Gene Updater

The automatic conversion of genes to dates in Excel can be problematic, as the converted dates are not recognised in pathway databases. This web tool thus serves to convert the old gene names or dates back into the updated gene names as recommended by the HUGO Gene Nomenclature Committee (HGNC). The running instance of the app is deployed at: https://share.streamlit.io/kuanrongchan/date-to-gene-converter/main/date_gene_tool.py

Instructions for using web tool

Users can upload their .csv or .xlsx file or files. Ensure that the first column contains the gene names. Having a Gene Description on the second column is useful for mapping the Mar-01 and Mar-02 genes, although this step is not mandatory. Checkbox is provided for users to inspect their data. If no data is uploaded, a demo dataset consisting of a restricted list of genes are pre-loaded. Users may use the pre-loaded demo dataset to explore the features and functionalities of the web tool.

If the first column contains the old gene names, these genes will be updated to the new gene names using the webtool. If the first column contains dates, they will be converted to the updated gene names, with the exception of Mar-01 and Mar-02 as these terms can be mapped to more than one gene.

When there are duplicate Mar-01 values, Mar-01 will be annotated as Mar-01_1st and Mar-01_2nd. Users will have to manually assign the corresponding gene names to the values using the widgets provided. If gene description is provided in the dataset, users will just need to match the gene name to the gene description. Otherwise, users will have to check their raw dataset to ascertain what the Mar-01_1st and Mar-01_2nd mean. The same process goes for Mar-02 values as well.

Finally, users can key in the genes of interest (e.g. MARCHF1) to inspect if the gene expression data has indeed been updated with the new gene names.

Running the Gene Updater tool locally

Please execute the following steps to run the Gene Updater tool locally:

Technical requirements

Please install the following:

1. Install Python 3.7 (or later) at https://www.python.org/downloads/
2. Install any text editor (e.g. Sublime or Visual Studio Code) to allow editing of Python (.py) files

Installing Streamlit locally

To install Streamlit, run the following code in terminal:

pip install streamlit

Installing packages for date_gene_tool

Install the following packages locally by typing the following commands in terminal:

pip install pandas
pip install numpy
pip install regex
pip install inflect
pip install dateparser
pip install openpyxl
pip install xlrd
pip install XlsxWriter
pip install streamlit-tags

Organizing Streamlit apps locally

To create a new folder called streamlit_apps and make it our current directory, type the following in the terminal:

mkdir streamlit_apps
cd streamlit_apps

Creating date_gene_tool.py file locally

Execute the following commands in the terminal:

mkdir date_gene_tool
cd date_gene_tool
touch date_gene_tool

This will generate a local file named that is named as date_gene_tool.py. After locating the date_gene_tool.py file, open the file in text editor (e.g. Sublime or Visual Studio Code).

When you open the file, copy and paste the codes that is located at: https://github.com/kuanrongchan/date-to-gene-converter/blob/main/date_gene_tool.py.

Remember to save the file after typing in the codes.

Downloading demo and HGNC symbol conversion files

In the GitHub address (https://github.com/kuanrongchan/date-to-gene-converter), download the following 2 files and place the 2 files within the date_gene_tool folder (together with the date_gene_tool.py file):

1. demo.csv
2. hgnc-symbol-check2.csv

Running Gene Updater tool locally

You can run the program locally by typing in terminal:

streamlit run date_gene_tool.py

This should open a new tab with the Gene Updater app appearing in your default browser

Summary

In summary, to run the file locally, please download this repository, install the requirements and run the script with the following codes in the command line

cd path/to/folder
pip install -r requirements.txt
streamlit run date_gene_tool.py

Note that users can also directly download all the files within GitHub in the ZIP file format by pressing the "Code" dropdown widget to run the program locally.

You may also access the files directly from Zenodo

Credits

This app is developed by Clara Koh, Justin Ooi and Kuan Rong Chan from Duke-NUS Medical School, Singapore. For more details on what we do, please visit our website at: kuanrongchan.com

Citation

To cite your use of Gene Updater, please reference this article (https://www.nature.com/articles/s41598-022-17104-3):

Koh, C.W.T., Ooi, J.S.G., Joly, G.L.C. et al. Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names. Sci Rep 12, 12743 (2022). https://doi.org/10.1038/s41598-022-17104-3