About the algorithms used on this site:

• Seed-based systematic discovery of specific transcription factor target genes by Ralf Mrowka, Nils Blüthgen, and Michael Fähling  FEBS J. 2008 Jun;275(12):3178-92) 
• Statistical modeling of transcription factor binding affinities predicts regulatory interactions. Manke T, Roider HG, Vingron M., PLoS Comput Biol. 2008 Mar 21;4(3):e1000039. 

About this webserver:

• Targetfinder.org: a resource for systematic discovery of transcription factor target genes.Szymon M Kielbasa ,Nils Blüthgen , Michael Fähling , and Ralf Mrowka . Nucleic Acids Res. 2010 May 11.

About the prediction of target genes based on sequence information:

• Wasserman WW and Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287

Sources of the transcription factor target sample data provided on this site:

• Wu JT, Kral JG. The NF-kappaB/IkappaB signaling system: a molecular target in breast cancer therapy. J.Surg.Res.; 123: 158-69.2005
• Bracken AP, Ciro M, Cocito A, Helin K. E2F target genes: unraveling the biology. Trends Biochem.Sci.; 29: 409-17.2004
• Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res.; 17: 1550-61.2007
• Sementchenko VI, Watson DK. Ets target genes: past, present and future. Oncogene.; 19: 6533-48.2000
• Hollenhorst PC, Shah AA, Hopkins C, Graves BJ. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev.; 21: 1882-94.2007
• Semenza GL. Targeting HIF-1 for cancer therapy. Nat.Rev.Cancer.; 3: 721-32.2003
• Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B. Genomic targets of the human c-Myc protein. Genes Dev.; 17: 1115-29.2003