TiGER Documentation

Version 1.0, March 2008


TiGER (Tissue-specific Gene Expression and Regulation) is a database for generating comprehensive information about human tissue-specific gene regulation, including both expression and regulatory data.

Currently, the database contains tissue-specific expression profiles for ~20,000 UniGene genes, combinatorial regulation for 7,341 interacting transcription factor (TF) pairs, and 6,232 cis-regulatory modules (CRMs) for tissue-specific genes.

Data Organization

The data are organized as a relational database, which provides three different views: gene view, TF view, and tissue view. Each view has a query interface and associated underlying database tables/entities:

Data Quality

EST Enrichment

We have included P-values for the enrichment scores in EST download file, where the 1st column is tissue name, the 2nd column is the enrichment score, and the 3rd column is the –log10(P) value. We define a gene as tissue-specific gene if it satisfies the two criteria: the enrichment score is greater than 5 and the P-value is smaller than 10-3.5.

TF Interaction

We have included P-values for TF interaction in summary table and download file. To evaluate TF interaction results, we use known interactions as positive control due to the scarcity of tissue-specific interaction. More than 40% of the known interactions are recovered, with 84-fold enrichment compared to the expected.

CRM Identification

We have sensitivity of 12% and enrichment of 10 using known regulatory regions as positive control.

Data Up-To-Dateness

We obtained DNA sequences and annotations (such as RefSeq) from the Human May 2004 (hg17) assembly of UCSC genome browser. Conservation score data was also downloaded from the multiple alignments of 8 vertebrate genomes with Human (hg17) at UCSC genome browser. The EST database was downloaded from NCBI website in 2005.

As more experimental data accumulates related to the nature of TF-DNA interactions, we plan to further develop our predictions on tissue-specific TF interactions. We also plan to extend our work on CRM detection by relating regulatory elements with temporal (e.g., development) and spatial (e.g., cell types) attributes. As new predictions on tissue-specific gene regulation accumulate, the TiGER database will need to be further expanded and modified. We will update the content of the database on a regular basis.


TiGER is constructed for free access and use. The downloadable data formats include standard .txt text files and .png images.