Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,836 bioRxiv papers from 309,131 authors.

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

By Genevieve L. Stein-O’Brien, Jacob L Carey, Wai-shing Lee, Michael Considine, Alexander V Favorov, Emily Flam, Theresa Guo, Sijia Li, Luigi Marchionni, Thomas Sherman, Shawn Sivy, Daria A Gaykalova, Ronald D McKay, Michael F. Ochs, Carlo Colantuoni, Elana J. Fertig

Posted 26 Oct 2016
bioRxiv DOI: 10.1101/083717 (published DOI: 10.1093/bioinformatics/btx058)

Non-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. Availability: PatternMarkers & GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license.

Download data

  • Downloaded 531 times
  • Download rankings, all-time:
    • Site-wide: 21,098 out of 70,836
    • In bioinformatics: 3,064 out of 6,933
  • Year to date:
    • Site-wide: 50,332 out of 70,836
  • Since beginning of last month:
    • Site-wide: 50,843 out of 70,836

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News