The aim of PACdb is to aid researchers in understanding how genetic variation contributes to differences in drug response and cytotoxicity.
PACdb is a database of pharmacology-related phenotypes that integrates genotypic and gene expression data.
This database provides:
- Whole Genome Analysis of Genotype and Cytotoxicity Association. SNP genotypes were downloaded from the International HapMap database. SNPs with evidence of Mendelian allele transmission errors and those with a minor allele frequency <5% were filtered out, giving a total of >2 million SNPs for the association analysis in each population. The quantitative transmission disequilibrium test (QTDT) was performed to identify genotype-cytotoxicity associations using QTDT software. This was performed separately within each population.
- Summary analysis which identifies differentially expressed transcript clusters between populations.
- Analysis of genotype and gene expression association.
- Summary information of relationship between gene expression and drug phenotypes.
- Summary information available from public databases such as physical and functional annotations.
For each SNP, the SCAN database is intended to provide:
- Summary information available from public data bases such as physical and functional annotations, frequencies in HapMap reference samples, FST values, and whether the SNP is on (or tags) a haplotype implicated in genomic studies identifying the signature of natural selection
- Linkage Disequilibrium (LD) information, including what genes have variation in strong LD (pairwise or multi-locus LD) with the variant, how well the SNP is interrogated (i.e. multi-locus LD measure) by SNPs on each of the high-throughput platforms
- Summary information from analyses conducted to characterize HapMap SNP associations to gene expression in the full set of HapMap lymphoblastoid cell lines derived from individuals of European (CEU) and African (YRI) ancestry for 9,156 transcript clusters evaluated using the Affymetrix GeneChip® Human Exon 1.0 ST Array. This information would be summarized both globally (all transcript clusters showing association at a user-specified threshold with the chosen variant) and locally (associations to local transcript clusters with at least nominal significance, including information on rank for local associations)
- Summary information from other genome-wide association studies (e.g. all phenotypes showing association at a user-specified threshold)
In addition, for each gene, we provide annotations on:
- All SNPs showing association with the transcript cluster relevant for the gene (user-specified thresholds for cis- and trans-regulators)
- How well all variants in the HapMap at that gene are interrogated on each high-throughput platform (average multi-locus LD coefficient for each SNP within and up to 2 kbp from the gene)