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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

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Showing Results 121 - 130 of 249
Scientific News
Silencing the FOXP2 Speech Gene Causes Breast Cancer Cells to Metastasize
BIDMC investigators make the surprising discovery that a gene associated with speech and language is linked to advanced breast cancer.
Fast Modeling Of Cancer Mutations
New genome-editing technique enables rapid analysis of genes mutated in tumors.
TGAC Leads Research To Help Identify Animal-To-Human Transmitted Diseases
The Genome Analysis Centre (TGAC) will lead research into the development of bioinformatics to support the identification and characterisation of viruses through metagenomics.
Shaking Up Cell Biology
Researchers focus in on decades old mystery.
Researchers Describe New Method for Cell Line Authentication
SNP profiling, an effective method to detect misidentification, contamination, and chromosomal abnormalities in mouse cell lines.
New Lead for Potential Parkinson’s Treatment
Effects of high-risk Parkinson’s mutation are reversible.
New Test can Help Doctors Choose Best Treatment for Ovarian Cancer
ADNEX discriminate between benign and malignant tumours with a high level of accuracy.
Novel Mutations Discovered In Cats Provide Insight Into Human Eye Diseases
99 Lives Cat Genome Sequencing Initiative makes discoveries using Maverix analytic platform.
Study Finds Link Between Neural Stem Cell Overgrowth and Autism-like Behavior in Mice
UCLA researchers demonstrates how, in pregnant mice, inflammation can trigger an excessive division of neural stem cells.
All the Cell’s a Stage
Brian Strahl, PhD, and his band of biochemists unravel the complicated mysteries of the epigenetic code to find a culprit in cancer development.
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