PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.

BMC Genomics
Jumamurat R BayjanovSacha A F T van Hijum

Abstract

Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances). Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/) that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene) selection is based. Preprocessed data is used in feature (e.g., gene) selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value) ...Continue Reading

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Citations

Apr 30, 2013·Briefings in Functional Genomics·Bas E DutilhSacha A F T van Hijum
Jul 13, 2012·Briefings in Bioinformatics·Wouter G TouwSacha A F T van Hijum
Mar 28, 2013·BMC Microbiology·Jumamurat R BayjanovSacha A F T van Hijum
Dec 8, 2014·Food Microbiology·J W SandersM Wels
Nov 12, 2013·Applied and Environmental Microbiology·Annereinou R DijkstraJeroen Hugenholtz
Jan 3, 2013·Current Opinion in Biotechnology·James SteeleJan Kok
Dec 4, 2012·Current Opinion in Biotechnology·Filipe Branco dos SantosBas Teusink
Sep 11, 2012·Current Opinion in Biotechnology·Sacha A F T van HijumRudi F Vogel
Mar 5, 2016·Annual Review of Food Science and Technology·Marjon H J Wells-BennikTjakko Abee
Jun 18, 2015·Briefings in Bioinformatics·Wynand AlkemaSacha A F T van Hijum
Oct 26, 2016·The ISME Journal·Erwin M BerendsenMarjon H J Wells-Bennik
Dec 24, 2014·Archives of Microbiology·Cristiane C ThompsonFabiano L Thompson
Jun 7, 2014·Frontiers in Microbiology·Sascha KrausePaul L E Bodelier
Sep 14, 2016·Immunity, Inflammation and Disease·Lydie CassardRaphaëlle Bourdet-Sicard
Dec 3, 2016·BMC Genomics·Alice CibrarioMarguerite Dols-Lafargue
Jun 7, 2015·Applied and Environmental Microbiology·Corina CeapaMichiel Kleerebezem
Jul 29, 2016·Microbiology and Molecular Biology Reviews : MMBR·Konstantinos PapadimitriouJan Kok
Jun 8, 2017·Clinical Microbiology Reviews·Tarah LynchGary Van Domselaar
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Dec 5, 2016·Nucleic Acids Research·Maria BrbićFran Supek
Jul 17, 2018·FEMS Microbiology Letters·Adalberto CostessiWalter Pirovano
Apr 30, 2020·Cell Host & Microbe·Jordan E BisanzPeter J Turnbaugh

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Datasets Mentioned

BETA
GSE21729

Methods Mentioned

BETA
genotyping
footprinting

Software Mentioned

Minomics
R
PhenoLink
R package randomForest
randomForest R package

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