Programmed cell death-ligand 1 expression in correlation with human papillomavirus status in cervical cancer: A 1-year retrospective study by Kaumudi Konkay, Padmavathi Devi Chaganti, Radhika Medidi, Ann Mary Varghese, Maruthi Devi Karri

“…Records of patients with cervical cancer were reviewed, and 40 cases were taken for tissue microarray. Immunohistochemistry with p16 and PD-L1 was done, and association between PD-L1 expression with age, histopathological features and HPV status was studied. …”
Get full text

Androgen receptor (AR) antagonism triggers acute succinate‐mediated adaptive responses to reactivate AR signaling by Neetu Saxena, Eliana Beraldi, Ladan Fazli, Syam Prakash Somasekharan, Hans Adomat, Fan Zhang, Chidi Molokwu, Anna Gleave, Lucia Nappi, Kimberly Nguyen, Pavn Brar, Nicholas Nikesitch, Yuzhuo Wang, Colin Collins, Poul H Sorensen, Martin Gleave

“…Activation of this pathway was seen in tissue microarray analysis on prostatectomy tissues and patient‐derived xenografts. …”
Get full text

DETERMINATION OF THE THERAPEUTIC EFFECT OF VULPINIC ACID AND VULPINIC ACID-RESPONSIVE miR-197-3P IN BREAST CANCER TREATMENT BY IN VITRO AND IN VIVO STUDIES by Demet Cansaran Duman

“…Our study revealed molecular characterization and in vivo experimental studies of vulpinic acid and vulpinic acid-responsive miRNAs on breast cancer. miRNAs formed by the application of vulpinic acid on breast cancer and normal cells were determined by microarray analysis. The genes and pathway analyses targeted by miRNAs were determined using bioinformatics tools. …”
Get full text

MicroRNA biomarkers of type 2 diabetes: A protocol for corroborating evidence by computational genomics and meta-analyses. by Hongmei Zhu, Siu-Wai Leung

“…The corresponding reporting guidelines will be used to assess the quality of included studies according to their profiling methods (microarray, RT-PCR, and RNA-Seq).<h4>Ethics and dissemination</h4>No ethics approval is required since this study does not include identifiable personal patient data.…”
Get full text

Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression by Itai Yanai, L Ryan Baugh, Jessica J Smith, Casey Roehrig, Shai S Shen‐Orr, Julia M Claggett, Andrew A Hill, Donna K Slonim, Craig P Hunter

“…We used RNAi and time series, whole‐genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage‐specific transcriptional regulatory network. …”
Get full text

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults. by Carolin A Kolmeder, Jarkko Salojärvi, Jarmo Ritari, Mark de Been, Jeroen Raes, Gwen Falony, Sara Vieira-Silva, Riina A Kekkonen, Garry L Corthals, Airi Palva, Anne Salonen, Willem M de Vos

“…A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. …”
Get full text

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. by Barbara A Weissenmayer, James G D Prendergast, Amanda J Lohan, Brendan J Loftus

“…We extend previous microarray based studies as well as uncovering evidence of a complex regulatory architecture underpinned by numerous non-coding RNAs. …”
Get full text

Deciphering the transcriptional-regulatory network of flocculation in Schizosaccharomyces pombe. by Eun-Joo Gina Kwon, Amy Laderoute, Kate Chatfield-Reed, Lianne Vachon, Jim Karagiannis, Gordon Chua

“…Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP-chip analysis to identify the flocculin target genes. …”
Get full text

Immortalized Human Schwann Cell Lines Derived From Tumors of Schwannomatosis Patients. by Kimberly Laskie Ostrow, Katelyn Donaldson, Jaishri Blakeley, Allan Belzberg, Ahmet Hoke

“…Cell morphology was retained following multiple passaging and freeze/ thaw cycles. Gene expression microarray analysis was used to compare the cell lines with their respective parent tumors. …”
Get full text

TLR3 Plays Significant Roles against HBV-Associated HCC by Xiao-lan Chen, Yu-yin Xu, Li Chen, Gui-lan Wang, Yin Shen

“…To investigate the ability of TLR3 in regulating HBV replication in HCC, 80 cases of human HCC were collected and their tissue microarray was made. In HCC cells, the expression and location of TLR3, hepatitis-associated virus, and interstitial immunoreactive cells were assayed with immunohistochemical staining. …”
Get full text

Chronic Exposure of Renal Progenitor Cells (HRTPT) to As (III) Implicates Microfibril Associated Protein 5 (MFAP5) in the Activation of Carcinoembryonic Antigen Related Cell Adhesi... by Md Ehsanul Haque, Donald A. Sens, Scott H. Garrett

“…Our model consists of acute and chronic exposure of i-As (III) to “Human Renal Tubular Precursor TERT” (HRTPT). The microarray and gene validation study demonstrated a sudden induction of microfibril associated protein 5 (MFAP5) and carcinoembryonic antigen related cell adhesion molecule 5 and 6 (CEACAM 5 and 6) in chronic i-As (III)-exposed cells. …”
Get full text

Maternal cocaine administration in mice alters DNA methylation and gene expression in hippocampal neurons of neonatal and prepubertal offspring. by Svetlana I Novikova, Fang He, Jie Bai, Nicholas J Cutrufello, Michael S Lidow, Ashiwel S Undieh

“…Global DNA methylation, methylated DNA immunoprecipitation followed by CGI(2) microarray profiling and bisulfite sequencing, as well as quantitative real-time RT-PCR gene expression analysis, were evaluated in hippocampal pyramidal neurons excised by laser capture microdissection. …”
Get full text

Stability indicators in network reconstruction. by Michele Filosi, Roberto Visintainer, Samantha Riccadonna, Giuseppe Jurman, Cesare Furlanello

“…Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects), and we validate the analysis on a second dataset (166 subjects) with good reproducibility.…”
Get full text

Detection of host-derived sphingosine by Pseudomonas aeruginosa is important for survival in the murine lung. by Annette E LaBauve, Matthew J Wargo

“…The members of the SphR transcriptome were identified by microarray analyses, and DNA binding assays showed specific interaction of these promoters with SphR, which enabled us to determine the consensus SphR binding site. …”
Get full text

Expression and Promoter Analysis of Six Heat Stress-Inducible Genes in Rice by Wirat Rerksiri, Xianwen Zhang, Hairong Xiong, Xinbo Chen

“…Six highly heat responsive genes were identified in rice by microarray data analysis. The qRT-PCR analysis confirmed that the expression of these six genes were highly heat inducible and moderately responded to salt stress, polyethylene glycol, and abscisic acid treatment, but little affected by cold treatment. …”
Get full text

Evaluation of LRIG1 Expression in Larynx Pathologies by Yavuz Gündoğdu, Orhan Asya, Ayşegül Gönen, Tajaddin Muradov, Selim Yiğit Erçetin, Zeliha Leyla Cinel, Ali Cemal Yumuşakhuylu

“…Patients’ data were obtained from the medical records. The tissue microarray method was used to evaluate specimens. Results: There was a statistically significant difference between the tumor differentiation, diagnosis, and the expression of LRIG1 (respectively p=0.045, p&lt;0.001). …”
Get full text

Epigenome and three-dimensional genome architecture remodeling during NDM29-mediated retro-transformation of neuroblastoma cells. by Francesca Baldini, Aldo Pagano, Lama Zeaiter, Paolo Bianchini, Hawraa Zbeeb, Alberto Diaspro, Laura Vergani

“…Then we assessed the mRNA expression of the main epigenetic modifying enzymes by quantitative PCR, and the expression of NF-κB-regulated genes by cDNA microarray. Compared to malignant NB cells, the NDM29-overexpressing cells, assuming a neuron-like phenotype, exhibited smaller and more elongated nuclei, redistribution of H3K9-acetylated and -methylated chromatin domains and DNA hypermethylation. …”
Get full text

Ubiquitin Specific Protease 26 (USP26) expression analysis in human testicular and extragonadal tissues indicates diverse action of USP26 in cell differentiation and tumorigenesis. by Matthew S Wosnitzer, Anna Mielnik, Ali Dabaja, Brian Robinson, Peter N Schlegel, Darius A Paduch

“…Immunofluorescence colocalization studies were performed with formalin-fixed/paraffin-embedded and frozen tissues using primary and secondary antibodies to detect USP26 and AR protein expression. Human microarray dot blots were used to identify protein expression in extra-gonadal tissues. …”
Get full text

Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures. by Danilo Licastro, Margherita Mutarelli, Ivana Peluso, Kornelia Neveling, Nienke Wieskamp, Rossella Rispoli, Diego Vozzi, Emmanouil Athanasakis, Angela D'Eustacchio, Mariateresa Pizzo, Francesca D'Amico, Carmela Ziviello, Francesca Simonelli, Antonella Fabretto, Hans Scheffer, Paolo Gasparini, Sandro Banfi, Vincenzo Nigro

“…We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. …”
Get full text

Comprehensive analysis of intervention and control studies for the computational identification of dengue biomarker genes. by Jibon Kumar Paul, Mahir Azmal, Tasnim Alam, Omar Faruk Talukder, Ajit Ghosh

“…This study conducted a comprehensive analysis of differential gene expression in dengue fever patients using multiple microarray datasets from the NCBI GEO database. Through bioinformatics approaches, 163 potential biomarker genes were identified, with some overlapping previously reported biomarkers and others representing novel candidates. …”
Get full text