A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Abstract

Background: Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the complexity of the MAGE-ML format has made its use impractical for laboratories lacking dedicated bioinformatics support.

Results: We propose a simple tab-delimited, spreadsheet-based format, MAGE-TAB, which will become a part of the MAGE microarray data standard and can be used for annotating and communicating microarray data in a MIAME compliant fashion.

Conclusion: MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

Figure 1

An example of an investigation design graph for a simple one-channel array experiment. Three samples are used: liver, kidney, and brain. Labeled RNA extracts from each sample are hybridized on an array (type HG_U95A). The RNA extraction and labeling are described in the Material processing protocol, P-XMPL-1. Raw data files (Data1.cel, Data2.cel and Data3.cel) are obtained, and then normalized and summarized as described in the Normalization protocol, P-XMPL-2, generating the file FGDM.txt.

Figure 2

An example investigation design graph. This graph depicts two samples hybridized on an array (design name SMD-10K) labeled by Cy3 and Cy5, generating the data file Data.txt.

Figure 3

An investigation design graph representing a two-channel experiment with extract pooling and reference RNA. This investigation is similar to the example in the Introduction (Figure 1), except that it uses a two-channel array and an RNA reference. The extract pooling protocol has been omitted for clarity.

Figure 5

An example of a more complex experimental design (data objects not shown). This is a real-world example, corresponding to the experiment with accession number E-MIMR-12 in Array Express.

Figure 4

Replicated design, dual channel with dye swap. Data objects are not shown as there is a simple one-to-one mapping between hybridizations and raw data files.

Figure 6

Graph with four possible paths between nodes. While four paths are possible between the nodes in this graph [(a → c → d), (a → c → e), (b → c → d), and (b → c → e)], only two full paths, e.g., (a → c → d) and (b → c → e), are required to capture all of the existing relationships between the nodes.