With steady progress in genomics, proteomics, metabolomics, lipidomics, and genetic engineering as well as an increased number of genomes sequenced and annotated, the modification of oilseed crops becomes a more straightforward practice.
In general, the available structural data refer to the protein chain for which PTMs are annotated, regardless of modifications are present in the solved structure.
Of the seven SNPs, six (rs6790260, rs6444285, rs4686483, rs4686484, rs6778720 and rs2030520) mapped to regions annotated with histone modifications H3K27ac, H3K4m1, H3k4 m2, H2A.Z and EZH2 identified in B- and T-cells (Fig. 1C and Supplementary Material, Table S5).
Since the post-translational modifications annotated by the BioGRID can be directly matched to standard PSI-MI terms (Supplementary Table 3), the script downloads the most recent BioGRID data set in TAB2 format, extracts this information and assigns appropriate PSI-MI terms for interaction type to the candidate biochemical reactions from iRefIndex that originate from the BioGRID.
A list of 230 S. cerevisiae genes annotated with "chromatin modification" or its child terms was obtained from the Gene Ontology database [6].
One is the GO database, from which 217 human genes annotated with 'Chromatin modification' or its child terms (see above) were downloaded.
Of all our candidate CM genes, 21 are annotated as "chromatin modification" or its child terms with the evidence code IEA (Inferred from Electronical Annotation) in the GO catalog when the annotations were initially downloaded.
For example, the functionally relevant phosphorylation of Acetyl Co-A Carboxylase 1 (ACACA) at S80 in human, S79 in mouse and S79 in rat have all been experimentally identified and are annotated as orthologous modification sites in PhosphoSitePlus.
Among them are many modified peptides not previously annotated to contain these modifications.
To this end, chromatin states and novel functional elements of the histone code [ 30] have been inferred and annotated, respectively, from histone modifications acting in a combinatorial fashion by using multivariate hidden Markov models [ 2, 31, 32], dynamic Bayesian networks [ 33, 34], or unsupervised machine learning [ 35].
