Harris, Benjamin D, Crow, Megan, Fischer, Stephan, Gillis, Jesse (May 2021) Single-cell co-expression analysis reveals that transcriptional modules are shared across cell types in the brain. Cell Systems. ISSN 2405-4712
Abstract
Gene-gene relationships are commonly measured via the co-variation of gene expression across samples, also known as gene co-expression. Because shared expression patterns are thought to reflect shared function, co-expression networks describe functional relationships between genes, including co-regulation. However, the heterogeneity of cell types in bulk RNA-seq samples creates connections in co-expression networks that potentially obscure co-regulatory modules. The brain initiative cell census network (BICCN) single-cell RNA sequencing (scRNA-seq) datasets provide an unparalleled opportunity to understand how gene-gene relationships shape cell identity. Comparison of the BICCN data (500,000 cells/nuclei across 7 BICCN datasets) with that of bulk RNA-seq networks (2,000 mouse brain samples across 52 studies) reveals a consistent topology reflecting a shared co-regulatory signal. Differential signals between broad cell classes persist in driving variation at finer levels, indicating that convergent regulatory processes affect cell phenotype at multiple scales.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression organism description > animal > mammal > rodent > mouse Investigative techniques and equipment > assays > Single cell sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Gillis Lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 10 May 2021 |
| Date Deposited: | 26 May 2021 15:25 |
| Last Modified: | 26 Jul 2021 13:12 |
| PMCID: | PMC8298279 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/40171 |
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