NDLI: PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays

Content Provider	PubMed Central
Author	Nurtdinov, Ramil N. Vasiliev, Mikhail O. Ershova, Anna S. Lossev, Ilia S. Karyagina, Anna S.
Copyright Year	2009
Abstract	Standard Affymetrix technology evaluates gene expression by measuring the intensity of mRNA hybridization with a panel of the 25-mer oligonucleotide probes, and summarizing the probe signal intensities by a robust average method. However, in many cases, signal intensity of the probe does not correlate with gene expression. This could be due to the hybridization of the probe to a transcript of another gene, mapping of the probe to an intron, alternative splicing, single nucleotide polymorphisms and other reasons. We have developed a database, PLANdbAffy (available at http://affymetrix2.bioinf.fbb.msu.ru), that contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. We have determined the probes matching the transcript-coding regions in the correct orientation. For each such probe alignment region, we determined the mRNA and EST sequences that contain the probe sequence. In the textual part of the database interface we summarize the data on the sequences that cover the probe alignment region and SNPs that are located inside it. The graphical part of our database interface is implemented as custom tracks to the UCSC genome browser that allows one to utilize all the data that are offered by UCSC browser.
Related Links	http://dx.doi.org/10.1093/nar/gkp969
Starting Page	726
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	Database issue
Volume Number	38
Language	English
Publisher	Oxford University Press
Publisher Date	2010-01-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays

Integrating probe-level expression changes across generations of Affymetrix arrays

Salvaging Affymetrix probes after probe-level re-annotation

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays

Salvaging Affymetrix probes after probe-level re-annotation

Summaries of Affymetrix GeneChip probe level data

Integrating multiple genome annotation databases improves the interpretation of microarray gene expression data

Integrating probe-level expression changes across generations of Affymetrix arrays

PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays

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PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays