The models of nucleotide sequence evolution for the different datasets were identified with jModeltest 2 [ 98, 99] using the corrected Akaike and Bayesian Information Criteria.
Applying an unpublished, enhanced version of CARMA to the unfiltered GS FLX dataset, EGTs were identified for 167,134 (32%) of the reads, while only 133,337 (22%) EGTs were reported in the previous study.
While 30 of those specific-dataset peptides were identified for protein hits in conjunction with other peptides (indicating that the gene product detection is correct), 5 of these peptides were observed given our identification criteria of "1 peptide per hit".
A total of 21,853 datasets of severely injured patients were identified for further analysis.
Based on the normalized tissue-specific expression pattern in root tissues in the soybean Affymetrix gene chip dataset [ 34], key genes were identified for quantitative RT-PCR analysis.> -wrap-foot>> -wrap-foot>> -wrap-foot> aThe genes specific to G. soja with a deleterious mutation were obtained from Kim et al. [ 6, 8].
In addition, the parametric gamma regressions fitted to the per-gene dispersion estimates α and gene expression means μ (Supplementary Fig. S25) were identified for each dataset: (4) (5) (6) Subsequently, simulation parameters for each dataset were fixed as follows.
Unique haplotypes in each dataset were identified and used for subsequent phylogenetic analyses [Genbank: KJ870103-KJ870137 & KJ870139-KJ870149] (Additional file 5: Table S7).
Gene ontology terms were identified for mRNAs overlapping with in-house dataset using DAVID bioinformatics tool.
Also, 56 candidate genes were identified for follow up in the Illig et al. dataset.
The genes, appearing in all the three dataset, were identified and cumulative rank score for each gene was calculated using the following equation - where, Based on their rank score the genes were re-ranked with one having the lower cumulative rank score getting the higher rank.
