MaGIC: a program to generate targeted marker sets for genome-wide association studies by Claire L. Simpson, Valerie K. Hansen, Pak C. Sham, Andrew Collins, John F. Powell, Ammar Al-Chalabi

“…Because it is currently impractical to use all available markers, a subset is typically selected on the basis of required saturation density. …”
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Multi-Scale Genomic, Transcriptomic and Proteomic Analysis of Colorectal Cancer Cell Lines to Identify Novel Biomarkers. by Romina Briffa, Inhwa Um, Dana Faratian, Ying Zhou, Arran K Turnbull, Simon P Langdon, David J Harrison

“…Selecting colorectal cancer (CRC) patients likely to respond to therapy remains a clinical challenge. …”
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Biomarker-Based Nomogram to Predict Neoadjuvant Chemotherapy Response in Muscle-Invasive Bladder Cancer by Meritxell Pérez, Juan José Lozano, Mercedes Ingelmo-Torres, Montserrat Domenech, Caterina Fernández Ramón, J. Alfred Witjes, Antoine G. van der Heijden, Maria José Requena, Antonio Coy, Ricard Calderon, Begoña Mellado, Antonio Alcaraz, Antoni Vilaseca, Maria J. Ribal

“…Gene expression patterns were analysed in 34 samples from transurethral resection of the bladder (TURB) using Illumina microarrays. The expression levels of 45 selected differentially expressed genes between responders and non-responders to NAC were validated by quantitative PCR in an independent cohort of 157 patients. …”
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Comprehensive analysis of microRNA expression profile in malignant glioma tissues by Monika Piwecka, Katarzyna Rolle, Agnieszka Belter, Anna Maria Barciszewska, Marek Żywicki, Marcin Michalak, Stanisław Nowak, Mirosława Z. Naskręt-Barciszewska, Jan Barciszewski

“…We investigated the global miRNA profile of malignant glioma tissues with miRNA microarrays, deep sequencing and meta‐analysis. We selected miRNAs that were most frequently deregulated in glioblastoma tissues, as well as in peritumoral areas, in comparison with normal human brain. …”
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Revealing new mouse epicardial cell markers through transcriptomics. by Lars Bochmann, Padmini Sarathchandra, Federica Mori, Enrique Lara-Pezzi, Domenico Lazzaro, Nadia Rosenthal

“…<h4>Methodology</h4>Using laser capture microscopy, we isolated the epicardial layer from the adult murine heart before or after cardiac infarction in wildtype mice and mice expressing a transgenic IGF-1 propeptide (mIGF-1) that enhances cardiac repair, and analyzed the transcription profile using DNA microarrays.<h4>Principal findings</h4>Expression of epithelial genes such as basonuclin, dermokine, and glycoprotein M6A are highly enriched in the epicardial layer, which maintains expression of selected embryonic genes involved in epicardial development in mIGF-1 transgenic hearts. …”
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Nonlinear Quantitative Radiation Sensitivity Prediction Model Based on NCI-60 Cancer Cell Lines by Chunying Zhang, Luc Girard, Amit Das, Sun Chen, Guangqiang Zheng, Kai Song

“…Important radiation therapy (RT) related genes were selected by significance analysis of microarrays (SAM). …”
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Classification of gliomas based on genome-wide DNA methylation profiles and immunohistochemical analysis: a short study by Olga Taryma-Leśniak, Kamil Buczkowski, Tomasz Klepinowski, Maciej Jankowski, Szymon Retfiński, Bartłomiej Sagan, Leszek Sagan, Ewa Szutowicz, Kacper Winiarski, Marta Masztalewicz, Przemysław Nowacki, Marta Sobalska-Kwapis, Dominik Strapagiel, Wojciech Kloc, Beata Lipska-Ziętkiewicz, Ewa Iżycka-Świeszewska, Tomasz K. Wojdacz

“…The performed analyses did not supply new data according to the unexpected clinical course of the selected cases. Immunohistochemical evaluation with p16 and PTEN antibodies was consistent with the CDKN2A and PTEN status in most cases. …”
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Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. by John G Rowland, Xin Pang, Iwane Suzuki, Norio Murata, William J Simon, Antoni R Slabas

“…We have characterised the acclimation physiology of selected gene 'knockouts' to elucidate possible gene function in the response.…”
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Serum LncRNAs Profiles Serve as Novel Potential Biomarkers for the Diagnosis of HBV-Positive Hepatocellular Carcinoma. by Kang Wang, Wei Xing Guo, Nan Li, Chun Fang Gao, Jie Shi, Yu Fu Tang, Feng Shen, Meng Chao Wu, Shan Rong Liu, Shu Qun Cheng

“…<h4>Methods</h4>lncRNA microarrays were utilized to measure the differential expression of lncRNAs between tumor tissues and corresponding non-tumor tissues in HBV-positive hapatocellular carcinoma. uc001ncr and AX800134 were selected as candidate lncRNAs and detected in three independent cohorts containing a total of 684 participants (healthy individuals and chronic HBV patients and HBV-positive HCC patients) who were recruited between March 2011 and December 2012. …”
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Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. by Salvatore San Paolo, Stepanka Vanacova, Luca Schenk, Tanja Scherrer, Diana Blank, Walter Keller, André P Gerber

“…In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA-related processes. …”
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Interleukin-13 receptor alpha 2 expression in tumor cells is associated with reduced disease-free survival in patients with luminal subtype invasive breast cancer by Hee Jung Kwon, Jung Eun Choi, Young Kyung Bae

“…This study shows interleukin-13 receptor alpha 2 expression could be a useful prognostic marker for selecting patients with luminal breast cancer likely to follow a clinically aggressive course despite receiving systemic therapy.…”
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Applicability of epigenetic age models to next-generation methylation arrays by Leonardo D. Garma, Miguel Quintela-Fandino

“…As new methylation microarrays are developed and older models discontinued, existing epigenetic clocks might become obsolete. …”
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NONO regulates m5C modification and alternative splicing of PTEN mRNAs to drive gastric cancer progression by Gaichao Zhao, Ruochen liu, Lingjun Ge, Dan Qi, Qishu Wu, Zini Lin, Houji Song, Liping Zhong, Hongjuan Cui

“…Abstract Background The effect of m5C modification on oncogene mRNAs has been well studied, while little is known about its influence on mRNAs of tumor suppressor genes (TSGs). …”
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Alliin, a Garlic (Allium sativum) Compound, Prevents LPS-Induced Inflammation in 3T3-L1 Adipocytes by Saray Quintero-Fabián, Daniel Ortuño-Sahagún, Manuel Vázquez-Carrera, Rocío Ivette López-Roa

“…However its potential anti-inflammatory effect is unknown. We examined the effects of alliin in lipopolysaccharide- (LPS-) stimulated 3T3-L1 adipocytes by RT-PCR, Western blot, and microarrays analysis of 22,000 genes. …”
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Five immune‐gene‐signatures participate in the development and pathogenesis of Kawasaki disease by Han Nie, Shizhi Wang, Quanli Wu, Danni Xue, Weimin Zhou

“…We constructed coexpression networks, and used the cytohobbe tool in Cytoscape to analyze the coexpression networks and select the immune genes that played a key role in them. …”
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Interaction networks among miRNA, protein, and metabolite fingerprints identify the regulatory networks and key players in the pathogenesis of diabetic cardiomyopathy by Bhaswati Chatterjee, Suman S. Thakur

“…The regulatory networks and key players involved in the pathogenesis of diabetic cardiomyopathy are not clearly known. We selected the miRNA, protein, and metabolite fingerprints that play a significant role in DCM and manually constructed miRNA–protein–metabolite interaction networks from the miRNA–protein and protein–metabolite interaction networks. …”
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Genetic Dissection of Learning and Memory in Mice by Yann S. Mineur, Wim E. Crusio, Frans Sluyter

“…Next, we briefly review more recently developed techniques, such as microarrays and RNA interference. In addition, we focus on gene-environment interactions and endophenotypes. …”
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ASF1B promotes gastric cancer progression by modulating H2AC20 and activating PI3K/AKT and ERK1/2 pathways by Mengyuan Zhao, Junchang Zhang, Yanjun He, Chongge You

“…With the continuous enrichment of treatment methods, GC has entered an era of comprehensive treatment oriented toward precision and standardization.MethodsThrough the application of bioinformatics and assessments of tissue microarrays, this study has selected the histone chaperone Anti-Silencing Function 1B (ASF1B) for detailed analysis, including clinical specimens. …”
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Characterization of tumor-infiltrating lymphocytes and their spatial distribution in triple-negative breast cancer by Eunkyung Han, Hye Yeon Choi, Hyun Jung Kwon, Yul Ri Chung, Hee-Chul Shin, Eun-Kyu Kim, Koung Jin Suh, Se Hyun Kim, Jee Hyun Kim, So Yeon Park

“…Methods We analyzed TNBC samples through PanCancer Immune Profiling using NanoString nCounter assays to identify immune-related genes that are expressed differentially in relation to TIL levels and evaluated protein expression of selected markers through immunohistochemical staining on tissue microarrays. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of shared T-cell epitopes for cancer immunotherapy regardless of the tumor mutational burden.Methods A transcriptomic analysis based on RNA sequencing was developed to quantify the expression of HERV-K sequences containing the selected epitopes. The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. …”
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