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. 2009 Jan;37(Database issue):D803-9.
doi: 10.1093/nar/gkn756. Epub 2008 Nov 4.

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

Alexander R Pico  1 , Ivan V Smirnov, Jeffrey S Chang, Ru-Fang Yeh, Joseph L Wiemels, John K Wiencke, Tarik Tihan, Bruce R Conklin, Margaret Wrensch
Affiliations

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

Alexander R Pico et al. Nucleic Acids Res. 2009 Jan.

Abstract

SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data.

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Figures

Figure 1.
Figure 1.
Overview of resource collection and integration into SNPLogic for a unique selection, annotation and analysis tool. A semi-automatic process periodically extracts SNP, pathway and genomic information from various public resources (blue cylinders), which is then integrated into a single SNP annotation database. The SNPLogic web site provides access, unique functionality and presentation of the integrated database.
Figure 2.
Figure 2.
Gene Browser interface for SNP selection. User input fields and functions are highlighted on this screenshot of the web interface.
Figure 3.
Figure 3.
Filtering and ranking SNP lists using the My SNPs interface. The main features of ranking are highlighted on this screenshot of the web interface.
See this image and copyright information in PMC

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