Installation:

This requires docker. If you don't have docker, download from https://docs.docker.com/engine/install/.

docker pull ghcr.io/ttsutsui-analysis/pub2gene_key:2.1
docker run --rm -d --name pub2gene_key -p 10020:3838 ghcr.io/ttsutsui-analysis/pub2gene_key:2.1

You can access index page via http://localhost:10020

Introduction

pub2gene_human

This app will show genes of which publication enriched in certain search words in pubmed. I believe that this app will be useful when researcher need to know typical gene for certain pubmed search result. So far, this app only adapt human genes only. Usage introduction written below.

1. If you work under proxy server, please fill its URL.
2. Fill search words and select used CPUs and push search button.
3. App will search your words in pubmed and obtain all PMIDs. Then calculate overlapping PMIDs for each gene links. The genes which has many overlapping PMIDs with search words up-sift from regression curve. So your interesting genes will show higher standard residual value. You may want to decide cut-off value for standard residual depend on your research interest arbitrarily.
4. Select your cut-off value for each option and push cut-off button. FYI, since residuals are standarized, 1.96 means top 5%.
5. You can have cut-off result. This result can be downloaded as csv file. In the csv, you can find overlapped PMIDs for each gene with search words.

pub2keyword_human

This app will obtain keywords from pubmed search result articles. Obtained keywords will be subjected to word enrichment analysis comparing with background keywords from ~1 million articles all of those are linked to human genes. Usage of this app is below.

1. Fill your entrez API key and proxy URL, if you want.
2. Fill your interest search words and push search button.
3. App will search recent top 1000 articles for your search words. So far, only top 1000 articles are used for further enrichment analysis due to computation speed.
4. You can see two table and one plot. First table is for title corresponding keywords for each article and second table represent enrichment analysis result for each keyword.
5. You can adjust plot by slidebars below.
   

Reference

TO BE DETERMIND