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Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example.

Rauwerda H, de Jong M, de Leeuw WC, Spaink HP, Breit TM - BMC Res Notes (2010)

Bottom Line: If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence.With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy.The annotation of the microarray is carried out simultaneously with the design.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microarray Department & Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. t.m.breit@uva.nl.

ABSTRACT

Background: A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous sequence information that can be used as input for an up-to-date microarray design.

Findings: Our algorithm consists of four steps. In the first step transcripts from different resources are grouped into Transcription Clusters (TCs) by looking at the similarity of all transcripts. TCs are groups of transcripts with a similar length. If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence. Secondly, all TCs are mapped to a genome assembly and gene information is added to the design. Thirdly TC members are ranked according to their trustworthiness and the most reliable sequence is used for the probe design. The last step is the actual array design. We have used this strategy to build an up-to-date zebrafish microarray.

Conclusions: With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy. By changing the parameters in the procedure it is possible to control the similarity within the TCs and thus the amount of candidate sequences for the design. The annotation of the microarray is carried out simultaneously with the design.

No MeSH data available.


Mapping of four gene repositories in the Zebrafish Model Organism Database. Using the mapping tables supplied by the Zebrafish Information Network (ZFIN) [14] (March 2010) on the Unigene, Vega, Ensembl and Refseq genome resources, indicated by colored shades, the number of ZFIN identifiers common to each combination of resources are shown.
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Figure 1: Mapping of four gene repositories in the Zebrafish Model Organism Database. Using the mapping tables supplied by the Zebrafish Information Network (ZFIN) [14] (March 2010) on the Unigene, Vega, Ensembl and Refseq genome resources, indicated by colored shades, the number of ZFIN identifiers common to each combination of resources are shown.

Mentions: Orthogonal to the genome and transcriptome resources are the organism-centric resources, such as the Mouse Genome Informatics (MGI) [14] and the Zebrafish Information Network (ZFIN) http://zfin.org[15], which offer an integrated view on the genome of a selected organism. However, if we were, for instance to base the design of a zebrafish microarray solely on the ZFIN genes, we would exclude a substantial number of genes that is present in one or more of the other resources (Figure 1).


Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example.

Rauwerda H, de Jong M, de Leeuw WC, Spaink HP, Breit TM - BMC Res Notes (2010)

Mapping of four gene repositories in the Zebrafish Model Organism Database. Using the mapping tables supplied by the Zebrafish Information Network (ZFIN) [14] (March 2010) on the Unigene, Vega, Ensembl and Refseq genome resources, indicated by colored shades, the number of ZFIN identifiers common to each combination of resources are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2913925&req=5

Figure 1: Mapping of four gene repositories in the Zebrafish Model Organism Database. Using the mapping tables supplied by the Zebrafish Information Network (ZFIN) [14] (March 2010) on the Unigene, Vega, Ensembl and Refseq genome resources, indicated by colored shades, the number of ZFIN identifiers common to each combination of resources are shown.
Mentions: Orthogonal to the genome and transcriptome resources are the organism-centric resources, such as the Mouse Genome Informatics (MGI) [14] and the Zebrafish Information Network (ZFIN) http://zfin.org[15], which offer an integrated view on the genome of a selected organism. However, if we were, for instance to base the design of a zebrafish microarray solely on the ZFIN genes, we would exclude a substantial number of genes that is present in one or more of the other resources (Figure 1).

Bottom Line: If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence.With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy.The annotation of the microarray is carried out simultaneously with the design.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microarray Department & Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. t.m.breit@uva.nl.

ABSTRACT

Background: A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous sequence information that can be used as input for an up-to-date microarray design.

Findings: Our algorithm consists of four steps. In the first step transcripts from different resources are grouped into Transcription Clusters (TCs) by looking at the similarity of all transcripts. TCs are groups of transcripts with a similar length. If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence. Secondly, all TCs are mapped to a genome assembly and gene information is added to the design. Thirdly TC members are ranked according to their trustworthiness and the most reliable sequence is used for the probe design. The last step is the actual array design. We have used this strategy to build an up-to-date zebrafish microarray.

Conclusions: With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy. By changing the parameters in the procedure it is possible to control the similarity within the TCs and thus the amount of candidate sequences for the design. The annotation of the microarray is carried out simultaneously with the design.

No MeSH data available.