GeneRIF

This tool is useful when you need to find out what is a function of your genes of interest (in Humans), when you have their gene symbols and want to use information from GeneRIF database.

What is GeneRIF: https://www.ncbi.nlm.nih.gov/gene/about-generif - GeneRIF provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene

Gene symbols and their alternatives - HGNC - https://www.genenames.org/

Install

1. If you have git installed

git clone https://github.com/pristanna/GeneRIF.git

2. If you don´t have git installed

simply download and unpack the ZIP file

Downloading files

At the beginning you will need to download GeneRIF and HGNC Gene symbols. Simply run this command:

cd GeneRIF 

# if you are working on unix system, get rid of windows line endings
dos2unix update.sh filter_multiple_genes.sh filter_one_gene.sh

# make the scripts executable
chmod u+x filter_multiple_genes.sh filter_one_gene.sh

# update databse
./update.sh

Also run the ./update.sh whenewever you want to update the database

Filter results for one gene symbol

Set gene name as parameter 1, eg.

./filter_one_gene.sh DNAJC5

Results will be saved in filtering folder as eg. filtering/DNAJC5.results.txt

Filter results for multiple gene symbol

Create a file in filtering folder - one gene symbol per line - and put the name of file as parameter 1, eg.

./filter_multiple_genes.sh file_with_gene_names

Results will be saved in filtering folder as eg. file_with_gene_names.results.txt"

Example usage

Taks: Find out information about genes from within region of interest, eg. chr19:1000000-7000000

Find which genes are within the region of interest:

Go to http://www.ensembl.org/biomart/

Get Gene symbols

Save as chr19_1-7mb.genesymbols into filtering folder

Run the query:

filter_multiple_genes.sh chr19_1-7mb.genesymbols

Find the results in filtering/chr19_1-7mb.genesymbols.results.txt