Open Access Methodology article

A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database

Kshitish K Acharya12*, Darshan S Chandrashekar1, Neelima Chitturi1, Hardik Shah1, Varun Malhotra1, Sreelakshmi KS1, Deepti H1, Akhilesh Bajpai1, Sravanthi Davuluri1, Pranami Bora1 and Leena Rao1

Author Affiliations

1 Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bangalore - 560100, Karnataka state, India

2 Shodhaka Life Sciences Pvt. Ltd., IBAB, Biotech Park, Bangalore - 560100, India

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BMC Genomics 2010, 11:467  doi:10.1186/1471-2164-11-467

Published: 11 August 2010

Additional files

Additional file 1:

Notes S1. Details of gene-set collection and fixed vocabulary usage in the database creation.

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Additional file 2:

Table S1. Illustration of scoring derived from multiple data sets for specific ESLCs ('transcribed' or 'dormant' in normal human adult testis).

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Additional file 3:

Figure S1. Schematic representation of creation and functioning of MGEx-Tdb.

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Additional file 4:

Table S2. References and URLs for various databases/repositories used/referred in the study.

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Additional file 5:

Table S3. Summary of manually curated data (MCD, from reports on individual gene studies) for the genes selected for final comparison of databases.

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Additional file 6:

Table S4. Scoring method for assessing the extent of agreement between the manually curated data (MCD, from reports on individual gene studies) vs. the information from databases.

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Additional file 7:

Notes S2. Procedure for comparison of MCD with the information from the databases.

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Additional file 8:

Table S5. Procedure for relative assessment of amount and details of information, and agreement with reports from individual gene studies.

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Additional file 9:

Notes S3. Procedure for comparison of results from various resources for gene expression under different physiological conditions and developmental stages in testis.

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Additional file 10:

Notes S4. An overview of MGEx-Tdb use, with the help of screen-shots.

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