The MOAI has been published in Briefings in Bioinformatics.
Journal: Briefings in Bioinformatics
Publisher: OXFORD
Indexed in Journal Citation Report (JCR)
Indexed in WoS (Q1)
Impact Factor: 11.622
Rank: 2/58 [97.41%], MATHEMATICAL & COMPUTATIONAL BIOLOGY
Cite
Yu-Da Lin, Yi-Chen Lee, Chih-Po Chiang, Sin-Hua Moi, Jung-Yu Kan, MOAI: a multi-outcome interaction identification approach reveals an interaction between vaspin and carcinoembryonic antigen on colorectal cancer prognosis, Briefings in Bioinformatics, 23(1):bbab427, 2022 https://doi.org/10.1093/bib/bbab427
Why MOAI?
MOAI was motivated by the limitations of the process of estimating the interaction that simultaneously occurred in multi-outcomes and by the success of the Pareto set filter operator for identifying multi-outcome interaction.
MOAI can consider multi-outcome for identifying the interaction between risk factors. The multi-outcome interaction might explain differences in a disease risk and effect on the multiple disease pathogenesis.
MOAI applies CV to avoid the overfitting of a training model (i.e., selecting the optimal multifactor combination) and reduces the false positives in the statistical analysis.
MOAI is nonparametric (distribution-free), making it suitable for small samples; thereby, it can be used to test differences between independent samples. Nonparametric methods do not need to assume the distribution of data before statistical analysis, which can avoid the small effect size problems in identifying multi-outcome interaction.
MOAI is model-free, indicating that it does not assume a specific disease model of inheritance because the characteristics of multi-outcome interaction between risk factors are usually unclear.
We demonstrated that the MOAI could successfully identify multi-outcome interaction in simulated high-dimensional multi-outcome data with epistatic effects and real-world CRC data.
Install Java
You use firstly ORACLE implementation of the Java Platform, Standard Edition Development Kit (JDK 16). Download the Java SE 16 to the Desktop:
Click on Download JDK button next to Java SE 16.0.1 Downloads. Be sure to choose the JDK, not the JRE.
Accept the Oracle Binary Code License Agreement for Java SE.
Choose the Windows x64 (for example) product by clicking the link jdk-16.0.1_windows-x64_bin.exe.
Once it is downloaded, install it by double clicking the file jdk-16.0.1_windows-x64_bin.exe.
We recommend all of the default options.
Note the installation directory for later—probably something like C:\Program Files\Java\jdk1.16.0_1.
Execute the MOAI Program
Input file format
The genotype data can be stored in a file for control (0) and case (1), respectively. The input file format is illustrated as below,
where the class label is either 0 (control) or 1 (case). The genotype is represented with {0, 1, 2} corresponding to homozygous reference genotype (AA), heterozygous genotype (Aa), and homozygous variant genotype (aa), respectively.
File and Folder
The MOAI.jar is execution files for MOAI program.
User manual
Command-Line Interface