A local average connectivity-based method for identifying essential proteins from the network level

Min Li, Jianxin Wang, Xiang Chen, Huan Wang, YiPan

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

LAC is a local average connectivity-based method that identifies essential proteins from the network level by evaluating the relationship between a protein and its neighbors.

Software download: LAC

DataSet

The original protein-protein interaction data was downloaded from DIP (http://dip.doe-mbi.ucla.edu/) and BioGrid (http://thebiogrid.org/ ). The final protein interaction networks used in this paper is given as DIP.txt and BioGRID.txt. The details of two networks are shown in table1. A list of essential proteins of S. cerevisiae are collected from the following databases: MIPS, SGD, DEG, and SGDP. The essential proteins used in this paper is given as Essential.txt.

Table 1 The yeast protein interaction networks obtained from two different databases: DIP and BioGRID.

Databases	Proteins	Interactions	The average degree	Essential proteins	non-essential proteins	Unknown proteins
DIP	4746	15166	6.39	1130	3328	288
BioGRID	5616	52833	18.82	1199	4026	391

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 LAC software, please send me an e-mail.

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

Min Li, Jianxin Wang, Xiang Chen, Huan Wang and Yi Pan.

A local average connectivity-based method for identifying essential proteins from the network level. Computational Biology and Chemistry 35 (2011), pp. 143-150

doi: 10.1016/j.compbiolchem.2011.04.002