High-throughput identification of protein functional similarities using a gene-expression-based siRNA screen
Year: 2020
Type: data-paper
Abstract: A gene expression-based siRNA screen was used to evaluate functional similarity between genetic perturbations to identify functionally similar proteins. A siRNA library (siGenome library, Dharmacon) consisting of multiple siRNAs per gene that have been pooled in to one well per gene was arrayed in a 384-well format and used to individually target 14,335 proteins for depletion in HCT116 colon cancer cells. For each protein depletion, the gene expression of eight genes was quantified using the multiplexed Affymetrix Quantigene 2.0 assay in technical triplicate. As a proof of concept, six genes (BNIP3, NDRG1, ALDOC, LOXL2, ACSL5, BNIP3L) whose expression pattern reliably reflect the disruption of the molecular scaffold KSR1 were measured upon each protein depletion. The remaining two genes (PPIB and HPRT) are housekeeping genes used for normalization. The gene expression signatures from this screen can be used to estimate the functional similarity between any two proteins and successfully identified functional relationships for specific proteins such as KSR1 and more generalized processes, such as autophagy.
Source: Scientific Data
Authors: Beth K. Neilsen, David L. Kelly, Binita Chakraborty, Hyun Seok Kim, Michael A. White, Robert E. Lewis, Kurt W. Fisher
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,870
Awards: G1314705203, G2482780363, G2782664826, Discovering Vulnerabilities in Ras-driven Cancers, A druggable dependency in low-MITF/high-AXL melanoma: preclinical efficacy and mechanism of action in a key treatment-resistant subclass., The role of PGC1beta and ERRalpha as novel targets for therapy in colorectal cancer, Nebraska Center for the Prevention of Obesity Diseases through Dietary Molecules, G4020073524, G5989231044, G7555581465, Novel Effectors of Colon Tumorigenesis, G9000064439, G9000108264, G9000112066, Nebraska Center for Molecular Target Discovery and Development, Buffett Cancer Center Support Grant, Cancer Biology Training Program
OpenAlex ID: W3001578194