PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 12824349

ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.

Sheng Zhong·Cheng Li·Wing Hung Wong
View original source ↗Export metadata ↓

Abstract

To date, assembling comprehensive annotation information for all probe sets of any Affymetrix microarrays remains a time-consuming, error-prone and challenging task. ChipInfo is designed for retrieving annotation information from online databases such as NetAffx and Gene Ontology and organizing such information into easily interpretable tabular format outputs. As companion software to dChip and GoSurfer, ChipInfo enables users to independently update the information resource files of these software packages. It also has functions for computing related summary statistics of probe sets and Gene Ontology terms. ChipInfo is available at http://biosun1.harvard.edu/complab/chipinfo/.

Explore related subjects

DNA ProbesDatabases, GeneticGene Expression ProfilingInternetOligonucleotide Array Sequence AnalysisSoftwareSystems IntegrationJournal ArticleResearch Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sheng Zhong, Cheng Li, Wing Hung Wong. 2003-07-01. ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis.. https://doi.org/10.1093/nar%2Fgkg598

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Comparison of GenoType MTBC with RFLP-PCR and multiplex PCR to identify Mycobacterium tuberculosis complex species.

The aims of the work presented here were to evaluate a commercial system based on DNA hybridization technology on nitrocellulose strips (GenoType MTBC; Hain Diagnostika, Nehren, Germany) for identifying Mycobacterium tuberculosis complex isolates to the species level and to compare the results with those obtained using the RFLP-PCR and multiplex PCR molecular techniques, biochemical tests and susceptibility testing. The commercial system correctly identified 102 of 103 (99.03%) strains studied, indicating it is capable of discriminating among the tuberculosis complex species.

DNA Probes↗
PubMed2006

Microarray-in-a-tube for detection of multiple viruses.

BACKGROUND: The detection of multiple viruses is important for pathogenic diagnosis and disease control. Microarray detection is a good method, but requires complex procedures for multiple virus detection. METHODS: We developed a novel PCR assay, the microarray-in-a-tube system, which integrates multiple PCR processes and DNA microarrays for multiple virus detection. A 5 x 5 oligonucleotide microarray for detecting 4 respiratory tract viruses (severe acute respiratory syndrome-associated coronavirus, influenza A virus, influenza B virus, and enterovirus) with inner controls was arranged on the inner surface of a specially designed Eppendorf cap with a flat, optically transparent window. RESULTS: We were able to perform all detection processes in the encapsulated system without opening the cap. The 4 viruses were successfully amplified by one-step reverse transcription-PCR in the encapsulated tube. After the PCR process, the microarray-in-a-tube was inverted, and the fluorescence-labeled PCR products were directly hybridized on the microarray. Hybridization signals were obtained with an ordinary fluorescent microscope. The sensitivity of the system for virus detection reached 10(2) copies/microL. With the help of inner controls, the system provided reliable results without false negatives and false positives. CONCLUSIONS: The microarray-in-a-tube system is a rapid, labor-saving tool for multiple virus detection with several advantages, such as convenience, prevention of cross-contamination of the PCR products, and potential for multiple-gene detection.

DNA Probes↗