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To examine simultaneously the effects of multiple standard parameters and lymphocyte-specific kinase (LCK) metagene expression on survival, a Cox proportional-hazards regression model was applied among ER-negative samples.
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Locus amplification primers (LAPs) for multiple target genes were designed using standard parameters as previously described [ 48].
(a) Standard parameters for cost analysis; (b) standard parameters except K = 2 (high carrying capacity); (c) standard parameters except h = 2 (long handling time).
Multiple sequence alignments were made by Muscle 3.6 using standard parameters.
The ClustalW program [ 25] with standard parameters was used for pairwise and multiple amino acid sequences alignments, followed by careful visual inspection.
Multiple sequence alignments were performed using ClustalW [ 39], with standard parameters.
Multiple amino acid sequence alignments were established with CLUSTALW2, a general purpose DNA/protein multiple sequence alignment program (http://www.ebi.ac.uk/Tools/msa/clustalw2/; [ 90]) using standard parameters.
By establishing multiple linear regression models using continuously distributed biomarker candidates and gold standard parameters (e.g. creatinine or proteinuria at time of biopsy), we identified a model consisting of 3 biomarkers (THBS1, TRIB1 and BMP7).
The multiple sequence alignments were used to build and calibrate HMMs with HMMER, using standard parameters.
(a) standard parameters (see Table 1); (b) standard parameters except K = 2 (higher carrying capacity); (c) standard parameters except h = 2 (long handling time).
Violin plots were created using the R package 'vioplot' using standard parameters.
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