Analysis of a data matrix and a graph: Metagenomic data and the phylogenetic tree

TL;DR

This paper explores integrating phylogenetic tree information into metagenomic data analysis by using a nonstandard inner-product space, enhancing the biological relevance of the results.

Contribution

It introduces a method to incorporate phylogenetic graphs into data analysis through a specialized inner-product space, improving interpretability.

Findings

Enhanced analysis results with phylogenetic information

More biologically meaningful insights obtained

Method applicable to other graph-structured data

Abstract

In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and nontrivial task. We look at the example of metagenomic data---data from a genomic survey of the abundance of different species of bacteria in a sample. Here, the graph of interest is a phylogenetic tree depicting the interspecies relationships among the bacteria species. We illustrate that analysis of the data in a nonstandard inner-product space effectively uses this additional graphical information and produces more meaningful results.