HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes

Carbon line formation and spectroscopy in O-type stars

The determination of chemical abundances constitutes a fundamental requirement for obtaining a complete picture of a star. Particularly in massive stars, CNO abundances are of prime interest, due to the nuclear CNO-cycle and various mixing processes which bring these elements to the surface. We aim at enabling a reliable carbon spectroscopy for our unified NLTE atmosphere code FASTWIND. We develop a new carbon model atom including CII/III/IV/V, and discuss problems related to carbon spectroscopy in O-type stars. We describe different tests to examine the reliability of our implementation, and investigate which mechanisms influence the carbon ionization balance. By comparing with high-resolution spectra from six O-type stars, we check in how far observational constraints can be reproduced by our new carbon line synthesis. Carbon lines are even more sensitive to a variation of temperature, gravity, and mass-loss rate, than hydrogen/helium lines. We are able to reproduce most of the observed lines from our stellar sample, and to estimate those specific carbon abundances which bring the lines from different ions into agreement. For hot dwarfs and supergiants earlier than O7, X-rays from wind-embedded shocks can impact the synthesized line strengths, particularly for CIV, potentially affecting the abundance determination. We have demonstrated our capability to derive realistic carbon abundances by means of FASTWIND, using our recently developed model atom. We found that complex effects can have a strong influence on the carbon ionization balance in hot stars. For a further understanding, the UV range needs to be explored as well. By means of detailed nitrogen and oxygen model atoms available to use, we will be able to perform a complete CNO abundance analysis for larger samples of massive stars, and to provide constraints on corresponding evolutionary models and aspects.Comment: 22 pages, 16 figures, 6 table