UMMS Affiliation
Department of Microbiology and Physiological Systems
Publication Date
2019-11-21
Document Type
Article
Disciplines
Bacterial Infections and Mycoses | Bioinformatics | Computational Biology | Microbiology
Abstract
BACKGROUND: Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described for identifying conditionally essential genes whose tolerance for insertions varies between two conditions. However, for large-scale experiments involving many conditions, a method is needed for identifying genes that exhibit significant variability in insertions across multiple conditions.
RESULTS: In this paper, we introduce a novel statistical method for identifying genes with significant variability of insertion counts across multiple conditions based on Zero-Inflated Negative Binomial (ZINB) regression. Using likelihood ratio tests, we show that the ZINB distribution fits TnSeq data better than either ANOVA or a Negative Binomial (in a generalized linear model). We use ZINB regression to identify genes required for infection of M. tuberculosis H37Rv in C57BL/6 mice. We also use ZINB to perform a analysis of genes conditionally essential in H37Rv cultures exposed to multiple antibiotics.
CONCLUSIONS: Our results show that, not only does ZINB generally identify most of the genes found by pairwise resampling (and vastly out-performs ANOVA), but it also identifies additional genes where variability is detectable only when the magnitudes of insertion counts are treated separately from local differences in saturation, as in the ZINB model.
Keywords
Essentiality, Mycobacterium tuberculosis, TnSeq, Transposon insertion library, Zero-inflated negative binomial distribution
Rights and Permissions
© The Author(s) 2019. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
DOI of Published Version
10.1186/s12859-019-3156-z
Source
BMC Bioinformatics. 2019 Nov 21;20(1):603. doi: 10.1186/s12859-019-3156-z. Link to article on publisher's site
Journal/Book/Conference Title
BMC bioinformatics
Related Resources
PubMed ID
31752678
Repository Citation
Subramaniyam S, DeJesus MA, Zaveri A, Smith CM, Baker RE, Ehrt S, Schnappinger D, Sassetti CM, Ioerger TR. (2019). Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression. Open Access Articles. https://doi.org/10.1186/s12859-019-3156-z. Retrieved from https://escholarship.umassmed.edu/oapubs/4042
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Bacterial Infections and Mycoses Commons, Bioinformatics Commons, Computational Biology Commons, Microbiology Commons