17 papers · ranked by Valyu relevance
Donna K. Slonim, Itai Yanai, Olga G. Troyanskaya
Gene expression microarrays provide a snapshot of all the transcriptional activity in a biological sample. Unlike most traditional molecular biology tools, which generally allow the study of a single gene or a small set of genes, microarrays facilitate the discovery of totally novel and unexpected functional roles of…
Greg Gibson
Microarrays can survey genome-wide expression patterns. Not only can these gene expression profiles be used to identify a few genes of interest, they are now being creatively applied for hypothesis generation and testing
Shirley Bikel, Leonor Jacobo-Albavera, Fausto Sánchez-Muñoz, Fernanda Cornejo-Granados + 8 more
'Fernanda Cornejo-Granados' 'Samuel Canizales-Quinteros' 'Xavier Soberón' 'Rogerio R. Sotelo-Mundo' 'Blanca E. del Río-Navarro' 'Alfredo Mendoza-Vargas' 'Filiberto Sánchez' 'Adrian Ochoa-Leyva' 'Shree Ram Singh'] Background In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for…
Paul K. Korir, Paul Geeleher, Cathal Seoighe
Background Quantifying gene expression by RNA-Seq has several advantages over microarrays, including greater dynamic range and gene expression estimates on an absolute, rather than a relative scale. Nevertheless, microarrays remain in widespread use, demonstrated by the ever-growing numbers of samples deposited in…
Teresa Lettieri
Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be used both to provide information about the mechanism of action of the toxicant and to form a sort of “genetic signature”…
Markus Weniger, Julia C Engelmann, Jörg Schultz
Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure the expression level of thousands of mRNAs at the same time, allowing insight into or comparison of different cellular…
Pratik Jaluria, Konstantinos Konstantopoulos, Michael Betenbaugh, Joseph Shiloach
'Joseph Shiloach'] With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as…
Rajesh K Sharma, William E Orr, Allyson D Schmitt, Dianna A Johnson
Background Retinal pigment epithelium cells play an important role in the pathogenesis of age related macular degeneration. Their morphological, molecular and functional phenotype changes in response to various stresses. Functional profiling of genes can provide useful information about the physiological state of cells…
Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam + 1 more
'Shivkumar Venkatasubrahmanyam' 'Atul J Butte'] Background The amount of gene expression data in the public repositories, such as NCBI Gene Expression Omnibus (GEO) has grown exponentially, and provides a gold mine for bioinformaticians, but has not been easily accessible by biologists and clinicians. Results We…
Yilin Dai, Ling Guo, Meng Li, Yi-Bu Chen
Background Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have…
Sandra L. Spurgeon, Robert C. Jones, Ramesh Ramakrishnan, Cathal Seoighe
'Cathal Seoighe'] We describe a high throughput gene expression platform based on microfluidic dynamic arrays. This system allows 2,304 simultaneous real time PCR gene expression measurements in a single chip, while requiring less pipetting than is required to set up a 96 well plate. We show that one can measure the…
Robert Plomin, Leonard C Schalkwyk
Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA…
Tyler J. Wilson, Steven X. Ge
Recent advances in microarray technologies have resulted in a flood of genomics data. This large body of accumulated data could be used as a knowledge base to help researchers interpret new experimental data. ArraySearch finds statistical correlations between newly observed gene expression profiles and the huge source…
Laura Saba, Paula L. Hoffman, Cheryl Hornbaker, Sanjiv V. Bhave + 1 more
'Boris Tabakoff'] Researchers from a wide variety of backgrounds and with a broad range of goals have utilized high-throughput screening technologies (i.e., microarray technologies) to identify candidate genes that may be associated with an observable characteristic or behavior (i.e., phenotype) of interest. However…
Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W Hentze + 2 more
'Thomas Dandekar' 'Martina U Muckenthaler'] Background Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA…
Alberto Risueño, Celia Fontanillo, Marcel E Dinger, Javier De Las Rivas
'Javier De Las Rivas'] Background Genome-wide expression studies have developed exponentially in recent years as a result of extensive use of microarray technology. However, expression signals are typically calculated using the assignment of "probesets" to genes, without addressing the problem of "gene" definition or…
Tarana Siddika, Ilka U. Heinemann
MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis.…