The graph also revealed that TMPRSS3 interacts with all these proteins, which is consistent with the findings presented in Fig. 5a. Fig. 5 First shell (colored) and second shell (white) interactors of TMPSS3 protein predicted by protein–protein interaction analysis by STRING database (a). ...
The graph shows the average hemoglobin expression per individual measured 3 times (* indicates P value of < 0.1; *** indicates a P value of < 0.001; Tukey’s multiple comparisons test was used for A and B, for C an unpaired student T-test on In(Lu) vs control donors groups...
Variant calling was performed using the GATK Unified Genotyper (v2.3.6). Single nucleotide variants (SNVs) and small indels were annotated using ANNOVAR [19]. In addition, we rescreened all variants for splice sites, which are likely to be missed by conven- tional...
Sequence alignment to the human reference genome (GRCh37) was performed using Burrows-Wheeler Aligner, and variant calling was performed using Genome Analysis Tool Kit (GATK v4.0, Broad Institute)26. Variants were annotated by ANNOVAR (http://wannovar.wglab.org/)27. DNA and protein sequence ...
Tumour purities ranged from 13 to 88% (mean of 48%), as estimated by Sequenza (v2.1.2) [15]. Somatic structural variant calling and gene annotation Somatic SVs were called using Manta (v1.6.0) [16] and GRIDSS (v2.8.3) [17, 18] for each pair of tumour and normal samples. High-...
(see the inset for the mutation type color code). Genes in magenta represent the significantly mutated genes (SMGs) as discerned by MuTSigCV. The right bar graph shows the rate of mutations per gene, split by mutation type.bFor the three SMGs, non-silent mutations are observed in the ...
L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8):907-915. If BRAKER was executed using RNA-Seq data in FASTQ format, cite HISAT2: Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). ...
Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. Biotechnol Biofuels. 2018;11:1–15. https://doi.org/10.1186/s13068-018-1167-z. Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-...
NATURE COMMUNICATIONS | DOI: 10.1038/ncomms6969 ARTICLE such as storing of variant population frequencies and alternative haplotypes within a reference possibly through a population sequence graph. Population-wide de novo assembly will certainly be needed to facilitate discovery of complex variants, and ...
The variant calling was performed using the complete human reference genome (GRCh37/hg19). ClinVar database was used to check the previously reported mutations and associated phenotypes. Exclusion of intronic, synonymous, inframe insertions/deletions (InDels) and mutations in untranslated regions ...