Unknown

Dataset Information

0

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.


ABSTRACT: Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree, a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

SUBMITTER: Stevens JR 

PROVIDER: S-EPMC5512180 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

altmetric image

Publications

<i>SigTree</i>: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

Stevens John R JR   Jones Todd R TR   Lefevre Michael M   Ganesan Balasubramanian B   Weimer Bart C BC  

Computational and structural biotechnology journal 20170706


Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant c  ...[more]

Similar Datasets

| S-EPMC5029162 | biostudies-literature
| S-EPMC4012501 | biostudies-literature
| S-EPMC3729670 | biostudies-literature
| S-EPMC2654800 | biostudies-other
| S-EPMC3467245 | biostudies-literature
| S-EPMC3416384 | biostudies-literature
| S-EPMC7658449 | biostudies-literature
2022-08-01 | GSE199797 | GEO
| S-EPMC5096847 | biostudies-literature
| S-EPMC4076506 | biostudies-literature