TiGER: a database for tissue-specific gene expression and regulation.
paper
Cited
Public
- Authors
- Liu, Xiong; Yu, Xueping; Zack, Donald J; Zhu, Heng; Qian, Jiang
- Year
- 2008
- Journal
- BMC bioinformatics
- PMID
- 18541026
- DOI
- 10.1186/1471-2105-9-271
- PMCID
- PMC2438328
BACKGROUND: Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. RESULTS: The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. CONCLUSION: We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.
Tissue-specific gene expression and TF interactions. (A) An example of gene expression profile. The gene RPE65 (RefSeq ID: NM_000329; UniGene ID: Hs.2133; Ensembl ID: ENSG00000116745) is preferentially expressed in the eye with an expression enrichment value greater than 13. (B) Distribution of -log10(p) values for 307 tissue-specific TF interactions in the eye. The most significant is the interaction between FOXJ2 and POU3F2, with a -log10(p) value greater than 39 (p-value < 10-39).
Conservation profile, density profile and energy profile for the eye-specific gene BFSP1 (RefSeq ID: NM_001195; UniGene ID: Hs.129702; Ensembl ID: ENSG00000125864). The energies less than -1 indicate the existence of TF modules. The upper panel depicts the conservation scores of the regions between 5 k upstream to translational start site. The middle panel shows the density of all known TF binding sites in a sliding window along the region. The bottom panel shows the potential energy based TF interactions. The dashed line is the thresholds for determining a cis-regulatory module.
A diagram of the TiGER views, illustrating three ways a user may search for tissue-specific gene expression and combinatorial regulation. In (A), the user could type a gene name and obtain a view of gene expressions and crm profiles. In (B), the user could type a TF name and obtain a view of co-regulations. In (C), the user could select a tissue name and obtain a view of gene expressions, crm detections and TF interactions.
| # | Section | Preview |
|---|---|---|
| 20 | Conclusion | There are fundamental issues relating to the computational prediction of human gene regulation.β¦ |
| 21 | Availability and requirements | Project name: TiGER |
| 22 | Availability and requirements | Project home page: [1] |
| 23 | Availability and requirements | Operating system(s): Platform independent. |
| 24 | Availability and requirements | Programming language: none. |
| 25 | Availability and requirements | License: no restriction. |
| 26 | Availability and requirements | Any restrictions to use by non-academics: no restriction. |
| 27 | Authors' contributions | XL, XY and JQ conceived the construction of the database. XL developed the database interface. XY⦠|
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