This track is part of the MaveDB track collection. It shows one heatmap per MaveDB score set: every measured position of the gene is a column, and every substitution tested there is a row, colored by its score.
Score sets that measured protein changes are drawn as protein heatmaps, with a column for each codon. This includes genome editing score sets whose variants are given as DNA changes and which MaveDB translated to protein changes; their intronic and untranslated region variants are only in the MaveDB Variants track. Score sets with no protein changes, such as assays of promoters, enhancers or splicing, are drawn as nucleotide heatmaps, with a column for each base.
Each heatmap is colored on its own scale, from the lowest score in that score set to the highest. The color in the middle is the arithmetic midpoint of the two, not the wild-type score. Score direction differs between assays: in some a high score means a normal protein, in others an abnormal one, so read the score set description on the details page before comparing colors.
| Lowest score in the score set | |
| Midpoint between the lowest and highest score | |
| Highest score in the score set | |
| The reference amino acid (protein heatmaps) or reference base (nucleotide heatmaps) at that position |
Rows of protein heatmaps are the 20 amino acids, then - for deletion of the residue, * for a stop codon and = for a synonymous change. Rows of nucleotide heatmaps are the four bases, on the forward strand of the genome. A codon split by an intron is drawn as two columns with the same values. An empty cell was not measured.
Where a score set reports the same change more than once, the cell is colored by the first score and marked with the number of measurements (+ for ten or more); hovering over the cell lists all of them. Hovering over any cell shows the MaveDB variant number, the change on the reference protein, and its score. Changes placed by UCSC rather than by MaveDB carry "(UCSC placement)"; the MaveDB Variants page explains what that means. Clicking a heatmap opens a page with the score set's description, abstract and methods, and a link to MaveDB.
Some score sets were measured on a construct that differs from the reference protein, at one position (for example a TP53 construct carrying the common Arg72 form) or by a few added residues at one end. Changes at those positions are not shown, and the details page names the difference. Score sets that report the same domain under two proteases (trypsin and chymotrypsin) and a combined score are shown here by the combined score only; all three are in the MaveDB Variants track.
Many score sets overlap at well studied genes. Use the score set filter on the track settings page to show one or a few. When the view is wider than 200,000 bases, the track shows a density graph of where heatmaps are instead of the heatmaps.
Each MaveDB score set lists its variants as changes to the sequence the experiment tested, and MaveDB maps them to human reference sequences: the tested sequence is aligned to GRCh38 with BLAT, a RefSeq transcript is chosen (preferring MANE Select), and an offset places the tested sequence on the reference protein (Arbesfeld et al., 2025). Details of each experiment are on its details page and on MaveDB.
The score sets, their metadata and their variants were downloaded from the MaveDB API (https://api.mavedb.org/api/v1, documented at api.mavedb.org/docs), including MaveDB's mapped terms and ClinGen allele IDs. Each variant was then placed on hg38 as described on the MaveDB Variants page, and every placed protein change was checked against the reference protein and the genome codon. Placed variants were grouped into one heatmap per score set and target. The steps are in the makeDoc file and the scripts in the MaveDB update directory of our source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=mavedb_maps.
For automated download and analysis, the heatmaps are stored in a bigBed file that can be downloaded from our download server. The file for this track is called mavedbMaps.bb. Individual regions or the whole file can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/maveDB/mavedbMaps.bb -chrom=chr17 -start=7660000 -end=7690000 stdout
The original data can be downloaded from MaveDB. Each score set carries its own license, shown on its MaveDB page.
Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N et al. Mapping MAVE data for use in human genomics applications. Genome Biol. 2025 Jun 25;26(1):179. PMID: 40563119; PMC: PMC12188674
Rubin AF, Stone J, Bianchi AH, Capodanno BJ, Da EY, Dias M, Esposito D, Frazer J, Fu Y, Grindstaff SB et al. MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. Genome Biol. 2025 Jan 21;26(1):13. PMID: 39838450; PMC: PMC11753097