Tissue-specific Profiles for Match
A number of tissue-specific profiles and a cell cycle-specific profile are provided with Match. Groups of transcription factors known to be active in a particular tissue have been collected for each profile from TRANSFAC. (Note: Although the selected factors are involved in the regulation of expression of tissue-specific genes, not all of the included factors themselves show strict tissue-specificity, i.e. besides tissue- (or condition-) specific factors the profiles may also include ubiquitous factors.) The matrices linked to these transcription factors in TRANSFAC were then used to build a profile. (Cut-offs included in the tissue-specific profiles, for command line use, were selected to minimize false negative matches.)
The following profiles are provided with Match:
Tissue-specific Profiles
Adipocyte-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of adipocyte-specific genes.
Immune Cell-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of genes whose transcription is induced upon immune response in T-cells, B-cells, mast cells, myeloid cells, natural killer cells, and macrophages.
Liver-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of liver-enriched genes.
Lung-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of lung-specific genes.
Muscle-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of muscle-specific genes.
Nerve System-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of nerve system-specific genes.
Pancreatic Beta Cell-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of pancreatic beta-cell-specific genes.
Pituitary-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of pituitary-specific genes.
Biological Process-specific Profiles
Cell Cycle-specific Profile
This profile is designed to search for potential binding sites within regulatory regions of genes whose expression is dependent on the stage of cell cycle.
All gene and factor lists are based on data from TRANSFAC.
Other Profiles
Three "vertebrate non-redundant profiles" are also provided, for the three cut-offs minFN, minFP, minSUM. The cut-offs in these three profiles are fixed. These profiles were constructed as follows: On the basis of matrix similarity and relatedness of the linked trancription factors, the vertebrate matrices were divided into groups and from each group just one "best" matrix was selected by the lowest number of hits (false positives) at minFN, minSUM, and minFP, for inclusion in the respective "non-redundant profile". The number of false negative hits was measured on the pooled sites linked to the factors of the respective matrix group. The number of false positive hits was measured on upstream sequences from TRANSPRO, -10,000 to -5,000 relative to the virtual transcription start sites.