Cell-cycle gene expression analysis using real time PCR in locally advanced squamous-cell head and neck cancer

Woźniak, Grzegorz; Herok, Robert; Jaksik, Roman; Misiołek, Maciej; Kolebacz, Bogdan; Fiszer-Kierzkowska, Anna; Miśkiewicz-Orczyk, Katarzyna; Szymczyk, Cezary; Maciejewski, Adam; Głowacki, Grzegorz; Suwiński, Rafał

doi:10.1016/j.advms.2016.03.009

Cited by 3 publications

(2 citation statements)

References 10 publications

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“…Quantitative real-time PCR (RT-qPCR) has emerged as a powerful and popular tool used for rapid and accurate assessment of changes in gene expression [ 1 – 3 ]. The reliability of gene expression measurements by RT-qPCR is strongly affected by technical factors, including template RNA quality, efficiency of complementary DNA (cDNA) synthesis, performance of primers, and normalization [ 4 – 6 ].…”

Section: Introductionmentioning

confidence: 99%

Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions

Jiang

Gao²,

Wáng³

et al. 2018

BioMed Research International

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Volvariella volvacea (V. volvacea), commonly referred to as Chinese (paddy straw) mushroom, is a basidiomycete with a protein-rich volva and pileus. Selecting appropriate reference genes is a crucial step in the normalization of quantitative real-time PCR data. Therefore, 12 candidate reference genes were selected from the V. volvacea transcriptome based on previous studies and then BestKeeper, geNorm, and NormFinder were used to identify reference genes stably expressed during different developmental stages and conditions. Of the 12 candidate reference genes, SPRY domain protein (SPRYp), alpha-tubulin (TUBα), cyclophilin (CYP), L-asparaginase (L-asp), and MSF1-domain-containing protein (MSF1) were the most stably expressed under different experimental conditions, while 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and beta-actin (ACTB) were the least stably expressed. This investigation not only revealed potential factors influencing the suitability of reference genes, but also identified optimal reference genes from a pool of candidate genes under a wide range of conditions.

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Section: Introductionmentioning

confidence: 99%

Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions

Jiang

Gao²,

Wáng³

et al. 2018

BioMed Research International

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“…As an example, Zheng et al applied a hybrid of K‐means and SVM algorithms in breast cancer diagnosis. In addition, N. Heintzman et al developed algorithms making use of the clustering technique (having chromatin signatures of the regulatory elements as a parameter) for predicting promoters and enhancers in the human genome, Wózniak et al applied a hierarchical clustering method in head and neck cancer, among other related papers …”

Section: Introductionmentioning

confidence: 99%

Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors

Dall'Alba

Casa

Notari

et al. 2018

J of Molecular Recognition

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Promoters are DNA sequences located upstream of the transcription start site of genes. In bacteria, the RNA polymerase enzyme requires additional subunits, called sigma factors (σ) to begin specific gene transcription in distinct environmental conditions. Currently, promoter prediction still poses many challenges due to the characteristics of these sequences. In this paper, the nucleotide content of Escherichia coli promoter sequences, related to five alternative σ factors, was analyzed by a machine learning technique in order to provide profiles according to the σ factor which recognizes them. For this, the clustering technique was applied since it is a viable method for finding hidden patterns on a data set. As a result, 20 groups of sequences were formed, and, aided by the Weblogo tool, it was possible to determine sequence profiles. These found patterns should be considered for implementing computational prediction tools. In addition, evidence was found of an overlap between the functions of the genes regulated by different σ factors, suggesting that DNA structural properties are also essential parameters for further studies.

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Determination of reference genes for ovine pulmonary adenocarcinoma infected lung tissues using RNA-seq transcriptome profiling

Yang

Zhang

Liu

2020

Journal of Virological Methods

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Cell-cycle gene expression analysis using real time PCR in locally advanced squamous-cell head and neck cancer

Cited by 3 publications

References 10 publications

Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions

Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions

Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors

Determination of reference genes for ovine pulmonary adenocarcinoma infected lung tissues using RNA-seq transcriptome profiling

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