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This article is part of the supplement: Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes

Open Access Proceedings

Facilitating functional annotation of chicken microarray data

Teresia J Buza12*, Ranjit Kumar12, Cathy R Gresham25, Shane C Burgess1234 and Fiona M McCarthy12

Author Affiliations

1 Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

2 Institute for Digital Biology, Mississippi State University, Mississippi State, MS 39762, USA

3 Life Sciences and Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762, USA

4 Mississippi Agricultural and Forestry Experiment Station, Mississippi State University, Mississippi State, MS 39762, USA

5 Department of Computer Science and Engineering, Bagley College of Engineering, Mississippi State University, Mississippi State, MS 39762, USA

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BMC Bioinformatics 2009, 10(Suppl 11):S2  doi:10.1186/1471-2105-10-S11-S2

Published: 8 October 2009

Additional files

Additional file 1:

Initial assessment of annotation of Affymetrix chicken genome array. Additional file descriptions text (including details of how to view the file, if it is in a nonstandard format).

Format: PDF Size: 22KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Example of output generated by the Array GO Mapper (AGOM). Unique identifier for the Arizona array (Oligo_ID) is displayed in column 1. Column 2–4 displays GenBank accessions, Entrez gene ID and Ensembl gene ID used for mapping. The array spot number is in column 5. The name of database and the corresponding gene product in Affymetrix annotations are shown in column 6 & 7. The GO and name of the GO term are displayed in column 8 & 9 with the evidence code for the annotation in column 10. Column 11 shows the aspects of gene ontology either molecular function (F), cellular component (C) or biological process (P). The GO Annotation Quality (GAQ) score for individual GO term is displayed in column 12 and the date the output was generated in column 13.

Format: XLS Size: 231KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Chicken array platform cross-reference. Each column represents one array platform showing the identifiers that can be used to search GO annotations from Affymetrix GO data. (+) indicates presence of identifier in the corresponding array platform. (-) indicates absence of identifier in the corresponding array platform.

Format: XLS Size: 24KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data