Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm. by Robert Darkins, Emma J Cooke, Zoubin Ghahramani, Paul D W Kirk, David L Wild, Richard S Savage

“…In this paper we focus on a particular application to microarray gene expression data. We define and analyse the randomised algorithm, before presenting results on both synthetic and real biological data sets. …”
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Integration of the transcriptome and glycome for identification of glycan cell signatures. by Sandra V Bennun, Kevin J Yarema, Michael J Betenbaugh, Frederick J Krambeck

“…Using the cancer progression model of androgen-dependent to androgen-independent Lymph Node Carcinoma of the Prostate (LNCaP) cells, the N-glycosylation model identified and quantified glycan structural details not typically derived from single-stage mass spectral or gene expression data. Differences between the cell types uncovered include increases in H(II) and Le(y) epitopes, corresponding to greater activity of α2-Fuc-transferase (FUT1) in the androgen-independent cells. …”
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Elucidating the immune infiltration in acne and its comparison with rosacea by integrated bioinformatics analysis. by Lu Yang, Yan-Hong Shou, Yong-Sheng Yang, Jin-Hua Xu

“…<h4>Methods</h4>Five microarray data-sets (GSE108110, GSE53795, GSE65914, GSE14905 and GSE78097) were downloaded from Gene Expression Omnibus. …”
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Transcription factor binding site analysis identifies FOXO transcription factors as regulators of the cutaneous wound healing process. by Karl Markus Roupé, Srinivas Veerla, Joshua Olson, Erica L Stone, Ole E Sørensen, Stephen M Hedrick, Victor Nizet

“…The search for significantly overrepresented and co-occurring transcription factor binding sites in the promoter regions of the most differentially expressed genes in microarray data sets could be a powerful approach for finding key regulators of complex biological processes. …”
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Omics Multi-Layers Networks Provide Novel Mechanistic and Functional Insights Into Fat Storage and Lipid Metabolism in Poultry by Farzad Ghafouri, Abolfazl Bahrami, Abolfazl Bahrami, Mostafa Sadeghi, Seyed Reza Miraei-Ashtiani, Maryam Bakherad, Herman W. Barkema, Samantha Larose

“…In the analysis of microarray and RNA-Seq data, 1,835 genes were detected by comparing the identified genes with significant expression differences (p.adjust &lt; 0.01, fold change ≥ 2 and ≤ −2). …”
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A computational screen for regulators of oxidative phosphorylation implicates SLIRP in mitochondrial RNA homeostasis. by Joshua M Baughman, Roland Nilsson, Vishal M Gohil, Daniel H Arlow, Zareen Gauhar, Vamsi K Mootha

“…We developed a computational procedure, which we call expression screening, which integrates information from thousands of microarray data sets in a principled manner to identify genes that are consistently co-expressed with a target pathway across biological contexts. …”
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RTP4, a Biomarker Associated with Diagnosing Pulmonary Tuberculosis and Pan-Cancer Analysis by Hao Li, Qin Zhou, ZhiXiang Ding, QingHai Wang

“…Pulmonary tuberculosis (PTB) is a global epidemic of infectious disease; the purpose of our study was to explore new potential biomarkers for the diagnosis of pulmonary tuberculosis and to use the biomarkers for further pan-cancer analysis. Methods. Four microarray gene expression sets were downloaded from the GEO public databases and conducted for further analysis. …”
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An attempt at a molecular prediction of metastasis in patients with primary cutaneous melanoma. by Melanie Gschaider, Friederike Neumann, Bettina Peters, Florian Lenz, Michael Cibena, Malgorzata Goiser, Ingrid Wolf, Jörg Wenzel, Cornelia Mauch, Wolfgang Schreiner, Stephan N Wagner

“…Significance analysis of microarrays identified the top 50 differentially expressed genes. …”
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MET overexpression contributes to STAT4-PD-L1 signaling activation associated with tumor-associated, macrophages-mediated immunosuppression in primary glioblastomas by Ying Zhang, Zheng Wang, Zheng Zhao, Tao Jiang, Shou-Wei Li, Yong-Jian Zhu, Qiang-Wei Wang, Li-Hua Sun, Zhi-Liang Wang, Kuan-Yu Wang, Guan-Zhang Li, Jian-Bao Xu, Chang-Yuan Ren, Wen-Ping Ma, Hong-Jun Wang, Zhao-Shi Bao

“…RNA expression data from a total of 1243 primary glioma samples (WHO grades 2–4) were assembled, incorporating The Cancer Genome Atlas, Chinese Glioma Genome Atlas, and GSE16011 data sets.Results Pearson’s correlation test from the three data sets indicated that MET showed a robust correlation with programmed death-ligand 1 (PD-L1) and STAT pathways. …”
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Bioinformatics-Driven Investigations of Signature Biomarkers for Triple-Negative Breast Cancer by Shristi Handa, Sanjeev Puri, Mary Chatterjee, Veena Puri

“…Microarray data set GSE65194 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus was used for identification of differentially expressed genes (DEGs) using R software. …”
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High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. by Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina Leslie

“…These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices (PSSMs), which may match large numbers of sites and produce an unreliable list of target genes. Recently, protein binding microarray (PBM) experiments have emerged as a new source of high resolution data on in vitro TF binding specificities. …”
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