Function2Gene is a search multiplexer which allows for the selection of genes from GeneCards, Harvester, and NCBI based on a set of keywords. You can use this program to order genes based on their association with a set of keywords for gene linkage studies to increase the power of gene linkage studies.
The sourcecode for function2gene is available in a tarball, a zip archive, or by using a subversion repository.
If you have questions about what function2gene does, please feel free to contact don@donarmstrong.com.
Function2Gene requires the following modules and programs to work properly:
All of the programs are located within the bin directory of the tarball (or zip archive) which is downloadable above. First, change directories to the bin directory (cd bin.) (If you are using cygwin, and you have unpacked the tarball (or zip archive) to the C:\function2gene directory (for example) you will need to open the cygwin terminal, and type cd /cygdrive/c/function2gene/bin.)
Then create a kewyords file which contains kewyords separated by newlines. You can optionally add a weight for each keyword separated by a tab. (That is, the file will contain lines of 'keyword<tab>0.3<newline>', for example.) You can do this in any text editor that is capable of saving text files, like vim, emacs or (shudder) notepad.
Finally, make a results directory (mkdir keyword_results), and run function2gene with the --keywords option specifying the keywords file that you have created and the --results option specifying the results directory you have created (./function2gene --keywords keywords.txt --results keyword_results.) You will need a new keyword_results directory for each set of keywords that you run.
The results will be in the keyword_results directory in a file called combined_results.txt, and a sumary table will be there as well, called combined_results_table.txt
The details of the operation of function2gene are explained in its documentation; type ./function2gene --man; to see it.
As a demonstration, you can simply do the following, which creates a keywords.txt file with a single keyword, 'transferrin', and runs the keywords:
cd bin; echo 'transferrin' > keywords.txt mkdir keyword_results; ./function2gene --keywords keywords.txt --results keyword_results;
which creates a keywords file with a single keyword, transferrin, and runs the various subscripts, putting the results in a keyword_results directory. The results will be in the keyword_results directory in a file called combined_results.txt, and a sumary table will be there as well in LaTeX table format, called combined_results_table.txt. (You can open up the latter as a fixed-width document in excel and delete the &.)