Description of the sample data

The algorithms provided on this site require seed data of known genes that are a target of a specific transcription factor of interest. We provide sample data that represent names from known transcription factor targets  for each of the following individual arbitrarily chosen transcription factors, namely NFkB, E2F, ETS1, HIF-1, HNF4, c-Myc. The seed data is given as ensemble gene identifiers.

Data Sources
The data of known transcription factors come from review papers. We used the following sources: NFkB [1],  E2F [2;3], ETS1 [4;5], HIF-1 [6], HNF4, c-Myc [7].


References

1. Wu JT, Kral JG. The NF-kappaB/IkappaB signaling system: a molecular target in breast cancer therapy. J.Surg.Res.; 123: 158-69.2005
2. Bracken AP, Ciro M, Cocito A, Helin K. E2F target genes: unraveling the biology. Trends Biochem.Sci.; 29: 409-17.2004
3. 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
4. Sementchenko VI, Watson DK. Ets target genes: past, present and future. Oncogene.; 19: 6533-48.2000
5. 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
6. Semenza GL. Targeting HIF-1 for cancer therapy. Nat.Rev.Cancer.; 3: 721-32.2003
7. 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