README.md

In huynguyen250896/GeneCluster: GeneCluster: Identification of subtype-specific genes

GeneCluster v0.1.0

I. Introduction

The package GeneCluster is built to serve as a support tool for the paper "Multi-omics analysis detects novel prognostic subgroups of breast cancer". A previous study defined subtype-specific genes are the ones mutated predominantly in the samples assigned to one single subtype than in the other subtypes [1]. Subsequently, those genes are features that reflect the difference between subgroups of heterogeneous cancers [1, 2]. To computationally detect subtype-specific genes, we built the R package GeneCluster from the idea of the reference paper [3]. In brief, given a gene from a list of genes of interest, it will be specifically distributed to either of predictive subgroups based on the mean values (e.g., CNA changes, MET changes, and expression levels). Then, a gene was considered as a subtype-specific one if P-value <= 0.05 (one-way ANOVA test).

[1] Cyll, K., et al., Tumour heterogeneity poses a significant challenge to cancer biomarker research. British journal of cancer, 2017. 117(3): p. 367-375.

[2] Alizadeh, A.A., et al., Toward understanding and exploiting tumor heterogeneity. Nature medicine, 2015. 21(8): p. 846-853.

[3] Shen, R., et al., Integrative Subtype Discovery in Glioblastoma Using iCluster. PLOS ONE, 2012. 7(4): p. e35236.

II. Understanding the tool

The following are parameters provided by GeneCluster: - omics: data.frame or matrix. The first input data includes its rows are samples and its columns are genes.

• cluster: Predictive subgroups correspond with samples after running a clustering tool for your own data (e.g., k-means, hclust,...).

• adjustedP: logical. Whether we should adjust the gained P-values (One-way ANOVA test) using the Benjamini-Hochberg procedure. Default is adjustedP = T.

Please see data_n_code to grasp a data format required by GeneCluster and its usage well.

III. Pipeline

Figure: Pipeline of the package GeneCluster.

IV. Implementation

Use the following command to install directly from GitHub;

devtools::install_github("huynguyen250896/GeneCluster")

Call the library;

library(GeneCluster)

running example:

SubtypeSpecificGene(omics = exp, cluster = groups)

IV. What's new

• 2021-01-26 : The function now can adjust gained P-values using the Benjamini-Hochberg procedure.

V. Citation

Please kindly cite the following paper (and Star this Github repository if you find this tool of interest) if you use the tool in this repo:

Author: Nguyen, Quang-Huy
Nguyen, Hung
Nguyen, Tin
Le, Duc-Hau
Year: 2020
Title: Multi-omics analysis detects novel prognostic subgroups of breast cancer
Journal: Frontiers in Genetics
Type of Article: ORIGINAL RESEARCH
DOI: 10.3389/fgene.2020.574661

Feel free to contact Quang-Huy Nguyen for any questions about the code and results.

huynguyen250896/GeneCluster documentation built on Feb. 20, 2021, 1:23 a.m.