Submit to Microarrays Review for Microarrays

Journal Menu

Journal Browser

► Journal Browser

Microarrays, Volume 5, Issue 3 (September 2016) – 6 articles

Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
You may sign up for e-mail alerts to receive table of contents of newly released issues.
PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

946 KiB

Open AccessFeature PaperArticle

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories

by Sriram Chockalingam, Maneesha Aluru and Srinivas Aluru

Microarrays 2016, 5(3), 23; https://doi.org/10.3390/microarrays5030023 - 19 Sep 2016

Cited by 11 | Viewed by 6068

Abstract

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp. Full article

(This article belongs to the Special Issue Next Generation Microarray Bioinformatics)

► Show Figures

Graphical abstract

1921 KiB

Open AccessArticle

Serology in the Digital Age: Using Long Synthetic Peptides Created from Nucleic Acid Sequences as Antigens in Microarrays

by Muhammad Rizwan, Bengt Rönnberg, Maksims Cistjakovs, Åke Lundkvist, Rudiger Pipkorn and Jonas Blomberg

Microarrays 2016, 5(3), 22; https://doi.org/10.3390/microarrays5030022 - 10 Aug 2016

Cited by 6 | Viewed by 5416

Abstract

Background: Antibodies to microbes, or to autoantigens, are important markers of disease. Antibody detection (serology) can reveal both past and recent infections. There is a great need for development of rational ways of detecting and quantifying antibodies, both for humans and animals. Traditionally, serology using synthetic antigens covers linear epitopes using up to 30 amino acid peptides. Methods: We here report that peptides of 100 amino acids or longer (“megapeptides”), designed and synthesized for optimal serological performance, can successfully be used as detection antigens in a suspension multiplex immunoassay (SMIA). Megapeptides can quickly be created just from pathogen sequences. A combination of rational sequencing and bioinformatic routines for definition of diagnostically-relevant antigens can, thus, rapidly yield efficient serological diagnostic tools for an emerging infectious pathogen. Results: We designed megapeptides using bioinformatics and viral genome sequences. These long peptides were tested as antigens for the presence of antibodies in human serum to the filo-, herpes-, and polyoma virus families in a multiplex microarray system. All of these virus families contain recently discovered or emerging infectious viruses. Conclusion: Long synthetic peptides can be useful as serological diagnostic antigens, serving as biomarkers, in suspension microarrays. Full article

(This article belongs to the Special Issue High-Throughput Microarray for Protein Biomarker Discovery)

► Show Figures

Graphical abstract

1809 KiB

Open AccessArticle

A Combinatorial Protein Microarray for Probing Materials Interaction with Pancreatic Islet Cell Populations

by Bahman Delalat, Darling M. Rojas-Canales, Soraya Rasi Ghaemi, Michaela Waibel, Frances J. Harding, Daniella Penko, Christopher J. Drogemuller, Thomas Loudovaris, Patrick T. H. Coates and Nicolas H. Voelcker

Microarrays 2016, 5(3), 21; https://doi.org/10.3390/microarrays5030021 - 10 Aug 2016

Cited by 5 | Viewed by 6503

Abstract

Pancreatic islet transplantation has become a recognized therapy for insulin-dependent diabetes mellitus. During isolation from pancreatic tissue, the islet microenvironment is disrupted. The extracellular matrix (ECM) within this space not only provides structural support, but also actively signals to regulate islet survival and function. In addition, the ECM is responsible for growth factor presentation and sequestration. By designing biomaterials that recapture elements of the native islet environment, losses in islet function and number can potentially be reduced. Cell microarrays are a high throughput screening tool able to recreate a multitude of cellular niches on a single chip. Here, we present a screening methodology for identifying components that might promote islet survival. Automated fluorescence microscopy is used to rapidly identify islet derived cell interaction with ECM proteins and immobilized growth factors printed on arrays. MIN6 mouse insulinoma cells, mouse islets and, finally, human islets are progressively screened. We demonstrate the capability of the platform to identify ECM and growth factor protein candidates that support islet viability and function and reveal synergies in cell response. Full article

(This article belongs to the Special Issue Cell-Based Microarrays)

► Show Figures

Graphical abstract

1176 KiB

Open AccessReview

The Potentials and Pitfalls of Microarrays in Neglected Tropical Diseases: A Focus on Human Filarial Infections

by Alexander Kwarteng and Samuel Terkper Ahuno

Microarrays 2016, 5(3), 20; https://doi.org/10.3390/microarrays5030020 - 2 Aug 2016

Cited by 1 | Viewed by 7319

Abstract

Data obtained from expression microarrays enables deeper understanding of the molecular signatures of infectious diseases. It provides rapid and accurate information on how infections affect the clustering of gene expression profiles, pathways and networks that are transcriptionally active during various infection states compared to conventional diagnostic methods, which primarily focus on single genes or proteins. Thus, microarray technologies offer advantages in understanding host-parasite interactions associated with filarial infections. More importantly, the use of these technologies can aid diagnostics and helps translate current genomic research into effective treatment and interventions for filarial infections. Studying immune responses via microarray following infection can yield insight into genetic pathways and networks that can have a profound influence on the development of anti-parasitic vaccines. Full article

(This article belongs to the Special Issue Microarrays in Immunology Research)

► Show Figures

Graphical abstract

1788 KiB

Open AccessArticle

Protein Profiling Gastric Cancer and Neighboring Control Tissues Using High-Content Antibody Microarrays

by Martin Sill, Christoph Schröder, Ying Shen, Aseel Marzoq, Radovan Komel, Jörg D. Hoheisel, Henrik Nienhüser, Thomas Schmidt and Damjana Kastelic

Microarrays 2016, 5(3), 19; https://doi.org/10.3390/microarrays5030019 - 8 Jul 2016

Cited by 4 | Viewed by 6432

Abstract

In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were analyzed on microarrays that contain 813 antibodies targeting 724 proteins. Only 17 proteins were found to be differentially regulated, with much fewer molecules than the numbers usually identified in studies comparing tumor to healthy control tissues. Insulin-like growth factor-binding protein 7 (IGFBP7), S100 calcium binding protein A9 (S100A9), interleukin-10 (IL‐10) and mucin 6 (MUC6) exhibited the most profound variations. For an evaluation of the proteins’ capacity for discriminating gastric cancer, a Receiver Operating Characteristic curve analysis was performed, yielding an accuracy (area under the curve) value of 89.2% for distinguishing tumor from non-tumorous tissue. For confirmation, immunohistological analyses were done on tissue slices prepared from another cohort of patients with gastric cancer. The utility of the 17 marker proteins, and particularly the four molecules with the highest specificity for gastric adenocarcinoma, is discussed for them to act as candidates for diagnosis, even in serum, and targets for therapeutic approaches. Full article

(This article belongs to the Special Issue Antibody Microarrays in Clinical Proteomics)

► Show Figures

Graphical abstract

764 KiB

Open AccessArticle

MicroRNA Profile of Lung Tumor Tissues Is Associated with a High Risk Plasma miRNA Signature

by Orazio Fortunato, Carla Verri, Ugo Pastorino, Gabriella Sozzi and Mattia Boeri

Microarrays 2016, 5(3), 18; https://doi.org/10.3390/microarrays5030018 - 5 Jul 2016

Cited by 6 | Viewed by 5494

Abstract

Lung cancer is the most common cause of cancer deaths worldwide. MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression. Many studies have reported that alterations in miRNA expression are involved in several human tumors. We have previously identified a circulating miRNA signature classifier (MSC) able to discriminate lung cancer with more aggressive features. In the present work, microarray miRNA profiling of tumor tissues collected from 19 lung cancer patients with an available MSC result were perform in order to find a possible association between miRNA expression and the MSC risk level. Eleven tissue mature miRNAs and six miRNA precursors were observed to be associated with the plasma MSC risk level of patients. Not one of these miRNAs was included in the MSC algorithm. A pathway enrichment analysis revealed a role of these miRNA in the main pathways determining lung cancer aggressiveness. Overall, these findings add to the knowledge that tissue and plasma miRNAs behave as excellent diagnostic and prognostic biomarkers, which may find rapid application in clinical settings. Full article

(This article belongs to the Special Issue Diagnostic, Prognostic and Predictive Cancer Biomarkers)

► Show Figures