Protein-Binding Microarray

Overview

Protein-binding microarrays (PBMs) are high-throughput platforms that measure the binding affinity of proteins (typically transcription factors) to large collections of DNA sequences simultaneously. Each array contains thousands of double-stranded DNA sequences; the protein of interest is applied, unbound protein is washed away, and binding is detected by fluorescence. PBMs can generate comprehensive sequence-to-binding-affinity maps (8-mer binding profiles) for TFs, enabling computational prediction of TF binding to any DNA sequence including somatic mutations in promoters.

Used by

• PBM data for 486 transcription factors integrated into the FIREFLY computational method applied to 70 CCA WGS samples; identified four gene sets enriched for promoter mutations that alter TF binding and produce concordant transcriptional dysregulation, two of which are PRC2/H3K27me3 targets enriched in the Cluster 1 (Fluke-Pos) CCA subtype PMID:28667006

Notes

• Used as a resource (TF binding profiles) rather than as a primary experimental assay in this context.
• PBM profiles for 486 TFs served as the reference binding database for FIREFLY.

Sources

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