Paper Info
Title
Tscca: A Tensor Sparse Cca Method For Detecting Microrna-Gene Patterns From Multiple Cancers
Abstract
Existing studies have demonstrated that dysregulation of microRNAs (miRNAs or miRs) is involved in the initiation and progression of cancer. Many efforts have been devoted to identify microRNAs as potential biomarkers for cancer diagnosis, prognosis and therapeutic targets. With the rapid development of miRNA sequencing technology, a vast amount of miRNA expression data for multiple cancers has been collected. These invaluable data repositories provide new paradigms to explore the relationship between miRNAs and cancer. Thus, there is an urgent need to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data in a pan-cancer paradigm. In this study, we present a tensor sparse canonical correlation analysis (TSCCA) method for identifying cancer-related miRNA-gene modules across multiple cancers. TSCCA is able to overcome the drawbacks of existing solutions and capture both the cancer-shared and specific miRNA-gene co-expressed modules with better biological interpretations. We comprehensively evaluate the performance of TSCCA using a set of simulated data and matched miRNA/gene expression data across 33 cancer types from the TCGA database. We uncover several dysfunctional miRNA-gene modules with important biological functions and statistical significance. These modules can advance our understanding of miRNA regulatory mechanisms of cancer and provide insights into miRNA-based treatments for cancer.Author summaryMicroRNAs (miRNAs) are a class of small non-coding RNAs. Previous studies have revealed that miRNA-gene regulatory modules play key roles in the occurrence and development of cancer. However, little has been done to discover miRNA-gene regulatory modules from a pan-cancer view. Thus, it is urgently needed to develop new methods to explore the complex cancer-related miRNA-gene patterns by integrating multi-omics data of multi-cancers. To build the connections between miRNA-gene regulatory modules across different cancer types, we propose a tensor sparse canonical correlation analysis (TSCCA) method. Our specific contributions are two-fold: (1) We propose a sparse statistical learning model TSCCA and an efficient block-coordinate descent algorithm to solve it. (2) We apply TSCCA to a multi-omics data set of 33 cancer types from TCGA and identify some cancer-related miRNA-gene modules with important biological functions and statistical significance.
Year
DOI
Venue
2021
10.1371/journal.pcbi.1009044
PLOS COMPUTATIONAL BIOLOGY
DocType
Volume
Issue
Journal
17
6
ISSN
Citations 
PageRank 
1553-734X
0
0.34
References 
Authors
0
4
Name
Order
Citations
PageRank
Wenwen Min1163.88
Tsung-Hui Chang2114272.18
Shihua Zhang342436.27
Xiang Wan412.04