IDEPA-XMBD: Individualized Differentially Expressed Protein Analysis

 

We evaluated five state-of-the-art tools (RankComp v1/v2, PenDA, Peng, and Quantile) through classic computational (precision, Type one error control, parameter evaluation, robustness, and similarity) and functional (pathway enrichment and survival analysis) criteria. We also integrated these tools into a user-friendly tool kit, IDEPA-XMBD , to facilitate individualized DEAs in proteomics studies.

1. Install

We use docker to encapsulate the command line version and the plotly version of IDEPA-XMBD separately.

1.1 Cmd Version

We provide a docker image with IDEPA-XMBD: https://registry.hub.docker.com/r/ychlouie/idepa_cmd

Pull the docker image of IDEPA-XMBD:

docker pull ychlouie/idepa_cmd:0.1

Create a docker container containing IDEPA-XMBD:

docker run -it ychlouie/idepa_cmd:0.1

1.2 Plotly Version

We provide a docker image with IDEPA-XMBD: https://hub.docker.com/r/lylan/idepa

Pull the image:

docker pull lylan/idepa:0.1

Create a docker container

docker run -it -d -p HostPort:8095 -v HostDirectory:/IDEPA/workdir lylan/idepa:0.1

Then, you can enter the IDEPA_plotly version by visiting HostIP:HostPort, and all output files will be saved in HostDirectory. For example: HostPort could be set to 38765, HostDirectory could be set to ~/IDEPA, HostDirectory must exist. These two parameters can be changed according to user needs.

such as,

mkdir ~/IDEPA

docker run -it -d -p 38765:8095 -v ~/IDEPA:/IDEPA/workdir lylan/idepa:0.1

Next, open 127.0.0.1:38765 in the local browser or remotely access ip:38765 (you should ensure that the machine can be accessed remotely).

The dependency of IDEPA-XMBD is: environment

2. Usage

2.1 Cmd versioin

After entering the container docker run -it ychlouie/idepa_cmd:0.1, use -h to view the IDEPA-XMBD module information:

python /IDEPA-XMBD/individual_depa.py -h

# View specific module information 
python /IDEPA-XMBD/individual_depa.py [moduleName] -h

# such as
python /IDEPA-XMBD/individual_depa.py comparison -h 

moduleName is the name of the module you want to run

We also provide example data for each module：

python /IDEPA-XMBD/individual_depa.py [moduleName] -p /IDEPA-XMBD/parameters_file/test_parameters.txt

## such as
python /IDEPA-XMBD/individual_depa.py stable -p /IDEPA-XMBD/parameters_file/test_parameters.txt

# Result workdir /IDEPA-XMBD/workdir

If you want to change the input data, you can change the content of /IDEPA-XMBD/parameters_file/test_parameters.txt

2.2 Plotly version

After entering the container, you can operate according to Procedure

3. Cite this article

[1] Liu Y, Lin Y, Yang W, et al. Application of individualized differential expression analysis in human cancer proteome[J]. Briefings in Bioinformatics, 2022.