SIN-Locator

code for "Ge-Wang, Min-Qi Xue, Hong-Bin Shen, and Ying-Ying Xu, Learning multi-view patterns of subcellular localization from protein imaging, sequence and network data"
Contact: Ying-Ying Xu, yyxu@smu.edu.cn 2021/06/08

1.datasets

The IHC and IF datasets are saved in ./data/0_datasetFiles/datasets, and the updated data can be found at ./data/0_datasetFiles/applicationDataset

2.features

All the features used in this study have been extracted and saved in ./data/7_constructedData folder. The code of feature extraction can be found at:

(1) SLF features

   http://murphylab.web.cmu.edu/software/2012_PLoS_ONE_Reannotation/
   http://murphylab.web.cmu.edu/software/2008_JProteomeResearch_HPA/

(2) GenP

   https://github.com/LorisNanni

(3) CNNs in Matlab

(4) Hum-mPLoc 3.0

   http://www.csbio.sjtu.edu.cn/bioinf/Hum-mPLoc3/

(5) DeepLoc

   https://github.com/JJAlmagro/subcellular_localization

(6) node2vec

   http://snap.stanford.edu/node2vec/

3.classification

Run mainProcess.m to recreate the results in the article. The code package has been tested using Matlab R2021a under Windows 7 in a 64bit architecture.