Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data

Bioinformatics
Qianqian ShiLuonan Chen

Abstract

Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called 'pattern fusion analysis' (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e.g. from each data type) into a global sample-pattern corresponding to phenotypes (e.g. across most data types). In particular, PFA can identify significant sample-patterns from different omics profiles by optimally adjusting the effects of each data type to the patterns, thereby alleviating the problems to process different platforms and different reliability levels of heterogeneous data. To validate the effectiveness of our method, we first tested PFA on various synthetic datasets, and found that PFA can not only capture the intrinsic sample clustering structures from the multi-omics data in contrast to the state-of-the-art methods, such as iClusterPlus, SNF and moCluster, but also provide an automatic weight-sche...Continue Reading

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Citations

May 14, 2019·Frontiers in Genetics·Hui TangLuonan Chen
Sep 10, 2019·Frontiers in Genetics·Qianqian ShiChuanchao Zhang
Feb 23, 2020·Bioinformatics and Biology Insights·Indhupriya SubramanianKrishanpal Anamika
Aug 14, 2020·Scientific Reports·Sayantan MitraMohammed Hasanuzzaman
Mar 25, 2020·Computational and Structural Biotechnology Journal·Edwin BaldwinHaiquan Li
Nov 17, 2020·Frontiers in Genetics·Tonmoy DasSajib Chakraborty
Jan 1, 2021·Bioinformatics·Milad Mokhtaridoost, Mehmet Gönen
Feb 23, 2021·Computational and Structural Biotechnology Journal·Otília Menyhárt, Balázs Győrffy
Jun 19, 2021·Computational and Structural Biotechnology Journal·Qianqian ShiLuonan Chen
Aug 13, 2021·PLoS Computational Biology·Ran DuanSongwei Jia
Apr 1, 2019·Journal of Biomedical Informatics·Juan C RodriguezElmer A Fernández
Nov 9, 2021·Frontiers in Oncology·Hung NguyenTin Nguyen

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