Topologically Associating Domain Knowledge Base (TADKB) is an integrated resource for exploring topologically associating domains (TADs). An example of 2D and 3D visualizations of a TAD can be found here. Learn more »
Liu T, Porter J, Zhao C, Zhu H, Wang N, Sun Z, Mo Y-Y, Wang Z. TADKB: Family classification and a knowledge base of topologically associating domains. BMC Genomics 2019, 20(1):217.
You can browse genome-wide TADs of ten cell types (i.e., 1. GM12878, 2. HMEC, 3. NHEK, 4. IMR90, 5. KBM7, 6. K562, 7. HUVEC for human and 8. CH12-LX, 9. Cortex, 10. ES for mouse) The domain definitions are called using normalized Hi-C data at the resolutions of 50 kb for the first eight cell lines and 40 kb for the last two cell lines.
For each chromosome, we create a table of TADs, including four columns:
For each TAD, we predict its 3D structure using multidimensional scaling method. We download protein-coding gene data from Ensembl and three lncRNA databases, including NONCODE 2016, LNCipedia 4.0, and lncRNAdb 2.0. We map genes onto TADs of each of the ten cell types by comparing their genomic positions. When you reach the domain detail webpage, you can select genes, check their positions on the 3D structure of the TAD, and obtain gene information.
You can provide a gene (i.e., protein coding gene or lncRNA) ID or sequence. TADKB will search databases and find matched TADs that the target gene belongs to. If you provide a gene sequence, TADKB will show the matched genes with the similar sequence and their TADs. You can select a TAD by clicking its row to show more details of this TAD.