Resources

1. Breast cancer GWAS SNPs
   
   
   
   
   
   • A list of breast cancer GWAS SNPs, their high LD SNPs and coordinates can be obtained from here.
   • The complete GWAS annotation catalog (April 2018 version) used in our database can be downloaded from here. The latest version is available on the EBI website.
2. WashU Epigenome Browser





• We use the WashU Epigenome Browser interface for showing data of different types.
• The source code for building the interface using Javascript and CSS can be found here.
3. TCGA data
   
   
   
   
   • Gene expression quantification (HTSeq - FPKM, open access) data was downloaded from the GDC data portal.
   • Raw data such as RNA-seq aligned reads and patient cohort genotypes was also obtained from the GDC data portal after receiving permission to access controlled data.
4. ENCODE data
   
   
   
   
   • ChIP-seq narrowPeak and broadPeak files were downloaded (April 2018 update) from the ENCODE portal.
   • The bam files are also downloaded from the ENCODE portal and sliced before using in the genome browser when relevant.
5. Motif databases
   • The following motif databases are included in the motif analysis: JASPAR, TRANSFAC, HOCOMOCO, HOMER, hPDI, FactorBook, Jolma.
   • Motif logos are generated using the R package seqLogo.