Overview

Silencers, which were first identified around 30 years ago as sequence-specific elements that induce negative effect on the transcription of particular genes, have started to receive growing attention. To facilitate the studies of silencers and their potential roles in transcriptional control during normal development and disease, we developed this comprehensive database of silencers, SilencerDB.

To date, SilencerDB contains:
    1. 32,851 validated silencers from both high-throughput and low-throughput experiments
    2. 5,045,664 predicted silencers from state-of-the-art machine learning/deep learning methods
SilencerDB has the following main features:
    1. Hierarchical categorization of silencers with species, organ, tissue, cell line
    2. Comprehensive gene annotation of silencers with the nearest gene and PECA predicted regulatory gene
Homo sapiens
Mus musculus
Other species
human body
Eye human_Eye
Breast human_Breast
Stomach human_Stomach
Intestine human_Intestine
Pancreas human_Pancreas
Kidney human_Kidney
Muscle human_Muscle
Skin human_Skin
Brain human_Brain
Lung human_Lung
Heart human_Heart
Liver human_Liver
Stem cell Stem cell
Blood human_Blood
Ovary human_Ovary
Others human_Others

Recent articles

Silencers in the spotlight. Della Rosa M, Spivakov M. Nature Genetics. 2020 Mar;52(3):244-5.
Systematic identification of silencers in human cells. Pang B, Snyder MP. Nature Genetics. 2020 Mar;52(3):254-63.
Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Ngan CY, Wong CH, Tjong H, Wang W, Goldfeder RL, Choi C, He H, Gong L, Lin J, Urban B, Chow J. Nature Genetics. 2020 Mar;52(3):264-72.
Candidate silencer elements for the human and mouse genomes. Jayavelu ND, Jajodia A, Mishra A, Hawkins RD. Nature communications. 2020 Feb 26;11(1):1-5.
Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts. Gisselbrecht SS, Palagi A, Kurland JV, Rogers JM, Ozadam H, Zhan Y, Dekker J, Bulyk ML. Nature Genetics. Molecular Cell. 2020 Jan 16;77(2):324-37.

News and updates

  • Added the silencers predicted by DeepSilencer.

    27 June 2020

  • Provided a demo for the analysis of silencers.

    15 June 2020

  • Version 1.0 of the database has been launched.

    03 June 2020