Additional file 2 of Microbial function and genital inflammation in young South African women at high risk of HIV infection
Creators: name: Arghavan Alisoltani
name: Manhanzva, Monalisa T.
name: Matthys Potgieter
name: Balle, Christina
name: Bell, Liam
name: Ross, Elizabeth
name: Iranzadeh, Arash
name: Plessis, Michelle Du
name: Radzey, Nina
name: Zac McDonald
name: Calder, Bridget
name: Allali, Imane
name: Mulder, Nicola
name: Smritee Dabee
name: Barnabas, Shaun
name: Hoyam Gamieldien
name: Godzik, Adam
name: Blackburn, Jonathan M.
name: Tabb, David L.
name: Linda-Gail Bekker
name: Jaspan, Heather B.
name: Jo-Ann S. Passmore
name: Masson, Lindi
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Table S2. List of protein BLAST results against UniProt and NCBI nr databases (DBs). Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 113 women from Cape Town, South Africa. Primary assigned taxa, obtained based on MaxQuant version 1.5.7.4, are presented in the second column. The curated taxa (third column) were obtained after considering the top similar and frequent BLAST hits for each protein. IDs: UniProt Identity codes. Table S3. List of differentially abundant taxa distinguishing women with low and high inflammation. Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 113 women from Cape Town, South Africa. The false discovery rate (FDR) corrected p-values were obtained based on the aggregated log2-transformed intensity-based absolute quantification of all proteins assigned to the same taxa applying the moderated t-test (limma R package), after adjusting for confounding variables including age, contraceptives, prostate specific antigen (PSA) and sexually transmitted infections (STIs). Taxa with FDR adjusted p-values &lt;0.05 and log2-transformed fold change &gt;1.2 or &lt; -1.2 were considered as differentially abundant taxa. Table S4. List of differentially abundant proteins distinguishing women with low, medium and high inflammation. Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 113 women from Cape Town, South Africa. The false discovery rate (FDR) corrected p-values were obtained based on the log2-transformed intensity-based absolute quantification of each protein applying the moderated t-test (limma R package), after adjusting for confounding variables including age, contraceptives, prostate specific antigen (PSA) and sexually transmitted infections (STIs). Proteins with FDR adjusted p-values &lt;0.05 and log2-transformed fold change &gt;1.2 or &lt; -1.2 were considered as differentially abundant proteins. IDs: UniProt Identity codes. Table S5. List of differentially abundant molecular function (MF) gene ontology terms distinguishing women with low and high inflammation. Liquid chromatography-tandem mass spectrometry was used to evaluate the metaproteome in lateral vaginal wall swabs from 113 women from Cape Town, South Africa. The false discovery rate (FDR) corrected p-values were obtained based on the aggregated log2-transformed intensity-based absolute quantification of all proteins assigned to the same MF term applying the moderated t-test (limma R package), after adjusting for confounding variables including age, contraceptives, prostate specific antigen (PSA) and sexually transmitted infections (STIs). Taxa with FDR adjusted p-values &lt;0.05 and log2-transformed fold change &gt;1.2 or &lt; -1.2 were considered as significantly abundant MFs. (PDF 6094 kb)