The MethyCancer search engine is composed of Methylation Search, Gene Search, Cancer Search, Clone Search, Repeat Search and Methy&Cancer, which help users to study interplay of DNA methylation, gene expression and cancer.
1. Methylation Search
Methylation Search provides different search options for methylation data, including methylation type, data source, experiment method, sample information and position on human genome. Users will acquire a detailed Methylation Report for each entry of methylation data, which contains methylation type, methylation status, sample information, related gene and repeat. Links to related public databases are also provided (Figure 1).
Figure 1. Methylation Report
2. Gene Search
MethyCancer contains more than 30,000 genes which were grouped into three categories with estimates of confidence of their relationship with cancer: 1) annotated cancer gene, 2) candidate cancer gene, and 3) other gene. Users may search for a specific category of genes. Gene Report contains 8 sections, namely Summary, Diseases (Cancers), Genomic Regions, Transcripts and Proteins, DNA Methylation and CGIs, Mutations, Pathway and Bibliography (Figure 2).
Figure 2. Gene Report
3． Cancer Search
MethyCancer collects more than 500 cancers (including cancer prone and leukemias). Cancer Report contains Summary, Clinics and Pathology, Related Genes, Cytogenetics and Bibliography (Figure 3).
Figure 3. Cancer Report
4． Clone Search
Clone search provides search options for both clones and sequences. We kept the same clone/sequence name as other databases, so users can easily find their data. Clone Report shows the reads of the clone while exist. Users can link to the related Methylation Report and MethyView from Clone Report.
5． Repeats Search
MethyCancer contains repetitive sequences predicted by RepeatMasker. Repeat search offers position, repeat name and repeat family as search options. From Repeat Report, users can link to related methylation report.
6． Methy&Cancer Search
In order to elucidate the interplay of DNA methylation, gene expression and cancer types, we annotated methylation data to genes by genomic mapping, and linked methylation data with cancers via cancer genes. All genes in MethyCancer were further classified into 9 categories based on this analysis:
Ø Annotated cancer gene
n Annotated cancer gene with experimental methylation data
n Annotated cancer gene with CGI prediction
n Annotated cancer gene without methylation data
Ø Candidate cancer gene
n Candidate cancer gene with experimental methylation data
n Candidate cancer gene with CGI prediction
n Candidate cancer gene without methylation data
Ø Other gene
n Other gene with experimental methylation data
n Other gene with CGI prediction
n Other gene without methylation data
Users may select gene category and input the cancer types or define specific expression tissues and genes with methylation data in promoter regions. A list of genes and methylation data will be returned and a factual detailed report could be shown upon demand. An example of search result is shown in Figure 4, where users can link to gene, cancer, MethyView and expression library pages.
Figure 4. Search results of Methy&Cancer