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Proteomes 2018, 6(1), 10; https://doi.org/10.3390/proteomes6010010

Revealing Subtle Functional Subgroups in Class A Scavenger Receptors by Pattern Discovery and Disentanglement of Aligned Pattern Clusters

1
VaryWave Technology Co., Ltd., 538A, Core Building 2, Hong Kong Science Park, Shatin, NT, Hong Kong
2
VerticalScope Inc., 111 Peter Street, Suite 900, Toronto, ON M5V 2H1, Canada
3
Systems Design Engineering, 5th, 6th Floor, 200 University Avenue West, University of Waterloo, Waterloo, ON N2L 3G1, Canada
*
Author to whom correspondence should be addressed.
Received: 24 November 2017 / Revised: 1 February 2018 / Accepted: 1 February 2018 / Published: 8 February 2018
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Abstract

A protein family has similar and diverse functions locally conserved as aligned sequence segments. Further discovering their association patterns could reveal subtle family subgroup characteristics. Since aligned residues associations (ARAs) in Aligned Pattern Clusters (APCs) are complex and intertwined due to entangled function, factors, and variance in the source environment, we have recently developed a novel method: Aligned Residue Association Discovery and Disentanglement (ARADD) to solve this problem. ARADD first obtains from an APC an ARA Frequency Matrix and converts it to an adjusted statistical residual vector space (SRV). It then disentangles the SRV into Principal Components (PCs) and Re-projects their vectors to a SRV to reveal succinct orthogonal AR groups. In this study, we applied ARADD to class A scavenger receptors (SR-A), a subclass of a diverse protein family binding to modified lipoproteins with diverse biological functionalities not explicitly known. Our experimental results demonstrated that ARADD can unveil subtle subgroups in sequence segments with diverse functionality and highly variable sequence lengths. We also demonstrated that the ARAs captured in a Position Weight Matrix or an APC were entangled in biological function and domain location but disentangled by ARADD to reveal different subclasses without knowing their actual occurrence positions. View Full-Text
Keywords: residue association; pattern discovery; disentanglement; protein; class A scavenger receptors residue association; pattern discovery; disentanglement; protein; class A scavenger receptors
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Zhou, P.-Y.; Lee, E.-S.A.; Sze-To, A.; Wong, A.K.C. Revealing Subtle Functional Subgroups in Class A Scavenger Receptors by Pattern Discovery and Disentanglement of Aligned Pattern Clusters. Proteomes 2018, 6, 10.

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