Proposing a novel molecular subtyping scheme for predicting distant recurrence-free survival in breast cancer post-neoadjuvant chemotherapy with close correlation to metabolism and... by Jin Huang, Jin Huang, Jian-Lin Zhang, Lin Ang, Ming-Cong Li, Min Zhao, Yao Wang, Qiang Wu, Qiang Wu

“…To optimize the surveillance regimen for distant recurrence after neoadjuvant chemotherapy (NAC), we conducted a comprehensive analysis using bioinformatics and machine learning approaches.Materials and methodsMicroarray data were retrieved from the GEO database, and differential expression analysis was performed with the R package ‘Limma’. …”
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Association between Incidental Pelvic Inflammation and Aggressive Prostate Cancer by Dimple Chakravarty, Parita Ratnani, Li Huang, Zachary Dovey, Stanislaw Sobotka, Roy Berryhill, Harri Merisaari, Majd Al Shaarani, Richa Rai, Ivan Jambor, Kamlesh K. Yadav, Sandeep Mittan, Sneha Parekh, Julia Kodysh, Vinayak Wagaskar, Rachel Brody, Carlos Cordon-Cardo, Dmitry Rykunov, Boris Reva, Elai Davicioni, Peter Wiklund, Nina Bhardwaj, Sujit S. Nair, Ashutosh K. Tewari

“…Alteration in tumor transcriptome and inflammatory markers in patients with and without pelvic inflammation were studied using microarray analysis, immunohistochemistry, and culture supernatants derived from inflamed sites used in functional assays. …”
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CCL2 Expression in Tumor Cells and Tumor-Infiltrating Immune Cells Shows Divergent Prognostic Potential for Bladder Cancer Patients Depending on Lymph Node Stage by Markus Eckstein, Elena Epple, Rudolf Jung, Katrin Weigelt, Verena Lieb, Danijel Sikic, Robert Stöhr, Carol Geppert, Veronika Weyerer, Simone Bertz, Astrid Kehlen, Arndt Hartmann, Bernd Wullich, Helge Taubert, Sven Wach

“…We analyzed the expression of CCL2 by immunohistochemistry (IHC) in 168 muscle invasive BCa samples using a tissue microarray. Application of a single cut-off for the staining status of tumor cells (TCs; positive vs. negative) and immune cells (ICs; ≤6% of ICs vs. >6% of ICs) revealed 57 cases (33.9%) and 70 cases (41.7%) with CCL2-positive TCs or ICs, respectively. …”
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The prognostic value and biological significance of gap junction beta protein 2 (GJB2 or Cx26) in cervical cancer by Silu Meng, Silu Meng, Yuhuan Liu, Yuhuan Liu, Xiaoyan Wang, Xue Wu, Xue Wu, Wan Xie, Wan Xie, Xiaoyan Kang, Xiaoyan Kang, Xiaoyu Liu, Xiaoyu Liu, Lili Guo, Lili Guo, Changyu Wang, Changyu Wang

“…Based on The Cancer Genome Atlas data (TCGA cohort, n = 304) and tissue microarray samples (OBC cohort, n = 111), we explored the prognostic value of GJB2 for CC patients using bioinformatics analysis and IHC scoring. …”
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Identification of KIF11 as a Novel Target in Meningioma by Gerhard Jungwirth, Tao Yu, Mahmoud Moustafa, Carmen Rapp, Rolf Warta, Christine Jungk, Felix Sahm, Steffen Dettling, Klaus Zweckberger, Katrin Lamszus, Christian Senft, Mario Loehr, Almuth F. Keßler, Ralf Ketter, Manfred Westphal, Juergen Debus, Andreas von Deimling, Matthias Simon, Andreas Unterberg, Amir Abdollahi, Christel Herold-Mende

“…Therefore, we re-analyzed our previous microarray dataset of benign, atypical, and anaplastic meningiomas (<i>n</i> = 62) and got evidence for differential expression of five kinesins (KIFC1, KIF4A, KIF11, KIF14 and KIF20A). …”
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Circulating Extracellular Vesicles and Particles Derived From Adipocytes: The Potential Role in Spreading MicroRNAs Associated With Cellular Senescence by Ionara Rodrigues Siqueira, Ionara Rodrigues Siqueira, Ionara Rodrigues Siqueira, Andressa de Souza Rodrigues, Marina Siqueira Flores, Eduarda Letícia Vieira Cunha, Madeleine Goldberg, Brennan Harmon, Rachael Batabyal, Robert J. Freishtat, Laura Reck Cechinel, Laura Reck Cechinel, Laura Reck Cechinel

“…Fatty acid-binding protein 4 (FABP4) was used for adipocyte-derived EVPs isolation; microRNA isolation and microarray expression analysis were performed. The analysis revealed 728 miRNAs, 32 were differentially between groups (p &lt; 0.05; fold change ≥ |1.1|), of which 15 miRNAs were upregulated and 17 were downregulated in circulating EVPs from aged animals compared to young adults. …”
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Tumor-suppressive role of the musculoaponeurotic fibrosarcoma gene in colorectal cancer by Hiroaki Itakura, Tsuyoshi Hata, Daisuke Okuzaki, Koki Takeda, Kenji Iso, Yamin Qian, Yoshihiro Morimoto, Tomohiro Adachi, Haruka Hirose, Yuhki Yokoyama, Takayuki Ogino, Norikatsu Miyoshi, Hidekazu Takahashi, Mamoru Uemura, Tsunekazu Mizushima, Takao Hinoi, Masaki Mori, Yuichiro Doki, Hidetoshi Eguchi, Hirofumi Yamamoto

“…Repeated administration of microRNAs inhibited polyp formation. Microarray analysis indicated that c-MAF, which reportedly shows oncogene-like behavior in multiple myeloma and T cell lymphoma, decreased in tumor samples but increased in microRNA-treated normal mucosa. …”
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Bioinformatic analysis of the molecular mechanisms underlying the progression of bone defects by Hao Liu, Hao Liu, Hao Liu, Xuan Zhao, Xuan Zhao, Xuan Zhao, Yin Li, Yin Li, Yin Li, Jiang Yi, Jiang Yi, Jiang Yi, Chenxi Zhang, Chenxi Zhang, Chenxi Zhang, Ziyang Zheng, Ziyang Zheng, Ziyang Zheng, Siming Dai, Siming Dai, Siming Dai, Guoyong Yin, Guoyong Yin, Guoyong Yin, Shujie Zhao, Shujie Zhao, Shujie Zhao

“…Our study was conducted to explore the molecular events related to the progression of bone defects a common clinical condition.MethodsFirst, microarray data of GSE20980 were obtained from the Gene Expression Omnibus (GEO) database, where 33 samples in total were used to analyze the molecular biological processes related to bone defects. …”
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Assessing equivalent and inverse change in genes between diverse experiments by Lisa Neums, Lisa Neums, Devin C. Koestler, Devin C. Koestler, Qing Xia, Qing Xia, Jinxiang Hu, Jinxiang Hu, Shachi Patel, Shachi Patel, Shelby Bell-Glenn, Shelby Bell-Glenn, Dong Pei, Dong Pei, Bo Zhang, Samuel Boyd, Samuel Boyd, Prabhakar Chalise, Prabhakar Chalise, Jeffrey A. Thompson, Jeffrey A. Thompson

“…Furthermore, applying the ECI bootstrap test and TOST to publicly available microarray expression data from pancreatic cancer showed that, while TOST was not able to identify any equivalently or inversely changed genes, the ECI bootstrap test identified genes associated with pancreatic cancer. …”
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Identification of Modulators of the <i>C.</i> <i>elegans</i> Aryl Hydrocarbon Receptor and Characterization of Transcriptomic and Metabolic AhR-1 Profiles by Lucie Larigot, Linh-Chi Bui, Marine de Bouvier, Ophélie Pierre, Grégory Pinon, Justine Fiocca, Mohammad Ozeir, Cendrine Tourette, Chris Ottolenghi, Sandrine Imbeaud, Clément Pontoizeau, Benjamin J. Blaise, Aline Chevallier, Céline Tomkiewicz, Béatrice Legrand, Bénédicte Elena-Herrmann, Christian Néri, Vanessa Brinkmann, Pierre Nioche, Robert Barouki, Natascia Ventura, Julien Dairou, Xavier Coumoul

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Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia by Jianhao Wang, Zhihui Sun, Huan Liu, Lin Yue, Fan Wang, Shuangrong Liu, Bohong Su, Baohui Liu, Fanjiang Kong, Chao Fang

“…Promoter analysis revealed that most Snf2 genes had <i>cis</i>-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. …”
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Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis by Jennifer Bolleyn, Matthias Rombaut, Nisha Nair, Steven Branson, Anja Heymans, Marinee Chuah, Thierry VandenDriessche, Vera Rogiers, Joery De Kock, Tamara Vanhaecke

“…In this study, we first investigated the impact of the ectopic expression of HNF4α in rLEC on both mRNA and microRNA (miR) level by means of microarray technology. We found that HNF4α transduction did not induce major changes to the rLEC phenotype. …”
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Rare recurrent copy number variations in metabotropic glutamate receptor interacting genes in children with neurodevelopmental disorders by Joseph T. Glessner, Munir E. Khan, Xiao Chang, Yichuan Liu, F. George Otieno, Maria Lemma, Isabella Slaby, Heather Hain, Frank Mentch, Jin Li, Charlly Kao, Patrick M. A. Sleiman, Michael E. March, John Connolly, Hakon Hakonarson

“…Methods Platforms aimed at investigating genetic-based associations, such as high-density microarray technologies, have been groundbreaking techniques in the field of complex diseases, aimed at elucidating the underlying disease biology. …”
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Identification of the circRNA–miRNA–mRNA regulatory network in osteoarthritis using bioinformatics analysis by Wen-Bin Xu, Vit Kotheeranurak, Vit Kotheeranurak, Huang-Lin Zhang, Jin-Yi Feng, Jing-Wei Liu, Chien-Min Chen, Chien-Min Chen, Chien-Min Chen, Guang-Xun Lin, Guang-Xun Lin, Gang Rui, Gang Rui

“…Therefore, this study aimed to construct a ceRNA regulatory network related to OA to explore the pathogenesis of OA.Methods: Differentially expressed circRNAs (DEcircRNAs), microRNAs (DEmiRNAs), and mRNAs (DEmRNAs) were obtained from the Gene Expression Omnibus microarray data (GSE175959, GSE105027, and GSE169077). …”
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Analysis of weighted gene co-expression networks and clinical validation identify hub genes and immune cell infiltration in the endometrial cells of patients with recurrent implant... by Zhenteng Liu, Zhenteng Liu, Shoucui Lai, Shoucui Lai, Qinglan Qu, Qinglan Qu, Xuemei Liu, Xuemei Liu, Wei Zhang, Wei Zhang, Dongmei Zhao, Dongmei Zhao, Shunzhi He, Shunzhi He, Yuxia Sun, Yuxia Sun, Hongchu Bao, Hongchu Bao

“…Nevertheless, the critical genes and genetic mechanisms underlying RIF are largely unknown.Methods:We first obtained three comprehensive microarray datasets “GSE58144, GSE103465 and GSE111974”. …”
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Cancer Stem Cell Markers—Clinical Relevance and Prognostic Value in High-Grade Serous Ovarian Cancer (HGSOC) Based on The Cancer Genome Atlas Analysis by Natalia Iżycka, Mikołaj Piotr Zaborowski, Łukasz Ciecierski, Kamila Jaz, Sebastian Szubert, Cezary Miedziarek, Marta Rezler, Kinga Piątek-Bajan, Aneta Synakiewicz, Anna Jankowska, Marek Figlerowicz, Karolina Sterzyńska, Ewa Nowak-Markwitz

“…Data on mRNA and protein levels assessed by microarray and mass spectrometry were retrieved from TCGA. …”
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Melatonin inhibits ESCC tumor growth by mitigating the HDAC7/β-catenin/c-Myc positive feedback loop and suppressing the USP10-maintained HDAC7 protein stability by Zhi-Qiang Ma, Ying-Tong Feng, Kai Guo, Dong Liu, Chang-Jian Shao, Ming-Hong Pan, Yi-Meng Zhang, Yu-Xi Zhang, Di Lu, Di Huang, Fan Zhang, Jin-Liang Wang, Bo Yang, Jing Han, Xiao-Long Yan, Yi Hu

“…IHC staining on ESCC tissue microarray and further survival analyses were performed to explore the relationship between target genes’ expression and prognosis of ESCC. …”
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Dietary Crocin is Protective in Pancreatic Cancer while Reducing Radiation-Induced Hepatic Oxidative Damage by Hamid A. Bakshi, Mazhar S Al Zoubi, Hakkim L. Faruck, Alaa A A Aljabali, Firas A. Rabi, Amin A. Hafiz, Khalid M Al-Batanyeh, Bahaa Al-Trad, Prawej Ansari, Mohamed M. Nasef, Nitin B. Charbe, Saurabh Satija, Meenu Mehta, Vijay Mishra, Gaurav Gupta, Salem Abobaker, Poonam Negi, Ibrahim M. Azzouz, Ashref Ali K Dardouri, Harish Dureja, Parteek Prasher, Dinesh K. Chellappan, Kamal Dua, Mateus Webba da Silva, Mohamed El Tanani, Paul A. McCarron, Murtaza M. Tambuwala

“…Concomitantly, crocin treatment-induced apoptosis by inducing the release of cytochrome c from mitochondria to cytosol. Microarray analysis of the expression signature of genes induced by crocin showed a substantial number of genes involved in cell signaling pathways and checkpoints (723) are significantly affected by crocin. …”
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Exploration and identification of anoikis-related genes in polycythemia vera by Wufuer Aini, Wufuer Aini, Wufuer Aini, Limin Xie, Limin Xie, Limin Xie, Wanyu Hu, Wanyu Hu, Wanyu Hu, Yuan Tang, Yuan Tang, Yuan Tang, Hongling Peng, Hongling Peng, Hongling Peng, Guangsen Zhang, Tuo Deng, Tuo Deng, Tuo Deng

“…However, few studies have focused on the role of anoikis in PV, especially on the development of PV.Methods: The microarray and RNA-seq results were screened from the Gene Expression Omnibus (GEO) database and the anoikis-related genes (ARGs) were downloaded from Genecards. …”
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Pharmacological targeting of MTHFD2 suppresses NSCLC via the regulation of ILK signaling pathway by Feng Zhou, Ziyi Yuan, Yuyan Gong, Luyao Li, Yanmao Wang, Xian Wang, Chunbo Ma, Lehe Yang, Zhiguo Liu, Liangxing Wang, Haiyang Zhao, Chengguang Zhao, Xiaoying Huang

“…Here, we show that MTHFD2 inhibition results in suppression of cell growth, migration, invasion and epithelial-mesenchymal transition (EMT) in NSCLC. Microarray analysis suggests that MTHFD2 is positively associated with ILK signaling based on western blotting results. …”
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