Advances in the development of human protein microarrays

@article{Duarte2017AdvancesIT,
  title={Advances in the development of human protein microarrays},
  author={Jessica Da Gama Duarte and Jonathan Michael Blackburn},
  journal={Expert Review of Proteomics},
  year={2017},
  volume={14},
  pages={627 - 641}
}
ABSTRACT Introduction: High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays… 
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References

SHOWING 1-10 OF 146 REFERENCES
Microarrays to characterize protein interactions on a whole‐proteome scale
TLDR
The ultimate form of a functional protein array consists of all of the proteins encoded by the genome of an organism; such an array would be the whole proteome equivalent of the whole genome DNA arrays that are now available.
Applications in high-content functional protein microarrays.
Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation
TLDR
This chapter describes a simple approach to the design and fabrication of cancer-antigen arrays suitable for cancer biomarker discovery through serological analysis of cancer patients and describes computational approaches to address these that enable quantitative assessment of serological protein microarray data.
Tissue-based map of the human proteome
TLDR
A genome-wide analysis of the tissue specificity of RNA and protein expression covering more than 90% of the putative protein-coding genes is reported, complemented with analyses of various subproteomes, such as predicted secreted proteins and membrane-bound proteins.
A critical comparison of protein microarray fabrication technologies.
TLDR
This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
An overview of innovations and industrial solutions in Protein Microarray Technology
TLDR
This review aims at assessing the developments in various commercial platforms, thus providing a holistic overview of various modalities, options, and compatibility of this powerful high‐throughput technology.
Protein chip technology.
Affinity‐based microarrays for proteomic analysis of cancer tissues
TLDR
This review highlights methodological aspects relevant for a biomedically useful analysis of cellular samples and discusses the potential of such studies, in particular, in view of personalised medicine approaches.
Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
TLDR
This study further optimized, validated, and standardized the next generation of the recombinant antibody microarray technology platform designed for clinical immunoproteomics, and presents one of the first antibody array studies in which these key biostatistics subjects have been studied in detail.
...
...