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Mistaken Identifiers

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Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett and John N Weinstein

BMC Bioinformatics 2004, 5:80
Abstract Link to article

Supplementary Material

SymbolMutationScan: scan your text files for gene names that were converted by Excel (for UNIX, including Mac OS X terminal UNIX command prompt)

usage: chmod +x SymbolMutationScan.sh
./SymbolMutationScan.sh filename
Download SymbolMutationScan.sh

Examples of Excel SymbolMutation for a Gene Name in a Major Public Database

We can compare screen shots taken on November 12, 2002 (left column) and the current database (right column) to validate that the inappropriately converted gene names in the screen shots have been corrected
has the Septin2 SymbolMutation error been fixed yet?
has the Septin7 SymbolMutation error been fixed yet?
has the Septin8 SymbolMutation error been fixed yet?
has the Septin9 SymbolMutation error been fixed yet?

Example of how symbol mutation can be introduced into the data processing stream

We can compare screen shots taken on November 14, 2003 of a web site hosting mouse genomic data without exhibiting the problem, and a site hosting human-mouse homology data which does exhibit the symbol mutation.
Symbol mutation in human-mouse homology data

Workarounds for the Excel SymbolMutation Conversion

Microsoft's Suggested Workarounds:
Current Microsoft Knowledge Base Workaround
Our Suggested Workarounds:
Our Suggested Workarounds

Contact Information: Barry Zeeberg


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