PXD010939

PXD010939 is an original dataset announced via ProteomeXchange.

Title	Univariate and classification analysis reveals potential diagnostic biomarkers for early-stage ovarian cancer type 1 and type 2
Description	Biomarkers for early detection of ovarian tumors are urgently needed. Tumors of the ovary grow within cysts and most are benign.Surgical sampling is the only way to ensure accurate diagnosis, but often leads to morbidity and loss of female hormones. The present study explored the deep proteome in well-defined sets of ovarian tumors, FIGO stage I, Type 1 (low-grade serous, mucinous, endometrioid; n=9), Type 2 (high-grade serous; n=9), and benign serous (n=9) using TMT-LC-MS/MS. We evaluated new bioinformatics tools in the discovery phase. This innovative selection process involved different normalizations, a combination of univariate statistics, and logistic model tree and naïve Bayes tree classifiers. We identified 142 proteins by this combined approach. One biomarker panel and nine individual proteins were validated in cyst fluid and serum: transaldolase-1, fructose-bisphosphate aldolase A (ALDOA), transketolase, ceruloplasmin, mesothelin, clusterin, tenascin- XB, laminin subunit gamma-1, and mucin-16. Six of the proteins were found significant (p<0.05) in cyst fluid while ALDOA was the only protein significant in serum. The biomarker panel achieved ROC AUC 0.96 and 0.57 respectively. We conclude that classification algorithms complement traditional statistical methods by selecting combinations that may be missed by standard univariate tests.
HostingRepository	PRIDE
AnnounceDate	2019-02-02
AnnouncementXML	Submission_2019-02-11_04:53:21.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sahlgrenska Academy Proteomics Core
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-30 01:23:21	ID requested
1	2019-02-01 18:40:20	announced
⏵ 2	2019-02-11 04:53:22	announced	Updated publication reference for PubMed record(s): 30710757.

Marci, š, auskas S, Ulfenborg B, Kristjansdottir B, Waldemarson S, Sundfeldt K, Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2. J Proteomics, 196():57-68(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Ovarian cancer, Cyst fluid, FIGO stage I type 1 and type 2, Proteomics, Biomarker, Q Exactive, Orbitrap Fusion

Karin Sundfeldt
contact affiliation	Professor, Department of Obstetrics and Gynecology at Institute of Clinical Sciences, Kvinnokliniken SU Östra 416 85 Gothenburg, Sweden
contact email	karin.sundfeldt@obgyn.gu.se
lab head
Sahlgrenska Academy Proteomics Core
contact affiliation	University of Gothenburg
contact email	egor.vorontsov@gu.se
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/2019/02/PXD010939

PRIDE project URI

• PRIDE
  1. PXD010939
     1. Label: PRIDE project
     2. Name: Univariate and classification analysis reveals potential diagnostic biomarkers for early-stage ovarian cancer type 1 and type 2