We have found that setting the aa-IDc < 40% can include TRs from the same protein family that are not functional homologs; while setting aa-IDc > 40% can filter functional homologs and limit the cross organism correlations.
One 2D LC/MS/MS run (20 x 1 h runs) (Dwivedi et al., [2008]) was conducted on an exponential phase sample from cells grown in low glycerol (170 mM) (see Additional file 1), primarily to survey the microorganism's proteome for future cross-organism and RNAseq studies.
To ensure that data were comparable across different platforms and species, gene signature identifiers were translated using both a universal gene dictionary to map them to a standard NCBI gene reference and a cross-organism dictionary to assign them to precomputed ortholog clusters (Methods).
These were entered into Geroprotectors in table format, facilitating cross-organism and cross-study comparison of results.
Major hindrances of a cross-organism comparison are differences in experimental approaches and the specific definition of essentiality used.
Motivation: Protein interaction networks contain a wealth of biological information, but their large size often hinders cross-organism comparisons.
The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching.
The cross-organism spearman correlation coefficient of TSS or TTS nCpG content was calculated based on all orthologous gene pairs between two organisms.
One aim of the InterMine project is not only to provide expanded querying capabilities within an individual MOD, but also to facilitate cross-organism querying between MODs.
Also on this page, pre-computed top-matched hits by BLAST search against genes from plantsUPS, Refseq and UniProt databases can be useful for cross-organism study.
