Metabolites were annotated using IDBrowser in Mass Profiler Professional (MPP, Agilent) using a combination of available databases, including METLIN, Human Metabolome Database (HMDB), LipidMaps, and Kyoto Encyclopedia of Genes and Genomes (KEGG).
In a way, these libraries also account for matrix effects and their use was preferred over the use of publicly available databases, because peak assignment could be performed with increased reliability.
With the ongoing genome sequencing projects in many different species and integrated efforts to annotate the functional content of fully sequenced genomes there is a need to complement existing automated genome annotations with a focused bioinformatics analysis of individual genes and gene families to make fully use of publicly available databases and resources.
We made use of publicly available databases to gain additional insight into chromatin structures surrounding promoters bearing the TCTCGCGAGA palindromic motif.
Availability and implementation: LigDig makes use of freely available databases, including ChEMBL, PubChem and SABIO-RK, and software programs, including cytoscape.js, PDB2PQR, ProBiS and Fconv.
Most proposed data mining approaches make use of available curated databases and predict gene-disease associations by using keyword similarity to known disease genes and phenotypes.
However for these projects to be fruitful, careful planning is needed to make full use of available tools and databases (see Table 4).
Using publicly available databases of the Consumer Product Safety Commission for 1985 through 2005, researchers found that 27 infants ages 1 month to 2 years had suffocated when they became wedged against the padded bumpers or were strangled by a bumper tie around the neck.
Manual interpretation of data using publically available databases such as KEGG pathways and the LipidMAPS databases may help place quantitated lipidomics results into a meaningful biological context.
Using public available databases of interaction BIOGRID and HPRD (http://www.thebiogrid.org/ and http://www.hprd.org/) we built an "interactome" among the transcriptional regulators of our list for which information was available (Figure 4).
