|Profiling formalin-fixed, paraffin-embedded (FFPE) samples on three Agilent microarray platforms|
Grazyna Fedorowicz, Srinka Ghosh, Steve Guerrero, Thomas Wu, and Zora Modrusan
Thousands of formalin-fixed, paraffin-embedded (FFPE) samples from clinical archives are available for retrospective studies. Such samples could provide crucial information for drug target discovery and diagnostics of various diseases. Here we used FFPE samples and their matched fresh-frozen (FF) counterparts to examine their performance on three types of microarrays including whole genome expression, comparative genomic hybridization (CGH) and microRNA.
|Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis|
Esteban Czwan, Benedikt Brors, David Kipling
Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate
| A major gene for grain cadmium accumulation in soybean (Glycine max [L] Merr)|
Eduardo Rodriguez Benitez1, Makita Hajika1, Tetsuya Yamada1, Koji Takahashi1 and Nobuhiko Oki1
Quantitative Trait Loci (QTL) analyses were conducted in a population derived from a cross of varieties which differ in their seed Cd accumulation. Results suggested that seed Cd accumulation might be controlled by one major gene
|DNA polymorphism in the pepper-Phytophthora capsici pathosystem|
Cristina Fernández-Otero1,2, Jesús Moreno-González1, and James P. Prince2
Phytophthora capsici is an important soilborne pathogen that produces a devastating disease on many crop species, including pepper. To analyze DNA polymorphism in the P. capsici-pepper pathosystem, six C. annuum lines with various degrees of resistance to P. capsici: Padrón, Couto,CM334,PI201234, SP-11 and JEP; and two P. capsici isolates,GSP1-1 and Ppc3, selected for different levels of virulence, were tested with a variety of molecular markers
|Reactome - a knowledgebase of human biological pathways|
Esther E Schmidt, Michael Caudy, David Croft, Bernard de Bono, Phani V Garapati, Gopal Gopinath, Marc Gillespie, Robin Haw, Bijay Jassal, Steven Jupe, Alexander Kanapin, Shahana Mahajan, Lisa Matthews, Bruce May, Gavin O’Kelly, Imre Vastrik, Guanming Wu, Ewan Birney, Peter D'Eustachio, Lincoln Stein
Reactome is a manually curated knowledgebase, created and peer-reviewed by experts in their field. Its robust data model describes life processes ranging from metabolism to signal transduction and the cell cycle. As of release 28, Reactome contains 3700 human proteins in 3200 reactions. Data is cross-referenced to publicly available web-based informatics resources. Reactome features the SkyPainter tool for analysis of high-throughput datasets, and the Mart query and data retrieval tool.
|Evaluation of a Novel Approach for the Measurement of RNA Quality|
Timothy Wilkes; Alison Devonshire; Carole Foy
The potential medical applications of microarrays have generated much interest, within the biomedical community. Numerous potential sources of variation have raised concerns regarding assay consistency and data quality. Previous studies have highlighted RNA integrity as having a major effect on data quality. We describe here a comparison of the performance characteristics of the Agilent (Bioanalyser) and Lab901 (Screen Tape System) platforms, and their capacity to determine sample RNA integrity.
|Differential metabolic response of tomato hybrids to herbivory|
Raghava T, Puja Ravikumar, Rajendra Hegde, Anil Kush
In this study we have documented the HIPVs produced by different plant organs in three agronomically important Lycopersicon esculentem (tomato) cultivars in the event of herbivory. The nocturnal and diurnal feeding of third instar Spodoptera littura larvae induces characteristic VOCs mainly terpenes, in all the three hybrids viz., All Rounder, Shaktiman and Lakshmi.
|Point-of-care testing for prostate cancer diagnosis |
Y. Uludag; I.E. Tothill
This presentation describes the potential of using a new fully automated QCM biosensor and a commercial SPR biosensor for the detection of PSA, a biomarker for prostate cancer. Initially a new buffer was formulated to eliminate 98% of the non-specific human serum protein binding to the sensors. Obtained results indicate that both instruments can be used for the fast and easy detection of PSA (0.29-150 ng/ml) in serum.
|A Web Interface for Automatic Microarray Analysis|
Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
DNA-Microarray technology provides a diagnostic tool for studying cancer and genetic diseases, allowing the experimenter to identify disease related genes and predict the tumour type for new cell samples. However, the statistical analysis of microarray data is a time-consuming and error-prone process. To address this problem we have developed a web interface for automatic DNA-microarray analysis, ArrayMining.net, which guides the user through the analysis process and performs automatic parameter