Int J Plant Genomics. 2008;2008:451327. Epub 2008 Oct 21.

Cross-chip probe matching tool: A web-based tool for linking microarray probes within and across plant species.

Ghanekar R, Srinivasasainagendra V, Page GP.

Source

Department of Electrical and Computer Engineering, University of Alabama at Birmingham, 35294-4461, USA.

Abstract

The CCPMT is a free, web-based tool that allows plant investigators to rapidly determine if a given gene is present across various microarray platforms, which, of a list of genes, is present on array(s), and which gene a probe or probe set queries and vice versa, and to compare and contrast the gene contents of arrays. The CCPMT also maps a probe or probe sets to a gene or genes within and across species, and permits the mapping of the entire content from one array to another. By using the CCPMT, investigators will have a better understanding of the contents of arrays, a better ability to link data between experiments, ability to conduct meta-analysis and combine datasets, and an increased ability to conduct data mining projects.

PMID:: 18949054; [PubMed]
PMCID: PMC2570748

Free PMC Article

Images from this publication.See all images (3) Free text

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. [BMC Bioinformatics. 2005]
Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements.
Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. BMC Bioinformatics. 2005 Apr 25; 6:107. Epub 2005 Apr 25.
Comparison of gene coverage of mouse oligonucleotide microarray platforms. [BMC Genomics. 2006]
Comparison of gene coverage of mouse oligonucleotide microarray platforms.
Verdugo RA, Medrano JF. BMC Genomics. 2006 Mar 21; 7:58. Epub 2006 Mar 21.
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. [Nucleic Acids Res. 2004]
Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.
Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Nucleic Acids Res. 2004 May 25; 32(9):e74. Epub 2004 May 25.
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling. [Nucleic Acids Res. 2005]
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling.
Bhattacharya S, Mariani TJ. Nucleic Acids Res. 2005 Oct 13; 33(18):e157. Epub 2005 Oct 13.
MAID : an effect size based model for microarray data integration across laboratories and platforms. [BMC Bioinformatics. 2008]
MAID : an effect size based model for microarray data integration across laboratories and platforms.
Borozan I, Chen L, Paeper B, Heathcote JE, Edwards AM, Katze M, Zhang Z, McGilvray ID. BMC Bioinformatics. 2008 Jul 10; 9:305. Epub 2008 Jul 10.

See reviews... See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC

Recent activity

Clear Turn Off Turn On

Cross-chip probe matching tool: A web-based tool for linking microarray probes w...
Cross-chip probe matching tool: A web-based tool for linking microarray probes within and across plant species.
Int J Plant Genomics. 2008 ;2008:451327. Epub 2008 Oct 21 .

PubMed
Ablation of ribosomal protein L22 selectively impairs alphabeta T cell developme...
Ablation of ribosomal protein L22 selectively impairs alphabeta T cell development by activation of a p53-dependent checkpoint.
Immunity. 2007 Jun ;26(6):759-72. Epub 2007 Jun 7 .

PubMed
Early results of laparoscopic biliopancreatic diversion with duodenal switch: a ...
Early results of laparoscopic biliopancreatic diversion with duodenal switch: a case series of 40 consecutive patients.
Obes Surg. 2000 Dec ;10(6):514-23; discussion 524.

PubMed
Interferon-alpha2a reduces MRI disease activity in relapsing-remitting multiple ...
Interferon-alpha2a reduces MRI disease activity in relapsing-remitting multiple sclerosis. Norwegian Study Group on Interferon-alpha in Multiple Sclerosis.
Neurology. 1999 Mar 23 ;52(5):1049-56.

PubMed
Inhaled nitric oxide versus aerosolized iloprost in secondary pulmonary hyperten...
Inhaled nitric oxide versus aerosolized iloprost in secondary pulmonary hypertension in children with congenital heart disease: vasodilator capacity and cellular mechanisms.
Circulation. 2001 Jan 30 ;103(4):544-8.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to:

Cross-chip probe matching tool: A web-based tool for linking microarray probes within and across plant species.

Source

Abstract

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information