Connectivity Characteristic of Transcription Factor

Transcription factors are a group of proteins that helps for interpreting the genetic information in DNA. Protein-protein interactions play a major role in the execution of key biological functions of a cell. These interactions are represented in the form of a graph with nodes and edges. Studies have showed that some nodes have high degree of connectivity and such nodes, known as hub nodes, are the inevitable parts of the network. In the present paper a method is proposed to identify hub transcription factor proteins using sequence information. On a complete data set of transcription factor proteins available from the APID database, the proposed method showed an accuracy of 77%, sensitivity of 79% and specificity of 76%.

Authors:

• T. Mahalakshmi
• Aswathi B. L.
• Achuthsankar S. Nair

Keywords:

• Transcription Factor Proteins
• Hub Proteins
• Shannon Index
• Transfer Free Energy to Surface (TFES).

References:

[1] Esti Yeger-Lotem, Shmuel Sttath, et.al, "Network motifs in integrated
cellular networks of transcription - regulation and protein-protein
interaction", PNAS, 2004, 101, 16, 5934:5939.
[2] Ideker T, Sharan R "Protein Networks in Disease", Genome Res, 2008,
18, 644-652.
[3] Michael Hsing, Kendall Grant Byler and Artem Cherkasov, "The use of
Gene Ontology terms for predicting highly-connected 'hub' nodes in
protein-protein interaction networks", BMC Systems Biology, 2008,
2:80
[4] Nizar N. Bataba, Laurence D. Hurst and Mike Tyers, "Evolutionary and
Physiological Importance of Hub Proteins", PLOS Computational
Biology, 2006, 2, 7, 748:756
[5] Diana Ekman, Sara Light, Asa K Bjorklund and Arne Eloffsson, "What
properties characterize the hub proteins of the protein-protein interaction
network of Saccharomyces cerevisiae?", Genome Biology 2006, 7:R45.
[6] www.biomedcentral.com dated 21st March 2009
[7] Keylock C.J., "Simpson diversity and the Shannon/Wiener index as
special cases of a generalized entropy", Earth and Biosphere Institute
and School of Geography, UK. OIKOS, 2005, 109:1
[8] Yanan Yu, Mya Breitbart, Pat McNairnie and Forest Rohwer,
"FastGroupII: A web-based bioinformatics platform for analyses of large
16S rDNA libraries", BMC Bioinformatics, 2006, 7:57
[9] Prieto C. and De Las Rivas J. , "APID: Agile Protein Interaction
DataAnalyzer." Nucl. Acids Res. 2006, 34: W298-W302.
[10] www.genome.ad.jp/aaindex
[11] CREX http://cbi.keralauniversity.edu dated December 15th 2008