Clover

Clover tool to mining differentially expressed genes (DEGs) in intaractive visualization tool. This tool rank DEGs by 4 different scores; Root, Dowsing, Ropeway, and Tresure hunt.

Installation

To run this app locally, clone this repository and open this app folder in your terminal/Command Prompt.

git clone https://github.com/G708/Clover.git
cd Clover

The project relies on several Python packages including Dash, Dash Bootstrap Components, Plotly, and Pandas. You can install these dependencies like this:

pip install -r requirements.txt

Download the data with:

python src/data_prep.py

Quick usase

This tool can use as command line tool and web application.

Command line tool

To run Clover as command line tool, run this command:

python clover.py -i imput_DEG_list.csv --id_type hgnc_symbol

Essential options

To run command line tool, you need to specify input file with -i option. This input file should be a csv file with FDR columns. For more options, please refer to this page.

-i, --input

Input expression matrix file with FDR columns. Default delimiter of the file is , , but user can specify by the additional option --sep.

--id_type

gene name / ID type in input file to convert ID and merge the columns. Choose from {hgnc_symbol, ensembl_gene_id, entrezgene_id}. Default is hgnc_symbol.

Web tool

For web application, this app implemented with Dash. To Run this app locally with:

python app.py

Open a browser at http://127.0.0.1:8050

Feature Data sources

• RNA-seq data from Genotype-Tissue Expression GTEx project v8 (THE GTEX CONSORTIUM, 2020) data in Human protein Atlas (https://www.proteinatlas.org/download/rna_tissue_gtex.tsv.zip).
• Publication data for each gene is publicly available at https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz.
• Score of DE prior is downloaded from

  Crow,M. et al. (2019) Predictability of human differential gene expression. Proceedings of the National Academy of Sciences, 116, 6491–6500. https://doi.org/10.1073/pnas.1802973116

• Human cell line essentiality data is downloaded from OGEE (https://v3.ogee.info/#/home)

  S. Gurumayum *, P. Jiang *, X. Hao, T.L Campos, N.D. Young, P.K. Korhonen, R.B. Gasser, P. Bork, X.M. Zhao, L.J. He, Chen, W.-H. (2020). "OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Research, gkaa884, doi: 10.1093/nar/gkaa884