FAANGMine

Features

• New template queries have for FAANG data.
• A new data collection called "Orthologue Cluster" allows retrieving OrthoDB orthologue clusters based on the cluster id.
• Duplicated NCBI gene ids are now handled with an underscore and digit(s) added to the duplicated ids to make them unique.

Data Sets

• New genome assemblies and gene sets for cat, dog, sheep and water buffalo.
• The dog genome hosted in FAANGMine is now for the German Shepherd breed.
• Updated Ensembl gene sets for chicken and pig.
• FAANG chromatin state data for bovine, chicken and pig. These are called "regulatory region" in the Regions Search.
• FAANG chromatin accessibility data for chicken. These include data based on ATAC-seq and DNase Hypersensitivity, which are called "open chromatin region" and "DNaseI hypersensitive site" in the Regions Search.
• FAANG CTCF binding site data generated using ChIP-seq for bovine, chicken, goat, and pig.
• FAANG chromatin architecture data generated using Hi-C for goat and pig. These include A/B compartments and TADs, which are called "Biological Region" and "Topologically Associated Domain" in the Regions Search.
• FAANG histone modification data generated using ChIP-seq have for bovine, chicken, horse and pig, and is called "Histone Binding Site" in the Regions Search.
• New FAANG RNA-seq based gene expression data for bovine, chicken, pig, sheep and water buffalo.

Features

• The regions search has an additional filter for analyses per organism.
• Homologues now include cluster ID and last common ancestor.
• Publications added for all FAANG species.

Data Sets

• Added data sets for Analyses, BioProjects, and BioSamples.
• Added data sets for Expressions and Experiments.
• Added OMIM data set.
• Excluded TreeFam data set.
• Pig variant and variant effect data issues resolved and are included in this release.
• FAANG histone modification data generated using ChIP-seq for horse.

This is the first public release of FAANGMine. There was a problem loading pig variant and variant effect data. This issue will be resolved in the next release.