Related papers: MOST: detecting cancer differential gene expressio…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
Microarray data are often used to determine which genes are differentially expressed between groups, for example, between treatment and control groups. There are methods of determining which genes have a high probability of differential…
Cancer is a heterogeneous disease with different combinations of genetic and epigenetic alterations driving the development of cancer in different individuals. While these alterations are believed to converge on genes in key cellular…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
With the increasingly available large-scale cancer genomics datasets, machine learning approaches have played an important role in revealing novel insights into cancer development. Existing methods have shown encouraging performance in…
Cancer cells evolve through random somatic mutations. "Beneficial" mutations which disrupt key pathways (e.g. cell cycle regulation) are subject to natural selection. Multiple mutations may lead to the same "beneficial" effect, in which…
Identifying the mutations that drive cancer growth is key in clinical decision making and precision oncology. As driver mutations confer selective advantage and thus have an increased likelihood of occurrence, frequency-based statistical…
Global expression analyses using microarray technologies are becoming more common in genomic research, therefore, new statistical challenges associated with combining information from multiple studies must be addressed. In this paper we…
We propose a method for detecting differential gene expression that exploits the correlation between genes. Our proposal averages the univariate scores of each feature with the scores in correlation neighborhoods. In a number of real and…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
In computational biology, gene expression datasets are characterized by very few individual samples compared to a large number of measurements per sample. Thus, it is appealing to merge these datasets in order to increase the number of…
In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
Statistical inference on the cancer-site specificities of collective ultra-rare whole genome somatic mutations is an open problem. Traditional statistical methods cannot handle whole-genome mutation data due to their…
In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subtypes of cancer. However, these alterations do not necessarily induce differential…
Four reasons why you might wish to read this paper: 1. We have devised a new statistical T test to determine differentially expressed genes (DEG) in the context of microarray experiments. This statistical test adds a new member to the…
Over the past decades, statisticians and machine-learning researchers have developed literally thousands of new tools for the reduction of high-dimensional data in order to identify the variables most responsible for a particular trait.…
Cancer detection is one of the key research topics in the medical field. Accurate detection of different cancer types is valuable in providing better treatment facilities and risk minimization for patients. This paper deals with the…
Two-component mixture models are particularly useful for identifying differentially expressed genes, but their performance can deteriorate markedly when the alternative distribution departs from parametric assumptions or symmetry. We…
Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…