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)  [NCBI]
• 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.  [NCBI]

About this webserver:

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

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 [NCBI]

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