PXD000416

PXD000416 is an original dataset announced via ProteomeXchange.

Title	Y chromosome-located gene, lysine-specific demethylase 5D, associated with prostate cancer
Description	The objective of Human Y Chromosome Proteome Project is to map and annotate all proteins encoded by genes on the MSY sequences. Lysine (K)-specific demethylase 5D (KDM5D) is located on the AZFb region of Y chromosome and encode for a JmjC-domain-containing protein. Changes in KDM5D transcript level in prostate cancer have shown in various studies. To investigation the function of KDM5D in prostate cancer, we knocked down the expression of KDM5D in human prostate cancer cell (DU-145) using siRNA approach. Down-regulation of KDM5D was confirmed by qRT-PCR and western-blot analyses. Cell cycle analysis and MTS assay revealed that down-regulation of KDM5D induces cell proliferation. Furthermore, we observed that KDM5D down-regulation could effectively decrease apoptosis, as measured by the propidium iodide flow cytometric assay. To further our study, we investigated the dynamic of KDM5D protein network using shotgun label free quantitative proteomics approach in knockdown and control cell line. In summary, 102 down-regulated and 107 up-regulated proteins were detected from 894 total proteins. Up-regulated proteins mainly activated ribosome biogenesis whereas down-regulated genes were mainly involved in proteolysis, cell death and metabolic process. The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI (Homo sapien) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
HostingRepository	PRIDE
AnnounceDate	2015-08-05
AnnouncementXML	Submission_2015-08-05_04:47:24.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mehdi mirzaei
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; monohydroxylated residue
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2013-08-15 02:21:53	ID requested
⏵ 1	2015-08-05 04:47:30	announced

Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH, Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J Proteome Res, 14(9):3492-502(2015) [pubmed]

submitter keyword: Human Y chromosome, KDM5D, Label-free shotgun proteomics

Mehdi mirzaei
contact affiliation	chemistry and biomolecular science department
contact email	mmirzaei@cbms.mq.edu.au
lab head
Mehdi mirzaei
contact affiliation	chemistry and biomolecular science department
contact email	mmirzaei@cbms.mq.edu.au
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/2015/08/PXD000416

PRIDE project URI

• PRIDE
  1. PXD000416
     1. Label: PRIDE project
     2. Name: Y chromosome-located gene, lysine-specific demethylase 5D, associated with prostate cancer