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

Ghanekar R, Srinivasasainagendra V, Page GP - Int J Plant Genomics (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

No MeSH data available.


Related in: MedlinePlus

CCPMT Arabidopsis BLASTworkflow. The workflow in CCPMT to get the probe set to AGI mappings is shown.
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fig1: CCPMT Arabidopsis BLASTworkflow. The workflow in CCPMT to get the probe set to AGI mappings is shown.

Mentions: In the case of Arabidopsis, allvendors provided the mappings between their probe sets and the correspondingAGI gene identifiers. However, due to evolving genome annotation, we derived anew set of mappings between the probe sets and the corresponding AGI IDs. Thesteps of the process are illustrated in Figure 1. The mapping was accomplishedusing the NCBI blastn [5] program. Blastn comparesa nucleotide query sequence against a nucleotide sequence database. Weused two different databases for blastn analysis. For the Affymetrix and Operonprobe sequences, which do not contain introns, the AGI CDS database at TAIR wasused as the sequence database due to the lack of introns and the UTRs in thisdatabase. The AGI CDS dataset is based on the TAIR6.0 release version, and wasreleased in November 2005. For the AFGCand CATMA arrays, which do contain some intronic and UTR sequences, the AGI Transcripts dataset was used. The AGITranscripts dataset includes all of the coding sequences from Arabidopsis, as well as containing the UTRs. Neither database contained intronic sequence.The AGI Transcripts dataset used the TAIR6.0 release version and was releasedin November 2005. The blastn expected value and percent identity cut-off were10−4 and 98%, respectively.


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

Ghanekar R, Srinivasasainagendra V, Page GP - Int J Plant Genomics (2008)

CCPMT Arabidopsis BLASTworkflow. The workflow in CCPMT to get the probe set to AGI mappings is shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2570748&req=5

fig1: CCPMT Arabidopsis BLASTworkflow. The workflow in CCPMT to get the probe set to AGI mappings is shown.
Mentions: In the case of Arabidopsis, allvendors provided the mappings between their probe sets and the correspondingAGI gene identifiers. However, due to evolving genome annotation, we derived anew set of mappings between the probe sets and the corresponding AGI IDs. Thesteps of the process are illustrated in Figure 1. The mapping was accomplishedusing the NCBI blastn [5] program. Blastn comparesa nucleotide query sequence against a nucleotide sequence database. Weused two different databases for blastn analysis. For the Affymetrix and Operonprobe sequences, which do not contain introns, the AGI CDS database at TAIR wasused as the sequence database due to the lack of introns and the UTRs in thisdatabase. The AGI CDS dataset is based on the TAIR6.0 release version, and wasreleased in November 2005. For the AFGCand CATMA arrays, which do contain some intronic and UTR sequences, the AGI Transcripts dataset was used. The AGITranscripts dataset includes all of the coding sequences from Arabidopsis, as well as containing the UTRs. Neither database contained intronic sequence.The AGI Transcripts dataset used the TAIR6.0 release version and was releasedin November 2005. The blastn expected value and percent identity cut-off were10−4 and 98%, respectively.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

No MeSH data available.


Related in: MedlinePlus