or had significant results in the meta-analysis of association studies. Ross et al., (2006) reviewed the evidence in four domains (association with schizophrenia, linkage to gene locus, biological plausibility, and altered expression in schizophrenia) and suggested 19 genes being candidates. We also included 27 genes with significant meta-analysis results performed by the SchizophreniaGene team (as of November 5, 2008). The genes were selected by having a nominally significant summary OR in all ethnic groups or Caucasian samples. After removing redundancy, the core gene set contains 38 genes.

2. 75 genes by COR

     The 75 genes by COR were prioritized by ranking more than 500 genes in more than 2000 association studies. The results has been published in our previous work ( Sun et al. 2008).

3. 160 by Lewis et al.

    In our recent work, we developed a multi-dimensional evidence-based candidate gene prioritization approach and identified 160 schizophrenia candidate genes, denoted here as "160 by Lewis et al.". This dataset is based on genetic studies for schizophrenia from four major categories: association studies, linkage analyses, gene expression, and literature search. Genes in these data sets are initially scored by category-specific scoring methods. Then, an optimal weight matrix is searched by a two-step procedure (core genes and unbiased P values in independent genome-wide association studies). Finally, genes are prioritized by their combined scores using the optimal weight matrix. The follow-up evaluation has suggested that this approach generates prioritized candidate genes that are promising for further analysis or replication.

4. 173 by Ng et al.

    The 173 by Ng et al. dataset is based on the same strategy as we used to get the 160 by Lewis et al. dataset, except the linkage dataset is collected from a most recently published genome scan meta-analysis (Ng et al. 2009). Click here to view this gene list.

  • Ng, M.Y.M., Levinson, D.F., Faraone, S.V., Suarez, B.K., DeLisi, L.E., Arinami, T., Riley, B., Paunio, T., Pulver, A.E., Irmansyah, et al. (2009) Meta-analysis of 32 genome-wide linkage studies of schizophrenia. Mol. Psychiatry Epub ahead of print
  • Ross, C.A., Margolis, R.L., Reading, S.A., Pletnikov, M., and Coyle, J.T. (2006 Oct 5) Neurobiology of schizophrenia. Neuron. 52(1): 139-53 PubMed
  • SchizophreniaGene Database: http://www.schizophreniaforum.org
  • Sun, J., Jia, P., Fanous, A.H., Webb, B.T., van den Oord, E.J.C.G., Chen, X., Bukszar, J., Kendler, K.S., and Zhao, Z. (2009) A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases - schizophrenia as a case. Bioinformatics 25(19):2595-2602. PubMed
  • Sun, J., Kuo, P.H., Riley, B.P., Kendler, K.S., and Zhao, Z. (2008) Candidate genes for schizophrenia: a survey of association studies and gene ranking. Am. J. Med. Genet. B Neuropsychiatr. Genet. 147B: 1173-1181 PubMed

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