Characterization of drug‐induced transcriptional modules: towards drug repositioning and functional understanding by Murat Iskar, Georg Zeller, Peter Blattmann, Monica Campillos, Michael Kuhn, Katarzyna H Kaminska, Heiko Runz, Anne‐Claude Gavin, Rainer Pepperkok, Vera van Noort, Peer Bork

“…Abstract In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug‐induced transcriptional modules from genome‐wide microarray data of drug‐treated human cell lines and rat liver, and first characterized their conservation. …”
Get full text

The Venus score for the assessment of the quality and trustworthiness of biomedical datasets by Davide Chicco, Alessandro Fabris, Giuseppe Jurman

“…We apply the Venus score to twelve datasets from multiple subdomains, including electronic health records, medical imaging, microarray and bulk RNA-seq gene expression, cheminformatics, physiologic electrogram signals, and medical text. …”
Get full text

The Construction of ceRNA Regulatory Network Unraveled Prognostic Biomarkers and Repositioned Drug Candidates for the Management of Pancreatic Ductal Adenocarcinoma by Busra Aydin, Keziban Okutan, Ozge Onluturk Aydogan, Raghu Sinha, Beste Turanli

“…The mRNA, miRNA, and circRNA expression profiles of PDAC were obtained from nine microarray datasets. Differentially expressed genes (DEGs), microRNAs (DEmiRNAs), and circular RNAs (DEcircRNAs) were identified. …”
Get full text

Quantitative Expression of SFN, lncRNA CCDC18-AS1, and lncRNA LINC01343 in Human Breast Cancer as the Regulator Biomarkers in a Novel ceRNA Network: Based on Bioinformatics and Exp... by Mehrnoush Rishehri, Tahereh Etemadi, Leila Pisheh, Ghazaleh Koufigar, Mansoureh Azadeh

“…Finding their dysregulation in cancer and evaluating their interaction with other molecules, such as short noncoding RNAs “microRNA (miRNAs)” as well as various genes, are the most important parts in cancer diagnostics. …”
Get full text

Exploration of the shared gene signatures and molecular mechanisms between cardioembolic stroke and ischemic stroke by Xuan Wang, Xuan Wang, Xueyuan Liu, Xueyuan Liu

“…ABCA1, CLEC4E, and IRS2 were identified as biomarkers for both CS and IS and performed well in predicting the onset risk of CS and IS. All three biomarkers were highly expressed in both CS and IS compared to their corresponding controls. …”
Get full text

Increased Expression of Long Noncoding RNA LOC100506314 in T cells from Patients with Nonsegmental Vitiligo and Its Contribution to Vitiligo Pathogenesis by Ning-Sheng Lai, Hui-Chun Yu, Hsien-Bin Huang, Hsien-Yu Huang Tseng, Ming-Chi Lu

“…This study aimed to identify the abnormal expression of long noncoding RNAs (lncRNAs) in T cells from patients with vitiligo and to investigate their functional roles in the immune system. Using microarray analysis, the expression levels of RNA transcripts in T cells from patients with vitiligo and controls were compared. …”
Get full text

Methylomics of breast cancer: Seeking epimarkers in peripheral blood of young subjects by Golnaz Khakpour, Mehrdad Noruzinia, Pantea Izadi, Fatemeh Karami, Mohammad Ahmadvand, Ramin Heshmat, Mahsa M Amoli, Javad Tavakkoly-Bazzaz

“…Critical roles of epigenomic alterations in the pathogenesis of breast cancer have recently seized great attentions toward finding epimarkers in either non-invasive or semi-non-invasive samples as well as peripheral blood. In this way, methylated DNA immunoprecipitation microarray (MeDIP-chip) was performed on DNA samples isolated from white blood cells of 30 breast cancer patients compared to 30 healthy controls. …”
Get full text

Methylation-based smoking signatures in blood and tissue samples for the prediction of self-reported smoking status and mortality in patients with colorectal cancer by Tanwei Yuan, Katrin E. Tagscherer, Wilfried Roth, Melanie Bewerunge-Hudler, Alexander Brobeil, Matthias Kloor, Hendrik Bläker, Hermann Brenner, Michael Hoffmeister

Get full text

The proteomics of colorectal cancer: identification of a protein signature associated with prognosis. by Donna O'Dwyer, Lynda D Ralton, Aisling O'Shea, Graeme I Murray

“…Fifteen proteins that showed increased expression were validated by immunohistochemistry using a well characterised colorectal cancer tissue microarray containing 515 primary colorectal cancer, 224 lymph node metastasis and 50 normal colonic mucosal samples. …”
Get full text

CDK5 Regulates Paclitaxel Sensitivity in Ovarian Cancer Cells by Modulating AKT Activation, p21Cip1- and p27Kip1-Mediated G1 Cell Cycle Arrest and Apoptosis. by Shu Zhang, Zhen Lu, Weiqun Mao, Ahmed A Ahmed, Hailing Yang, Jinhua Zhou, Nicholas Jennings, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, Roberto Miranda, Wei Qiao, Veera Baladandayuthapani, Zongfang Li, Anil K Sood, Jinsong Liu, Xiao-Feng Le, Robert C Bast

“…CDK5 protein was measured by immunohistochemical staining of an ovarian cancer tissue microarray to correlate CDK5 expression with overall patient survival. …”
Get full text

Deep sleep and parietal cortex gene expression changes are related to cognitive deficits with age. by Heather M Buechel, Jelena Popovic, James L Searcy, Nada M Porter, Olivier Thibault, Eric M Blalock

“…Despite sleep disruption's well-recognized negative influence on cognition, and its prevalence with age, surprisingly few studies have tested sleep's relationship to cognitive aging.…”
Get full text

Tazarotene-Induced Gene 3 (TIG3) Induces Apoptosis in Melanoma Cells Through the Modulation of Inhibitors of Apoptosis Proteins by Chun-Hua Wang, Lu-Kai Wang, Fu-Ming Tsai

“…In this study, we investigated the role of the retinoic acid-inducible gene TIG3 in regulating melanoma cell growth, as well as elucidating its involvement in apoptosis. …”
Get full text

Enucleation-Induced Rat Adrenal Gland Regeneration: Expression Profile of Selected Genes Involved in Control of Adrenocortical Cell Proliferation by Marianna Tyczewska, Marcin Rucinski, Agnieszka Ziolkowska, Marta Szyszka, Marcin Trejter, Anna Hochol-Molenda, Krzysztof W. Nowak, Ludwik K. Malendowicz

“…Therefore, we performed studies on regenerating rat adrenals. Microarray RNA analysis and QPCR revealed that enucleation resulted in a rapid elevation of expression of genes involved in response to wounding, defense response, and in immunological processes. …”
Get full text

Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor. by Ester Rozenblum, Jose R Sotelo-Silveira, Gina Y Kim, Jack Y Zhu, Christopher C Lau, Nicole McNeil, Susana Korolevich, Hongling Liao, James M Cherry, David J Munroe, Thomas Ried, Paul S Meltzer, Walter M Kuehl, Anna V Roschke

“…Newly developed near-diploid OVDM1 cell line offers an opportunity to evaluate tumorigenesis pathways/events in a minor clone of metastatic ovarian adenocarcinoma as well as mechanisms of chromothripsis.…”
Get full text

γ-Synuclein antibodies have neuroprotective potential on neuroretinal cells via proteins of the mitochondrial apoptosis pathway. by Corina Wilding, Katharina Bell, Sabine Beck, Sebastian Funke, Norbert Pfeiffer, Franz H Grus

“…The aim of this study was to investigate the effect of γ-synuclein antibody on the viability and reactive oxygen species levels of a neuroretinal cell line (RGC-5) as well as their interaction with cellular proteins. …”
Get full text

Rab7 inhibitor enhances stem cell differentiation into keratinocyte-like cells with anti-inflammatory properties by Raghad Alghazali, Mouna Tabebi, Mouna Tabebi, Moustafa Elmasry, Moustafa Elmasry, Ahmed El-Serafi, Ahmed El-Serafi

“…This treatment upregulated several epidermal markers, including P63, cytokeratin 5 and 14 and filaggrin, while downregulated the stem cell marker, vimentin. Microarray data showed upregulation of the anti-inflammatory gene HMOX-1, coupled with the downregulation of various inflammation-related pathways, such as TNF, chemokine, AGE-RAGE and IL-17 signalling cascades, as well as cytokine-cytokine receptor interaction pathways. …”
Get full text

Cyr61 Mediates Angiotensin II-Induced Podocyte Apoptosis via the Upregulation of TXNIP by Jingxue Ma, Ruiying Ma, Xiaoyue Zhao, Yingxiu Wang, Shengxue Liao, Cong Nong, Fengling Lu, Zhao Liang, Junhui Huang, Yan Huang, Zhengxi Zhu, Junjie Wang

“…Purpose. It is well documented that angiotensin II (Ang II) elevation promotes apoptosis of podocytes in vivo and vitro, but the potential mechanism is still oscular. …”
Get full text

A “proto” type galectin expressed in striped bass (Morone saxatilis) tissues is released to epidermal mucus and binds to bacterial and mucus glycans by Davin E. Henrikson, Davin E. Henrikson, Hafiz Ahmed, Hafiz Ahmed, Satoshi Tasumi, Satoshi Tasumi, Mahesh Gokara, Chiguang Feng, Chiguang Feng, Kelsey Abernathy, Kelsey Abernathy, Muddassar Iqbal, Muddassar Iqbal, Mario A. Bianchet, Gerardo R. Vasta, Gerardo R. Vasta

“…Msgal1-L1 agglutinated environmental bacterial species and strains, some of which are recognized fish pathogens, such as Vibrio and Edwardsiella spp. A microbial microarray analysis revealed that it preferentially binds to bacterial exopolysaccharides (e.g., Streptococcus and Shigella spp.) as well as various lipopolysaccharide O-antigen serotypes of Proteus spp. …”
Get full text

IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling. by Helen M Lazear, Alissa Lancaster, Courtney Wilkins, Mehul S Suthar, Albert Huang, Sarah C Vick, Lisa Clepper, Larissa Thackray, Margaret M Brassil, Herbert W Virgin, Janko Nikolich-Zugich, Ashlee V Moses, Michael Gale, Klaus Früh, Michael S Diamond

“…To define IRF-regulated gene signatures, we performed microarray analysis on WNV-infected mDC from wild type (WT), DKO, TKO, or Ifnar(-/-) mice, as well as from mice lacking the RIG-I like receptor adaptor protein MAVS. …”
Get full text

Comprehensive analysis of anoikis-related genes in diagnosis osteoarthritis: based on machine learning and single-cell RNA sequencing data by Jun-Song Zhang, Run-Sang Pan, Guo-Lu Li, Jian-Xiang Teng, Hong-Bo Zhao, Chang-Hua Zhou, Ji-Sheng Zhu, Hao Zheng, Xiao-Bin Tian

“…The objective of this work was to discover novel transcriptome-based anoikis-related biomarkers and pathways for OA progression.The microarray datasets GSE114007 and GSE89408 were downloaded using the Gene Expression Omnibus (GEO) database. …”
Get full text