PXD042954

PXD042954 is an original dataset announced via ProteomeXchange.

Title	Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge
Description	Multi-omics has the promise to provide a detailed molecular picture for biological systems. Although obtaining multi-omics data is relatively easy, methods that analyze such data have been lagging. In this paper, we present an algorithm that uses probabilistic graph representations and external knowledge to perform optimum structure learning and deduce a multifarious interaction network for multi-omics data from a bacterial community. Kefir grain, a microbial community that ferments milk and creates kefir, represents a self-renewing, stable, natural microbial community. Kefir has been shown to associate with a wide range of health benefits. We obtained a controlled bacterial community using the two most abundant and well-studied species in kefir grains: Lentilactobacillus kefiri and Lactobacillus kefiranofaciens. We applied growth temperatures of 30°C and 37°C, and ob-tained transcriptomic, metabolomic, and proteomic data for the same 20 samples (10 samples per temperature). We obtained a multi-omics interaction network, which generated insights that would not have been possible with single-omics analysis. We identified interactions among transcripts, proteins, and metabolites suggesting active toxin/antitoxin systems. We also observed multifarious interactions that involved the shikimate pathway. These observations helped explain bacterial adaptation to different stress conditions, co-aggregation, and increased activation of L. kefiranofa-ciens at 37°C.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:03:26.424.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sophe Alvarez
SpeciesList	scientific name: Lactobacillus kefiranofaciens; NCBI TaxID: 267818; scientific name: Lactobacillus kefiri; NCBI TaxID: 33962;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-13 12:56:59	ID requested
1	2023-08-18 05:16:16	announced
⏵ 2	2023-11-14 07:03:26	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Lactobacillus,proteomics, metabolomics, Lentilactobacillus, kefir

Sophie Alvarez
contact affiliation	Proteomics and Metabolomics Facility, University of Nebraska - Lincoln
contact email	salvarez@unl.edu
lab head
Sophe Alvarez
contact affiliation	University of Nebraska - Lincoln
contact email	salvarez@unl.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD042954
     1. Label: PRIDE project
     2. Name: Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge