Tutorial
1. Advanced Search 
In BDgene, handy and powerful ways for data searching and browsing are provided for users. Apart from the 'Search' bar on the home page which presents regular keyword search option, the 'Advanced Search', which includes ‘Search SNP’, ‘Search Gene’, ‘Search CNV’, ‘Search Haplotype’, ‘Search Other Variant’, ‘Search Region’, ‘Search Pathway’ and ‘Search Study’, presents many detailed options for users to facilitate users to choose their interested data. Taking ‘Search Gene’ as an example (Figure 1), users can search genes by defining detailed search options, such as gene symbol, location information, gene research status in BD and SZ/MDD and gene involved GO term or pathway. Figure 1 shows the list of genes obtained from searching options defined as “at least one positive result in both BD and SZ”.
By clicking the gene symbol in the search result, user can enter gene report page (Figure 2), which provides comprehensive information for the gene, including basic information, gene related studies, gene functional annotation (gene related GO terms, gene related KEGG pathways, gene related BioCarta pathways and gene related interactors from protein-protein interaction data in HPRD), correlation with other genetic factors (gene related SNPs, gene related CNVs, gene related other variants and gene related regions), overlap with SZ and MDD, and links for gBrowse. Two extra functions 'Add to My Gene Set’ and ‘Comment on Gene' were provided to help user collect their intersted genes and make comments on genes as shown in the "My Gene Set" part and "Forum" parts as below.
2. Disease Gene Overlap
'Disease Gene Overlap' is a module to present shared genetic factors among three mental disorders generated from both cross-disorder studies and candidate gene intersection analysis (Figure 3). Details of disease, data source and number of studies with different results are optional for users. In addition, referring to two options in “source”, ”Cross-disorder study” represents data from cross-disorder studies while ”Candidate gene intersection analysis” represents the results of candidate gene intersection analysis among BDgene, SZGene and MK4MDD.
3. Analysis
Based on the data from literature, BDgene implemented four aspects of data analyses and the analysis results were shown in ‘Analysis’ modules, including BD core genes from gene prioritization analysis, pathways from PBA (pathway-based analysis) for BD GWAS, and enriched pathway for both BD core genes and shared literature-reported positive genes. For enriched pathways, several parameters were provided to filter the pathways, including top results, P-value, total gene count and comparison result with pathways from PBA (only for enriched pathway for BD core genes).
4. Tools
4.1 My Gene Set
‘My Gene Set’ is a module designed to help users collect their interested genes and
further acquire a customized gene network to help understand the association of selected genes with diseases.
Users can select genes of interest from any gene search result page or gene report page
by clicking on ‘ADD’ button. On ‘My Gene Set’ page, gene network is
generated by using the selected genes and their interacted genes from
protein-protein interaction data in HPRD.
Different colors of nodes are used to
denote the genetic overlapping status among three diseases. Users can do further editing on the selected
genes to generate a dynamic data network. A demo search is shown in Figure 4.
4.2 gBrowse
GBrowse is a popular visualization tool for visualizing genetic and genomic data. GBrowse was
incorporated in BDgene to facilitate users to view the different types of genetic factors (variant/gene/CNV/region) simultaneously in the context of genomic regions.
Moreover, different colors are marked on genes and SNPs to denote the genetic overlap status among BD, SZ and MDD (Figure 5).
5. Forum
BDgene forum is a platform for users to make comment on specific genes or studies hosted by BDgene on line in real time (via "Comment on Gene" and "Comment on Study")(Figure 6). We also welcome researchers to propose complementary articles of BD genetic study (via "Upload Article"), make any comments and suggestions for the website or exchange ideas on BD genetics research (via "Add General Comment").
To submit any types of comments or upload complementary articles, registration is needed. Users can add comments either from Forum home page or from gene/study report page (Figure 7). Text fields for comment, references and weighting are provided for users to input to make comment on gene. There are four levels for gene weighting provided, namely 0 - no association, 1 - weak association, 2 - moderate association and 3 - strong association. Researchers can select gene weight according to their understanding of the genes, and thus to share their opinions with other researchers. Users can also make reply any existing comment or view all comments made by a given person.
