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Favorov, A.

Publications and source records attributed to Favorov, A..

5 recordsLinked to original sources

REVA: a rank-based multi-dimensional measure of correlation

The neighbors principle implicit in any machine learning algorithm says that samples with similar labels should be close to one another in feature space as well. For example, while tumors are heterogeneous, tumors that have similar genomics profiles can also be expected to have similar responses to a specific therapy. Simple correlation coefficients provide an effective way to determine whether this principle holds when features and labels are both scalar, but not when either is multivariate. A new class of generalized correlation coefficients based on inter-point distances addresses this need and is called \"distance correlation\". There is only one rank-based distance correlation test available to date, and it is asymmetric in the samples, requiring that one sample be distinguished as a fixed point of reference. Therefore, we introduce a novel, nonparametric statistic, REVA, inspired by the Kendall rank correlation coefficient. We use U-statistic theory to derive the asymptotic distribution of the new correlation coefficient, developing additional large and finite sample properties along the way. To establish the admissibility of the REVA statistic, and explore the utility and limitations of our model, we compared it to the most widely used distance based correlation coefficient in a range of simulated conditions, demonstrating that REVA does not depend on an assumption of linearity, and is robust to high levels of noise, high dimensions, and the presence of outliers. We also present an application to real data, applying REVA to determine whether cancer cells with similar genetic profiles also respond similarly to a targeted therapeutic.\n\nAuthor summarySometimes a simple question arises: how does the distance between two samples in multivariate space compare to another scalar value associated with each sample. Here, we propose theory for a nonparametric test to statistically test this association. This test is independent of the scale of the scalar data, and thus generalizable to any comparison of samples with both high-dimensional data and a scalar. We apply the resulting statistic, REVA, to problems in cancer biology motivated by the model that cancer cells with more similar gene expression profiles to one another can be expected to have a more similar response to therapy.

bioinformatics

Enter the matrix: Interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data

Omics data contains signal from the molecular, physical, and kinetic inter- and intra-cellular interactions that control biological systems. Matrix factorization techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in topics ranging from pathway discovery to time course analysis. We review exemplary applications of matrix factorization for systems-level analyses. We discuss appropriate application of these methods, their limitations, and focus on analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with matrix factorization enables discovery from high-throughput data beyond the limits of current biological knowledge--answering questions from high-dimensional data that we have not yet thought to ask.

systems biology

Untangling The Gene-Epigenome Networks: Timing Of Epigenetic Regulation Of Gene Expression In Acquired Cetuximab Resistance

BACKGROUNDTargeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. To determine the dynamics of these molecular changes, we obtained high throughput omics data weekly during the development of cetuximab resistance in a head and neck cancer in vitro model.\n\nRESULTSAn unsupervised algorithm, CoGAPS, was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically.\n\nCONCLUSIONSGenes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize resistance. These genes include FGFR1, which was associated with EGFR inhibitor resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. Our findings provide a relevant towards better understanding of the time course progression of changes resulting in acquired resistance to targeted therapies. This is an important contribution to the development of alternative treatment strategies that would introduce new drugs before the resistant phenotype develops.

cancer biology

Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis

Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, non-coding RNAs, post-translational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations, once thought to be crucial only for the malignant phenotype maintenance, are now recognized as critical also for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. While associated with cancer, the precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems, and bioinformatics algorithms for their analysis. Advances in bioinformatics data integration techniques that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer, and are therefore also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations to cause tumorigenesis initiation and progression. This deeper understanding is essential to future studies that will precisely infer patients prognosis and select patients who will be responsive to emerging epigenetic therapies.

cancer biology

PatternMarkers and Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS) for data-driven detection of novel biomarkers via whole transcriptome Non-negative matrix factorization (NMF)

SummaryNon-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g., time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF solutions can obscure biomarkers. Therefore, we developed a novel PatternMarkers statistic to extract genes for biological validation and enhanced visualization of NMF results. Finding novel and unbiased gene markers with PatternMarkers requires whole-genome data. However, NMF algorithms typically do not converge for the tens of thousands of genes in genome-wide profiling. Therefore, we also developed Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS), the first robust whole genome Bayesian NMF using the sparse, MCMC algorithm, CoGAPS. This software contains analytic and visualization tools including a Shiny web application, patternMatcher, which are generalized for any NMF. Using these tools, we find granular brain-region and cell-type specific signatures with corresponding biomarkers in GTex data, illustrating GWCoGAPS and patternMarkers ascertainment of data-driven biomarkers from whole-genome data.\n\nAvailabilityPatternMarkers & GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license.\n\nContactgsteinobrien@jhmi.edu; ccolantu@jhmi.edu; ejfertig@jhmi.edu

bioinformatics