ORTI (Open-access Repository of Transcriptional Interactions) is a rich and publicly-available database of experimentally-validated transcriptional interactions with the focus on mammalian species, which is accompanied with tools that can identify and predict transcriptional interactions.
To build the ORTI database, mammalian TFs and their associated TGs were retrieved from publicly available databases of TF-TG interactions, namely HTRI, TFactS, TRED, TRRD, PAZAR, and NFI-Regulome, as well as from the literature. Gene names were disambiguated by consulting with NCBI to include the official symbol of the gene for the specified species as provided by the HGNC. Any ambiguous cases were clarified by manual curation, consulting the original articles to determine the relevant TFs and TGs under examination, after which any remaining ambiguous cases were discarded. For transcriptional heterodimers (e.g. AP1), the TG was assigned to the individual TF components where possible (e.g. Fos, Jun). However, when the information source did not specify these TFs, the original heterodimer name was retained.
For each TF-TG interaction, ORTI provides the
The ranking was incorporated since many existing databases do not clearly separate out TF-TG interactions validated by low-throughput (LTP) experimental methods from those derived by high-throughput (HTP) screening techniques. This feature categorizes TF-TG interactions into three ranks:
If the supporting evidence for a TF-TG interaction was not provided by a database or was ambiguous (for instance, chromatin immunoprecipitation can be used as both as HTP and LTP technique), manual curation of the literature was performed to clarify the ambiguity. The composition of the ORTI database is depicted in figure below:
Together, ORTI encompasses 660 TFs and 72,817 factor-gene interactions, out of which 10,283 regulations are Rank 1. Table below shows the number of TFs, TGs, and TF-TG interactions across all databases with no ranking constraint (all interactions) or when only LTP verified interactions (Rank 1) are included:
|Database||# of TFs||# of TGs||# of TF-TG pairs|
Vafaee F, Krycer JR, Ma X, Burykin T, James DE, Kuncic Z. ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PloS one. 2016 Oct 10;11(10):e0164535.
Last updated on November 2016