SNPExpress search window (Figure 1)
This window is the main user-interafce working with the SNPExpress database. Figure 1 shows the componentes of this window:
[A] Main menu;
[B] Entry selection indicator. This panel displays the database entries, including genes, transcritps, exon probesets, and/or SNPs that are selected from navigation trees ([C]) or search bar ([E]). Selected entries are displayed in green. The selection status will then determine the availability of
[C] Plugin functions. Currently these functions include: [C-1] 'Expression by Genotype' becomes activated (available) when a gene AND a SNP are selected, as displayed in [B]. This function will plot the expression levels of each transcripts and exon probesets of the selected gene, grouped by the genotypes of the selected SNP. This function will also perform association tests, using a linear regression model corretced for age, sex, tissue sources, and EIGENSTRAT axes, for the plotted expression levels and the SNP genotype. Please note that these association tests are proformed in a real-time manner between any selected gene and SNP, and there is no assumption on the chromsome locational relavance ('cis-acting' effects) of genes and SNPs. This feature is unlike data preseneted in 'Probeset view->Plot' as displayed in Figure 1, part F, in which the P values were pre-calculated from 'cis-acting genetic regulation' screening, defined as associations between SNPs lying in 100kb surrounding region of the transcripts or exons. [C-2] 'PathwayExpress' becomes activated when a gene is selected. Clicking on this button will bring up a 'PathwayExpress' plugin window. The pathway analysis is based on KEGG database. The number in the square brackets ('[', ']') indicates how many pathways are known for the selected gene. As in the example in Figure 2-1, there is one known pathway for selected gene 'RPS26'. [C-3] 'GWAS Now' becomes activated only when a transcript OR an exon probetset is selected. Clicking on this button will bring up an on-demand genome-wide association test for the selected transcript or exon probeset in both brain and PBMC data sets. With a laptop equipped with Intel T2500 2.50 GHz CPU and 2GB RAM, this process will take around 20 minutes. If WGAViewer is installed, the results will be then loaded into the WGAViewer software for annotating.
[D] Navigation trees . The navigation trees are used to select database entries, which will then be displayed in part B. These include: [D-1] 'Probeset navagator' is used to select gene, transcript, or exon probeset; [D-2] 'SNP navigator' is used to select a SNP; and [D-3] 'P val rank navigator' is used to select genes and SNPs based on P values generated from 'cis-acting genetic regulation' screening.
[E] Search bar. The search bar is used to search for and select genes and/or SNPs in the SNPExpress database. These searching engines include: [E-1] 'By genomic location' takes chromosomal coordinates as inputs, and can be used to zoom in or out; [E-2] 'By Gene' takes HUGO gene symbol as inputs; [E-3] 'By SNP' takes SNP rs number as inputs; [E-4] 'By Gene X SNP' takes HUGO gene symbol and SNP rs number as inputs; and [E-5] 'By P val rank' takes the rank of P values generated from 'cis-acting genetic regulation' screening as inputs.
[F] Result panels. These are the main outputs for annotations and association tests. These panels include: [F-1] 'Probeset view' illustrates the genomic regions selected. This panel displays: (1) Chromosomal locations of genotyped SNPs; (2) P values for displayed SNPs generated from 'cis-acting genetic regulation' screening in brain; (3) P values for displayed SNPs generated from 'cis-acting genetic regulation' screening in PBMCs; (4) Ensmebl transcripts in displayed genomic region, based on the latest genome build; and (5) probesets assaysed. Please note the P values displayed (2 and 3) can be heavily overlapped by signals for a number of transctipts and exons, unless one select specific transcript or exon to display from navigation trees [D]. 'Probeset view' presents data in both graph and table, which can be saved or copied to spreadsheet. [F-2] 'Expression by genotype (brain)' respond to analysis generated from part [C-1]. Data are presented in both graph and table; [F-3] 'Expression by genotype (PBMC)' respond to analysis generated from part [C-1]. Data are presented in both graph and table.
[G] Result tool bar can be used to save or copy result tables in part [F].
[H] Log panel keeps a track of actions performed and their results. For example, it displays whether one certain gene is coverd in the SNPExpress database.
[I] Status bar keeps a track of system information and issues warning when needed, including (from left to right): (1) current database loaded; (2) current SNPExpress version; (3) version of JAVA environment; and (4) current usage of memory.