BASE

About:

BASE is a method to infer transcription factor activities by integrating microarray expression data and TF-gene binding (e.g. ChIP-chip) data.

Download:

WinBase: Program executable in Microsoft Windows system. The program is coded in C++ and complied with Visual Studio 6.0.

UnixBase: Program executable in UNIX system.

Readme: Description about format of input and output files for the above program.

Example microarrat data: An example microarray data which measured relative expression levels of yeast genes across cell cycle.

Exampe TF-gene affinity data: compiled TF-gene binding affinity data derived from ChIP-chip data from Richard Young's Lab.

run.bat: An example to show how to run the program.

Reference:

[1] Inferring activity changes of transcription factors by binding association with sorted expression profiles. Cheng C, Yan X, Sun F, Li LM. BMC Bioinformatics. 2007 Nov 16;8:452. [Pubmed]

[2] Systematic identification of cell cycle regulated transcription factors from microarray time series data. Cheng C, Li LM. BMC Genomics. 2008 Mar 3;9:116. [Pubmed]

[3] Systematic identification of transcription factors associated with patient survival in cancers. Cheng C, Li LM, Alves P, Gerstein M. BMC Genomics. 2009 May 15;10:225. [Pubmed]

Contact:

Chao Cheng