Supervised Wavelet Method to Predict Patient Survival from Gene Expression Data by Maryam Farhadian, Paulo J. G. Lisboa, Abbas Moghimbeigi, Jalal Poorolajal, Hossein Mahjub

“…In microarray studies, the number of samples is relatively small compared to the number of genes per sample. …”
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Next-generation sequencing for endocrine cancers: Recent advances and challenges by Padmanaban S Suresh, Thejaswini Venkatesh, Rie Tsutsumi, Abhishek Shetty

“…Microarray data can also elucidate the responses of endocrine tumors to therapeutic treatments. …”
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RETRACTED ARTICLE: Multi-stage biomedical feature selection extraction algorithm for cancer detection by Ismail Keshta, Pallavi Sagar Deshpande, Mohammad Shabaz, Mukesh Soni, Mohit kumar Bhadla, Yasser Muhammed

“…Early cancer detection is greatly aided by machine learning and artificial intelligence (AI) to gene microarray data sets (microarray data). Despite this, there is a significant discrepancy between the number of gene features in the microarray data set and the number of samples. …”
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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

“…In addition, the study demonstrates that discoveries made using neoglycoprotein-based microarrays can be readily migrated to a clinical assay.…”
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Deep learning-based spatial analysis on tumor and immune cells of pathology images predicts MIBC prognosis. by Chao Hu, Fan Wang, Hui Xu, XiQi Dong, XiuJuan Xiong, Yun Zhang, TianCheng Zhao, YuanQiao He, LiBin Deng, XiongBing Lu

“…The prognostic value of Lymph_inside % was validated in the HBlaU079Su01 microarray. Multiomics analysis demonstrated that Lymph_inside % demonstrated significant positive correlations with antitumor immune cell abundance and the apoptosis pathway. …”
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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. …”
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Prognostic role of FUT8 expression in relation to p53 status in stage II and III colorectal cancer. by Masaru Noda, Hirokazu Okayama, Yasuhide Kofunato, Shun Chida, Katsuharu Saito, Takeshi Tada, Mai Ashizawa, Takahiro Nakajima, Keita Aoto, Tomohiro Kikuchi, Wataru Sakamoto, Hisahito Endo, Shotaro Fujita, Motonobu Saito, Tomoyuki Momma, Shinji Ohki, Koji Kono

“…Utilizing multiple datasets of microarray and RNA sequence of CRC, FUT8 mRNA was found to be highly expressed in wild-type p53 tumors (n = 382) compared to those of mutant p53 (n = 437). …”
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Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways. by Andrew Filer, Philipp Antczak, Greg N Parsonage, Holly M Legault, Margot O'Toole, Mark J Pearson, Andrew M Thomas, Dagmar Scheel-Toellner, Karim Raza, Christopher D Buckley, Francesco Falciani

“…To test our hypothesis we utilized a bioinformatics approach to explore a publicly available microarray dataset including rheumatoid arthritis (RA), osteoarthritis (OA) and normal synovial tissue, then extended those findings in a new microarray dataset representing matched synovial, bone marrow and skin fibroblasts cultured from RA and OA patients undergoing arthroplasty. …”
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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

“…The results showed RNA degraded more after longer incubation at room temperature. However, microarray results showed only 240 genes (0.91%) altered significantly in response to thawing at room temperature. …”
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Protein detection enhanced by 3DNA dendrimer signal amplification by Johanna R. Mora, Tamara L. Zielinski, Bryce P. Nelson, Robert C. Getts

“…DNA dendrimers, conjugated with both anti-biotin antibodies and up to 350 labeling entities, were designed and adapted to protein microarray and enzyme-linked immunosorbent assay (ELISA) to improve the limits of protein detection with no additional steps or equipment. …”
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Clinical profile and cytogenetics of siblings with Jacobsen syndrome by Abinaya Gunalan, Priya Jose, Allen David, Peter Prasanth Kumar Kommu

“…Segmental duplication (22.2 Mb) on the long arm of chromosome 14 and deletion of 5.9 Mb on 11q24 were revealed by chromosomal microarray analysis.…”
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Attenuated monocyte apoptosis, a new mechanism for osteoporosis suggested by a transcriptome-wide expression study of monocytes. by Yao-Zhong Liu, Yu Zhou, Lei Zhang, Jian Li, Qing Tian, Ji-Gang Zhang, Hong-Wen Deng

“…<h4>Aim</h4>To identify osteoporosis-related genes, we performed microarray analyses of monocytes using Affymetrix 1.0 ST arrays in 42 (including 16 pre- and 26 postmenopausal) high hip BMD (bone mineral density) vs. 31 (including 15 pre- and 16 postmenopausal) low hip BMD Caucasian female subjects. …”
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Over-expression of either MECP2_e1 or MECP2_e2 in neuronally differentiated cells results in different patterns of gene expression. by Marija Orlic-Milacic, Liana Kaufman, Anna Mikhailov, Aaron Y L Cheung, Huda Mahmood, James Ellis, Peter J Gianakopoulos, Berge A Minassian, John B Vincent

“…DOCK8 was shown via microarray and qRT-PCR to be upregulated in both SK-N-SH cells and mouse fibroblasts. …”
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CFS-MOES Ensemble Model on Metaheuristic Search-Based Feature Selection by Santosini Bhutia, Bichitrananda Patra, Mitrabinda Ray

“…However, the tremendous dimensionality of the microarray cancer dataset is the greatest challenge in interpreting the data. …”
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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

“…We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL). …”
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Genes Related to Mitochondrial Functions, Protein Degradation, and Chromatin Folding Are Differentially Expressed in Lymphomonocytes of Rett Syndrome Patients by Alessandra Pecorelli, Guido Leoni, Franco Cervellati, Raffaella Canali, Cinzia Signorini, Silvia Leoncini, Alessio Cortelazzo, Claudio De Felice, Lucia Ciccoli, Joussef Hayek, Giuseppe Valacchi

“…LIMMA (Linear Models for MicroArray) and SAM (Significance Analysis of Microarrays) analyses on microarray data from 12 RTT patients and 7 control subjects identified 482 genes modulated in RTT, of which 430 were upregulated and 52 were downregulated. …”
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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. …”
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On-Chip DNA Assembly via Dielectrophoresis by Xichuan Rui, Lin-Sheng Wu, Xin Zhao

“…While there exist several microarray-based oligo synthesis technologies, on-chip gene assembly has yet to be demonstrated. …”
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The impact of focused Gene Ontology curation of specific mammalian systems. by Yasmin Alam-Faruque, Rachael P Huntley, Varsha K Khodiyar, Evelyn B Camon, Emily C Dimmer, Tony Sawford, Maria J Martin, Claire O'Donovan, Philippa J Talmud, Peter Scambler, Rolf Apweiler, Ruth C Lovering

“…This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome.…”
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Chapter 8: Biological knowledge assembly and interpretation. by Ju Han Kim

“…Most methods for large-scale gene expression microarray and RNA-Seq data analysis are designed to determine the lists of genes or gene products that show distinct patterns and/or significant differences. …”
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