scGRNdb

scGRNdb is a database of over 1000 tissue- and cell-type- specific gene regulatory networks (GRNs) and a web server for GRN analysis. You can provide your own single cell data to build a custom network or use one of the pre-built cell type networks across the following 12 human and mouse single cell atlases:

• GTEx
• Tabula Sapiens
• Human Allen Brain Atlas 10X
• Human Allen Brain Atlas SmartSeq
• Human Cell Landscape
• Mouse Cell Atlas
• Tabula Muris 10X
• Tabula Muris SmartSeq
• Tabula Muris Senis 10X
• Tabula Muris Senis SmartSeq
• Mouse Allen Brain Atlas 10X
• Mouse Allen Brain Atlas SmartSeq

We use the Single Cell Integrative Gene regulatory network (SCING) method, as an unbiased GRN method that has been demonstrated to outperform other GRN methods in predicting downstream effects of single cell gene knockout experiments (Littman et al., 2023). scGRNdb offers a variety of tools to model any given network or gene set. These tools for network analysis include network module detection and pathway annotation, gene set modeling and network prioritization, and key driver analysis, all of which are found in under the Network Analysis tab. All the networks can be visualized in the Explore Networks tab to understand coordinated gene mechanisms in cell types within and across tissues.

scGRNdb is being actively developed by the Yang Lab in the Department of Integrative Biology and Physiology at UCLA. The Yang Lab at UCLA uses integrative genomics and systems biology approaches to better understand the molecular mechanisms of complex disease. We maintain all our open-source analytical methods and pipelines, including SCING and scGRNdb, through our Github page.