Gene Expression Profiles for Predicting Metastasis in Breast Cancer: A Cross-Study Comparison of Classification Methods by Mark Burton, Mads Thomassen, Qihua Tan, Torben A. Kruse

“…This study compares the performance of seven classification methods and the effect of voting for predicting metastasis outcome in breast cancer patients, in three situations: within the same dataset or across datasets on similar or dissimilar microarray platforms. …”
Get full text

The role of sialyl glycan recognition in host tissue tropism of the avian parasite Eimeria tenella. by Livia Lai, Janene Bumstead, Yan Liu, James Garnett, Maria A Campanero-Rhodes, Damer P Blake, Angelina S Palma, Wengang Chai, David J P Ferguson, Peter Simpson, Ten Feizi, Fiona M Tomley, Stephen Matthews

“…The microarray analyses also reveal a lack of recognition of glycan sequences terminating in the N-glycolyl form of sialic acid by EtMIC3. …”
Get full text

Identification of Differentially Expressed Genes and Elucidation of Pathophysiological Relevance of ABCA1 in HaCaT Cells Induced by PM2.5 by Fen Peng, Chen-Hong Xue, Xiao-Jing Yang, Jing-Yi Huang, Zhou Chen, Jian-Zhong Zhang

“…Cell cycle distribution and apoptosis were detected by flow cytometry. Microarray analyses were used to find out the microarray gene expression profiling; data processing included gene enrichment and pathway analysis. …”
Get full text

Knockdown of A-kinase anchor protein 4 inhibits proliferation of triple-negative breast cancer cells and by Nirmala Jagadish, Sonika Devi, Namita Gupta, Vitusha Suri, Anil Suri

Get full text

Does Bilirubin Have a Causal Relationship With Vitiligo? A Mendelian Randomization Study and Bioinformatics Analysis by Xu D, Yin Y, Teng Y, Huang Y, Yu Y, Tao X, Fan Y, Ding X

“…This study aims to investigate the causal associations between bilirubin and vitiligo using Mendelian randomization (MR) analysis, complemented by bioinformatics validation to unravel the underlying molecular mechanisms.Methods: Genome-wide association study (GWAS) data pertaining to vitiligo and bilirubin were obtained, followed by the execution of a bidirectional MR analysis. Additionally, we performed a bioinformatics analysis using microarray datasets to identify differentially expressed genes (DEGs) in relation to bilirubin in patients with vitiligo. …”
Get full text

A systems biological approach reveals multiple crosstalk mechanism between gram-positive and negative bacterial infections: an insight into core mechanism and unique molecular sign... by R Muthukumar, V Alexandar, Berla Thangam, Shiek S S J Ahmed

“…Further, to identify candidate molecules, the TLRs specific nodes were prioritized using microarray differential expressed genes. Of the top prioritized TLR 2 molecules, 70% were co-expressed. …”
Get full text

Integrative Analysis of Clinical and Bioinformatics Databases to Reveal the Role of Peripheral Innate Immunity in Kawasaki Disease by Hongjun Ba, Lili Zhang, Huimin Peng, Jixun Lin, Youzhen Qin, Yao Wang

“…In this study, we analyzed public single-cell RNA sequencing (scRNA-seq) and microarray data of peripheral blood mononuclear cells from normal controls and KD patients. …”
Get full text

Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women. by Gemma C Sharp, James L Hutchinson, Nanette Hibbert, Tom C Freeman, Philippa T K Saunders, Jane E Norman

“…Appropriate analysis of large microarray experiments that compare gene expression in non-labouring and labouring gestational tissues is necessary to help bridge these gaps in our knowledge. …”
Get full text

Unravelling the Impact of an Additional Sex Chromosome in an Adult Female by Sigin George, Vikas Dagar, Barun Kumar Chakrabarty, N. Nagaraja

“…Interphase fluorescence in situ hybridisation was performed to confirm the diagnosis. Chromosomal microarray, which is a more expensive test, substantiated the presence of additional X chromosomes but failed to detect the presence of low level of mosaicism. …”
Get full text

Development and validation of a Luminex assay for detection of a predictive biomarker for PROSTVAC-VF therapy. by Julie L Lucas, Erin A Tacheny, Allison Ferris, Michelle Galusha, Apurva K Srivastava, Aniruddha Ganguly, P Mickey Williams, Michael C Sachs, Magdalena Thurin, James V Tricoli, Winnie Ricker, Jeffrey C Gildersleeve

“…Strategies to identify patients likely to respond well to a given therapy could significantly improve health care outcomes by maximizing clinical benefits while reducing toxicities and adverse effects. Using a glycan microarray assay, we recently reported that pretreatment serum levels of IgM specific to blood group A trisaccharide (BG-Atri) correlate positively with overall survival of cancer patients on PROSTVAC-VF therapy. …”
Get full text

Identification and Validation of a Potential Marker of Tissue Quality Using Gene Expression Analysis of Human Colorectal Tissue. by Nicole Lange, Florian T Unger, Monika Schöppler, Katja Pursche, Hartmut Juhl, Kerstin A David

“…Normal colorectal tissue and CRC tissue was analyzed using microarray and quantitative real-time PCR (qPCR). Comparing changes in gene expression between pre- and post-surgical tissue using microarray analysis identified a list of potential tissue quality biomarkers and this list was validated using qPCR. …”
Get full text

Renal tissue thawed for 30 minutes is still suitable for gene expression analysis. by Yi Ma, Xiao-Nan Kang, Wen-Bin Ding, Hao-Zheng Yang, Ye Wang, Jin Zhang, Yi-Ran Huang, Hui-Li Dai

“…We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis. …”
Get full text

AgileMultiIdeogram: Rapid Identification and Visualization of Autozygous Regions Using Illumina Short-Read Sequencing Data by Christopher M. Watson, Carolina Lascelles, Morag Raynor, Marilena Elpidorou, Ummey Hany, Laura Crinnion, Colin A. Johnson, Eamonn Sheridan, Alexander F. Markham, James A. Poulter, David T. Bonthron, Ian M. Carr

“…A well-established and effective way of identifying these “autozygous” genomic regions has been to search for runs of homozygous genotypes in microarray SNP data. …”
Get full text

An Ensemble Classification Method for High-Dimensional Data Using Neighborhood Rough Set by Jing Zhang, Guang Lu, Jiaquan Li, Chuanwen Li

“…Mining useful knowledge from high-dimensional data is a hot research topic. Efficient and effective sample classification and feature selection are challenging tasks due to high dimensionality and small sample size of microarray data. …”
Get full text

The absolute number of T lymphocyte subsets is beneficial for differential diagnosis of myelodysplastic syndrome with pure red cell aplastic anemia: a case report and review of the... by Liangjun Zhang, Huixiu Zhong

“…The result of the morphological examination of bone marrow, whole-genome microarray, and bone marrow biopsy all supported the diagnosis of MDS at the first clinical diagnosis. …”
Get full text

The expression levels of CYP3A4 and CYP3A5 serve as potential prognostic biomarkers in lung adenocarcinoma by Mao Qixing, Xu Juqing, Wang Yajing, Dong Gaochao, Xia Wenjie, Shi Run, Wang Anpeng, Xu Lin, Jiang Feng, Wang Jun

“…Lung adenocarcinoma remains to be a high-mortality disease with few effective prognostic biomarkers. Novel biomarkers are urgently demanded to supplement the current prognostic biomarkers. …”
Get full text

Profiling of Circulating Cell-free DNA Methylation Patterns Identifies Aberrant Methylated CTBP1 Promotor Sites for Prediction of Alzheimer’s Disease by Zhiwu Dong, Kewen Zhao, Hongjun Gu, Wenwei Yang, Xin Zhang

“…The R Bioconductor Linear Models for Microarray Data (LIMMA) package was employed to identify methylation variable positions (MVPs), and Probe Lasso was used to pinpoint differentially methylated regions (DMRs) linked to AD. …”
Get full text

Improving machine learning detection of Alzheimer disease using enhanced manta ray gene selection of Alzheimer gene expression datasets by Zahraa Ahmed, Mesut Çevik

“…However, the late enriched understanding of the genetic underpinnings of AD has been made possible due to recent advancements in data mining analysis methods, machine learning, and microarray technologies. However, the “curse of dimensionality” caused by the high-dimensional microarray datasets impacts the accurate prediction of the disease due to issues of overfitting, bias, and high computational demands. …”
Get full text

RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. by B Alex Merrick, Dhiral P Phadke, Scott S Auerbach, Deepak Mav, Suzy M Stiegelmeyer, Ruchir R Shah, Raymond R Tice

“…Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1), a potent hepatocarcinogen, on the male rat liver transcriptome prior to onset of histopathological lesions or tumors. …”
Get full text

An enhanced single base extension technique for the analysis of complex viral populations. by Dale R Webster, Armin G Hekele, Adam S Lauring, Kael F Fischer, Hao Li, Raul Andino, Joseph L DeRisi

“…This single base extension (SBE) based microarray platform was designed and optimized using poliovirus as the target genotype, but can be easily adapted to assay populations derived from any organism. …”
Get full text