Immunoregulatory actions of epithelial cell PPAR gamma at the colonic mucosa of mice with experimental inflammatory bowel disease. by Saroj K Mohapatra, Amir J Guri, Montse Climent, Cristina Vives, Adria Carbo, William T Horne, Raquel Hontecillas, Josep Bassaganya-Riera

“…Global gene expression analysis was profiled using Affymetrix microarrays. The IEC-specific deficiency of PPAR gamma in mice with a mixed background worsened colonic inflammatory lesions, but had no effect on disease activity (DAI) or weight loss. …”
Get full text

2R and remodeling of vertebrate signal transduction engine by Huminiecki Lukasz, Heldin Carl

“…We investigated 2R-associated nodes in the context of the human signalling network, as well as in an inferred ancestral pre-2R (AP2R) network, and found that hubs (particularly involving negative regulation) were preferentially retained, with high connectivity driving retention. Finally, microarrays and proteomics demonstrated a trend for gradual paralog expression divergence independent of the duplication mechanism, but inferred ancestral expression states suggested preferential subfunctionalisation among 2R-ohnologs (2ROs).…”
Get full text

EBV-positive Hodgkin lymphoma is associated with suppression of p21^cip1/waf1and a worse prognosis by Hsu Su-Ming, Tsai Ching-Hwa, Tsai Mong-Hsun, Lo Fei-Yun, Huang Mi-Hsin, Wu Shang-Ju, Liu Ting-Yun, Lin Chung-Wu

“…</p> <p>Results</p> <p><it>EBER1 </it>was transfected into two HL cell lines, KMH2 and L428, and microarrays were used to screen for <it>EBER1</it>-induced changes. …”
Get full text

A proteomic view of <it>Caenorhabditis elegans </it>caused by short-term hypoxic stress by Wu Yonghong, Gao Yan, Zhang Feilong, Hang Xingyi, Shi Jinping, Ren Changhong, Li Hualing, Xu Langlai, Chen Changsheng, Zhang Chenggang

“…Hypoxia-induced changes in the expression of a number of genes have been analyzed using whole genome microarrays in <it>C. elegans</it>, but the changes at the protein level in response to hypoxic stress still remain unclear.…”
Get full text

Expression of MTDH and IL-10 Is an Independent Predictor of Worse Prognosis in ER-Negative or PR-Negative Breast Cancer Patients by Pei-Yi Chu, Shin-Mae Wang, Po-Ming Chen, Feng-Yao Tang, En-Pei Isabel Chiang

“…Although tumor hypoxia has been found to promote tumor metastasis, the roles of HIF-1α-regulated genes and their application are not completely integrated in clinical practice. (2) Methods: We examined the correlation between HIF-1α, metadherin (MTDH), and interleukin (IL)-10 mRNA expression, as well as their expression patterns in the prognosis of breast cancer using the Gene Expression Profiling Interactive Analysis (GEPIA) databases via a web interface; tissue microarrays (TMAs) were stained for MTDH and IL-10 protein expression using immunohistochemistry. (3) Results: HIF-1α, MTDH, and IL-10 mRNA expression are highly correlated and strongly associated with poor prognosis. …”
Get full text

Regulation of the cardiomyocyte transcriptome <it>vs </it>translatome by endothelin-1 and insulin: translational regulation of 5' terminal oligopyrimidine tract (TOP) mRNAs by insu... by Sugden Peter H, Tham El L, Cullingford Timothy E, Marshall Andrew K, Markou Thomais, Clerk Angela

“…TOP mRNAs include those encoding ribosomal proteins, but the full panoply remains to be established. Here, we used microarrays to compare the effects of endothelin-1 and insulin on the global transcriptome of neonatal rat cardiomyocytes, and on mRNA recruitment to polysomes (i.e. the translatome).…”
Get full text

EGFR as a biomarker of smoking status and survival in oropharyngeal squamous cell carcinoma by Shanmugappiriya Sivarajah, Morris Kostiuk, Cameron Lindsay, Lakshmi Puttagunta, Daniel A. O’Connell, Jeffrey Harris, Hadi Seikaly, Vincent L. Biron

“…Retrospectively collected tumors were used to construct tissue microarrays (TMAs), which were stained with EGFR, p16, DAPI and Pan-cytokeratin, and digitally quantified. …”
Get full text

Maintenance of stemness in oxaliplatin-resistant hepatocellular carcinoma is associated with increased autocrine of IGF1. by Yang Bu, Qing-An Jia, Zheng-Gang Ren, Ju-Bo Zhang, Xue-Mei Jiang, Lei Liang, Tong-Chun Xue, Quan-Bao Zhang, Yan-Hong Wang, Lan Zhang, Xiao-Ying Xie, Zhao-You Tang

“…Metastatic potential, sensitivity to oxaliplatin, and expression of CSC-related markers in the xenografted tumor tissues were evaluated. DNA microarrays were used to measure changes in gene expression as a result of oxaliplatin treatment. …”
Get full text

Long Non-coding RNAs Expression Profile in HepG2 Cells Reveals the Potential Role of Long Non-coding RNAs in the Cholesterol Metabolism by Gang Liu, Xinxin Zheng, Yanlu Xu, Jie Lu, Jingzhou Chen, Xiaohong Huang

“…Our aim was to identify important lncRNAs that might play an important role in contributing to the benefits of epigallocatechin-3-gallate (EGCG) on cholesterol metabolism. Methods: Microarrays was used to reveal the lncRNA and mRNA profiles in green tea polyphenol(-)-epigallocatechin gallate in cultured human liver (HepG2) hepatocytes treated with EGCG and bioinformatic analyses of the predicted target genes were performed to identify lncRNA-mRNA targeting relationships. …”
Get full text

Transcription factors Mat2 and Znf2 operate cellular circuits orchestrating opposite- and same-sex mating in Cryptococcus neoformans. by Xiaorong Lin, Jennifer C Jackson, Marianna Feretzaki, Chaoyang Xue, Joseph Heitman

“…Here, we applied insertional mutagenesis via Agrobacterium-mediated transformation and transcription analysis using whole genome microarrays to identify factors involved in C. neoformans differentiation. …”
Get full text

Altered circular RNA expressions in extracellular vesicles from bronchoalveolar lavage fluids in mice after bacterial infections by Heedoo Lee, Heedoo Lee, Rokgi Hong, Yang Jin

“…The circRNAs identified using microarrays may be validated by RT-qPCR using primers specific to the circular but not the linear form. …”
Get full text

Novel bioinformatic methods and machine learning approaches reveal candidate biomarkers of the intensity and timing of past exposure to Plasmodium falciparum. by Sophie Bérubé, Tamaki Kobayashi, Douglas E Norris, Ingo Ruczinski, William J Moss, Amy Wesolowski, Thomas A Louis

“…Using a novel bioinformatic pipeline optimized for protein microarrays that minimizes between-sample technical variation, we used antibody responses to Plasmodium antigens as predictors in random forest models to classify samples from adults into these three regions of differing historical malaria transmission with high accuracy (AUC = 0.99). …”
Get full text

Epigenetic regulation of developmental expression of Cyp2d genes in mouse liver by Ye Li, Xiao-bo Zhong

“…DNA methylation (DNAme), histone 3 lysine 4 dimethylation (H3K4me2), and histone 3 lysine 27 trimethylation (H3K27me3) was established by ChIP-on-chip tiling microarrays from mouse livers at prenatal, neonatal, and adult stages. …”
Get full text

Iodine-131 dose dependent gene expression in thyroid cancers and corresponding normal tissues following the Chernobyl accident. by Michael Abend, Ruth M Pfeiffer, Christian Ruf, Maureen Hatch, Tetiana I Bogdanova, Mykola D Tronko, Armin Riecke, Julia Hartmann, Viktor Meineke, Houda Boukheris, Alice J Sigurdson, Kiyohiko Mabuchi, Alina V Brenner

“…We first hybridized 32 randomly allocated RNA specimen pairs (T/N) on 64 whole genome microarrays (Agilent, 4×44 K). Associations of differential gene expression (log(2)(T/N)) with dose were assessed using Kruskall-Wallis and trend tests in linear mixed regression models. …”
Get full text

Urine proteomic insights from the belimumab in lupus nephritis trial by Daniel Goldman, Chandra Mohan, Laurence Magder, Andrea Fava, Emma Weeding

“…At each time point, 1000 urinary proteins were quantified using antibody microarrays (Raybiotech Kiloplex), and their abundance was compared in responders (n=31) versus non-responders (n=22) and with belimumab treatment (n=28) versus standard of care therapy (n=26). …”
Get full text

National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research by Valdivieso Federico A, Milnes John T, Schneider Althea M, Whelan Nancy B, Winters Sharon B, Pople Andrew K, Farhat Ghada, Mohanty Sambit K, Schmandt Linda, Parwani Anil V, Amin Waqas, Feldman Michael, Pass Harvey I, Dhir Rajiv, Melamed Jonathan, Becich Michael J

“…</p> <p>Conclusion</p> <p>The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. …”
Get full text

Molecular network profiling of U373MG human glioblastoma cells following induction of apoptosis by novel marine-derived anti-cancer 1,2,3,4-tetrahydroisoquinoline alkaloids by Tabunoki Hiroko, Saito Naoki, Suwanborirux Khanit, Charupant Kornvika, Satoh Jun-ichi

“…</p> <p>Methods</p> <p>We studied the genome-wide gene expression profile on microarrays and molecular networks by using pathway analysis tools of bioinformatics.…”
Get full text

High Levels of Nucleolar Spindle-Associated Protein and Reduced Levels of BRCA1 Expression Predict Poor Prognosis in Triple-Negative Breast Cancer. by Li Chen, Liu Yang, Feng Qiao, Xin Hu, Shan Li, Ling Yao, Xue-Li Yang, Zhi-Ming Shao

“…This study investigated the prognostic value of NuSAP1 in breast cancer.Two sets of tissue microarrays (TMAs) that included samples from 450 breast cancer patients were constructed, of which 250 patients were training set and the other 200 patients were validation set. …”
Get full text

Deep serological profiling of the Trypanosoma cruzi TSSA antigen reveals different epitopes and modes of recognition by Chagas disease patients. by Guadalupe Romer, Leonel A Bracco, Alejandro D Ricci, Virginia Balouz, Luisa Berná, Juan C Villar, Janine M Ramsey, Melissa S Nolan, Faustino Torrico, Norival Kesper, Jaime Altcheh, Carlos Robello, Carlos A Buscaglia, Fernán Agüero

“…To optimize the serotyping performance of this molecule, we herein used a combination of immunosignaturing approaches based on peptide microarrays and serum samples from Chagas disease patients to establish a deep linear B-cell epitope profiling of TSSA.…”
Get full text

Intratumoral neutrophil extracellular traps are associated with unfavorable clinical outcomes and immunogenic context in pancreatic ductal adenocarcinoma by Xianlong Chen, Heng Ma, Shengwei Mo, Shuangni Yu, Zhaohui Lu, Jie Chen

“…We performed multiplex immunofluorescence staining to detect ET formation by neutrophils or macrophages using tissue microarrays obtained from 205 patients, and analyzed the immunohistochemistry data for PD-L1, PD-L2, B7-H3, and B7-H4. …”
Get full text