PXD008153

PXD008153 is an original dataset announced via ProteomeXchange.

Title	Integration of multilevel OMICs data based on the identification of regulatory modules from protein-protein interaction networks
Description	Complex scientific experiments provide researchers with a wealth of data and knowledge from heterogeneous sources. Analyzed in its entirety, OMICs data provide a deep insight into the overall biological processes of organisms. However, the integration of data from different cellular levels (e.g., transcriptomics and proteomics) is challenging. Analyzing lists of differentially abundant molecules from different cellular levels often results in a small overlap, which can be accounted to, e.g., different regulatory mechanisms, different temporal scales as well as inherent properties of the measurement method. Thus, there is a need for approaches that allow efficient integration of OMICs data from different cellular levels. In this study, we make use of transcriptome, proteome and secretome data from the human pathogenic fungus Aspergillus fumigatus challenged with the antifungal drug caspofungin. Caspofungin targets the fungal cell wall leading to a compensatory stress response. We analyze the experimental data based on two different approaches. First, we apply a simple approach based on the comparison of differentially regulated genes and proteins with subsequent pathway analysis. Second, we compare the cellular levels based on the identification of regulatory or functional modules by two module-detecting algorithms from protein-protein interaction networks in conjunction with transcriptomic and proteomic data. Our results show that both approaches associate the fungal caspofungin response with biological pathways like cell wall biosynthesis, fatty acid metabolism as well as carbohydrate metabolism. Compared to results of the simple approach, the use of regulatory modules shows a notably higher agreement between the different cellular levels. The additional structural information of the networks provided by the module-based approach allows for topological analysis as well as the analysis of the temporal evolution of cellular response at a molecular level. However, we also found that quality of the module-based results depends on the comprehensiveness of the underlying protein-protein interaction network itself. Thus, while our results highlight the benefits and potential provided by a module-based analysis of OMICs data from different cellular levels, future studies will have to focus on the expansion of organism specific protein-protein interaction networks.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:41:49.666.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Krüger
SpeciesList	scientific name: Neosartorya fumigata (Aspergillus fumigatus); NCBI TaxID: 746128;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iTRAQ4plex-116 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-07 04:46:16	ID requested
1	2018-10-25 05:45:29	announced
⏵ 2	2024-10-22 04:41:57	announced	2024-10-22: Updated project metadata.

Conrad T, Kniemeyer O, Henkel SG, Kr, ü, ger T, Mattern DJ, Valiante V, Guthke R, Jacobsen ID, Brakhage AA, Vlaic S, Linde J, Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol, 12(1):88(2018) [pubmed]

10.1186/s12918-018-0620-8;

curator keyword: Technical

submitter keyword: caspofungin, proteomics, LC-MS,Aspergillus fumigatus, secretome

Olaf Kniemeyer
contact affiliation	Leibniz Institute for Natural Product Research and Infection Biology, Department of Molecular and Applied Microbiology, Stress- and Immunoproteomics group
contact email	olaf.kniemeyer@leibniz-hki.de
lab head
Thomas Krüger
contact affiliation	Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute
contact email	thomas.krueger@leibniz-hki.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/10/PXD008153

PRIDE project URI

• PRIDE
  1. PXD008153
     1. Label: PRIDE project
     2. Name: Integration of multilevel OMICs data based on the identification of regulatory modules from protein-protein interaction networks