SilencerDB

The documentation of SilencerDB

A simple introduction about the database, with a global view of body maps of human and mouse.
- The body maps facilitate the quick browse of silencers across various organs and cell lines. Users can switch the body map by clicking the icon at the top right.
- The number of silencers in different cell lines can be accessed by clicking the organ icons.
- After choosing validated or predicted silencers of a specific cell line, it will jump to the corresponding Browse page to show more details.
Recent articles about silencers.
News and updates of SilencerDB.

Users can browse silencers of interest by selecting a species or cell line in the hierarchical tree.
We provide some statistics and visualization figures by species and cell line.
- The first pie plot figure shows the number distribution of silencers from one species or one cell line. For example, there are 43,495 silencers in K562 of Homo sapiens.
- The second bar plot figure shows the number of silencers in different chromosomes from one species or one cell line. For example, there are 267,674 silencers in Chromosome 12 of Homo sapiens.
- The third bar plot figure shows the size distribution of silencers from one species or one cell line. For example, there are 1,350,909 silencers of which size is in [120,160) in Homo sapiens.
- The fourth diagram of curves shows the number of genes around the silencers, which to some extent reflects the openness of the silencer regions from one species or one cell line. For example, in Homo sapiens, there are 214,893 silencers in 100kb around which the number of genes is in [20,25).
The corresponding silencers are displayed on a interactive table. Users can click the Silencer ID to access detailed information about this silencer on a new page.

Users can search for silencers of interest by selecting a species from the pull-down menu, and then selecting multiple tissues and cell lines from the pull-down menu with advanced features such as searching and selecting-all.
Users can also determine the scope of the silencer query by determining annotation method, associated gene, and genomic location for the results of interest.

Validated silencers were manually curated from high-throughput (e.g., MPRA, CRISPR, etc.) and low-throughput (e.g., transient transfection assays, reporter assays, etc.) experiments.
Predicted silencers were identified via correlation-based model (Huang et al., Genome Research, 2019), SVM model (Huang et al., Genome Research, 2019), gkmSVM model (Jayavelu et al., Nature Communications, 2020) and our newly developed deep learning model DeepSilencer.

We also provide an example to facilitate the usage of searching.
The results will be displayed on an interactive table.
- Users can click the Silencer ID to access detailed information about this silencer on a new page.
- By clicking the Download button, users can obtain the compressed results.

Overview information includes Silencer ID, categories (by species, organ, tissue, or cell line), annotation method, reference of source and corresponding PubMed ID, genomic location, size, external link to UCSC, and FASTA file.
To help users view proximity information of silencers in genomes, we developed a personalized genome browser using Dalliance with useful tracks. Users can add other genomic annotation, configure tracks and options, export results, and get support using the top right buttons.
We also provide detailed information about the nearest gene and the potential regulatory gene. We annotate the nearest gene according to the genomic location, and the potential regulatory gene by the PECA model. Users can click on the icons to external databases (GeneCards, UniProt and NCBI, etc.). The gene expression in different tissues is also displayed.

We categorize the silencers by species, method, and cell line. The data can be downloaded in different formats like BED, FASTA, and UCSC custom tracks.
The corresponding MD5 files are provided to ensure the integrity of the downloaded data.
We also provide advanced features such as searching and sorting for the convenient usage.

Using the validated silencers of human K562 cell line, we provide a demo for the analysis of silencers. We walk through the workflow for the analysis of the length distribution of silencers, the distance between silencers and genes, the GC content of silencers, and the cell line specificity of silencers.

The citation information of SilencerDB.
The interface for submitting data to SilencerDB. Users can submit their silencer data with the PubMed reference ID and optional information such as URL, name, and E-mail. The approved data will be public available in the coming release. We appreciate the users for their contribution.
The contact information of SilencerDB. Please feel free to contact us if you have any question about SilencerDB.