A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

Min Li,Hanhui Zhang,Jian-xin Wang,Yi Pan

School of Information Science and Engineering, Central South University, China

PeC is a new centrality measure based on the integration of protein-protein interaction and gene expression data.

Software download: PeC

DataSet

The original protein-protein interaction data was downloaded from DIP (http://dip.doe-mbi.ucla.edu/). The final protein interaction networks used in this paper is given as DIP.txt. The details of DIP network is shown in table1. A list of essential proteins of S. cerevisiae were collected from the following databases: MIPS, SGD, DEG, and SGDP. The essential proteins are given as Essential.txt.The gene expression data of Saccharomyces cerevisiae was retrieved from Tu et al., 2005, containing 6,777 gene products and 36 samples in total, with 4,858 genes involved in the yeast protein interaction network. The gene expression data are given as genedata.txt.

Table 1 The yeast protein interaction network obtained from database DIP.

Databases	Proteins	Interactions	The average degree	Essential proteins	non-essential proteins	Unknown proteins
DIP	5093	24743	9.72	1167	3591	335

Additional files: http://www.biomedcentral.com/1752-0509/6/15/additional

Collaboration
This software is a jar file. If you want to modify the source code and would like the modification to be included in a subsequent release, we would love to hear from you. Please send me an e-mail (limin@mail.csu.edu.cn).
If you have questions about PeC software, please send me an e-mail.

PeC Publication
Please see the following paper for more information about the algorithm:

Min Li, Hanhui Zhang, Jian-xin Wang, Yi Pan.
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data.
BMC Systems Biology 2012, 6:15 doi:10.1186/1752-0509-6-15.