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  4. Selecting control genes for RT-QPCR using public microarray data.
 
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Titre

Selecting control genes for RT-QPCR using public microarray data.

Type
article
Institution
UNIL/CHUV/Unisanté + institutions partenaires
Périodique
BMC Bioinformatics  
Auteur(s)
Popovici, V.
Auteure/Auteur
Goldstein, D.R.
Auteure/Auteur
Antonov, J.
Auteure/Auteur
Jaggi, R.
Auteure/Auteur
Delorenzi, M.
Auteure/Auteur
Wirapati, P.
Auteure/Auteur
Liens vers les personnes
Delorenzi, Mauro  
Wirapati, Pratyaksha  
Popovici, Vlad  
Goldstein, Darlene  
Liens vers les unités
Institut Suisse de Bioinformatique  
ISSN
1471-2105
Statut éditorial
Publié
Date de publication
2009
Volume
10
Première page
42
Peer-reviewed
Oui
Langue
anglais
Résumé
Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones.
Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/
Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable.
Sujets

Breast Neoplasms/diag...

Breast Neoplasms/gene...

Early Detection of Ca...

Female

Gene Expression Profi...

Humans

Oligonucleotide Array...

Reverse Transcriptase...

PID Serval
serval:BIB_2C446942B4A8
DOI
10.1186/1471-2105-10-42
PMID
19187545
WOS
000264007300001
Permalien
https://iris.unil.ch/handle/iris/114800
Open Access
Oui
Date de création
2012-02-23T11:07:47.468Z
Date de création dans IRIS
2025-05-20T19:41:28Z
Fichier(s)
En cours de chargement...
Vignette d'image
Nom

BIB_2C446942B4A8.P001.pdf

Version du manuscrit

preprint

Taille

806.58 KB

Format

Adobe PDF

PID Serval

serval:BIB_2C446942B4A8.P001

URN

urn:nbn:ch:serval-BIB_2C446942B4A89

Somme de contrôle

(MD5):a2c9f09452286ce5183f2f5f9bd0a1e1

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