Additional file 1 of HMMvar-func: a new method for predicting the functional outcome of genetic variants

Supplementary Tables. (XLSX 323 kb

Additional file 2 of HMMvar-func: a new method for predicting the functional outcome of genetic variants

Supplementary Figures. (PDF 102 kb

Additional file 1: of Performance evaluation of indel calling tools using real short-read data

Supplementary materials for Performance evaluation of indel calling tools using real short-read data. This additional file includes List of the input samples used in this study with corresponding population and read coverage, P-value for Chi-square statistical test of indel size distribution between the tools, Distribution of indels based on lengths (1 to 10 bp) for the tools, Intra-tool comparison among GATK_HC, Dindel, SAMtools, and Platypus for percentage of their own indels called by others, Average Recall, Precision, and F-Measure of each tool for insertion and deletion, average recall and precision for each tool for different lengths of indels, Comparison between Chromosome 11 and Chromosome 20 for HG00157, and Comparison between High (~64X) and Low (~5X) coverage samples for NA12878

Image_1_Genome-wide analysis of LysM gene family members and their expression in response to Colletotrichum fructicola infection in Octoploid strawberry(Fragaria × ananassa).tif

The cultivated octoploid strawberry (Fragaria × ananassa) is an economically important fruit that is planted worldwide. The lysin motif (LysM) protein family is composed of the major class of plant pattern recognition receptors, which play important roles in sensing pathogen-associated molecular patterns (PAMPs), and subsequently triggers downstream plant immunity. In the present study, a comprehensive, genome-wide analysis of F. × ananassa LysM (FaLysM) genes was performed to investigate gene structures, phylogenic relationships, chromosome location, collinear relationships, transcription factor binding sites, and protein model analysis. We aimed to identify the LysM genes involved in the defense against plant pathogens. A total of 14 FaLysM genes were identified in the F. × ananassa genome and divided into 2 subgroups (LYP and LYK) on the basis of the phylogenetic analysis. The Ka/Ks ratio for the duplicated pair of most FaLysM genes was less than 1, which indicates that the selection pressure was mostly subject to the purifying selection during evolution. The protein model analysis revealed that FaLysM2-10 contain conserved mode of chitin binding, which suggest the potential role of FaLysM2-10 in pathogen perception and plant immunity. The RNA-Seq results showed the differential regulation of 14 FaLysM genes in response to Colletotrichum fructicola infection, implying the complex interaction between C. fructicola and strawberry. Knockout of candidate effector gene CfLysM2, which was previously proved to be highly expressed during C. fructicola infection, resulted in the up-regulation of six FaLysM genes (FaLysM1, FaLysM2, FaLysM3, FaLysM7, FaLysM8, and FaLysM12), indicating the competitive relations between CfLysM2 and FaLysM genes. Overall, this study provides fundamental information on the roles of LysM proteins in octoploid strawberry and its interaction with C. fructicola, laying useful information for further investigation on the C. fructicola-strawberry interaction and strawberry resistance breeding.</p

Table_1_Genome-wide analysis of LysM gene family members and their expression in response to Colletotrichum fructicola infection in Octoploid strawberry(Fragaria × ananassa).xls

The cultivated octoploid strawberry (Fragaria × ananassa) is an economically important fruit that is planted worldwide. The lysin motif (LysM) protein family is composed of the major class of plant pattern recognition receptors, which play important roles in sensing pathogen-associated molecular patterns (PAMPs), and subsequently triggers downstream plant immunity. In the present study, a comprehensive, genome-wide analysis of F. × ananassa LysM (FaLysM) genes was performed to investigate gene structures, phylogenic relationships, chromosome location, collinear relationships, transcription factor binding sites, and protein model analysis. We aimed to identify the LysM genes involved in the defense against plant pathogens. A total of 14 FaLysM genes were identified in the F. × ananassa genome and divided into 2 subgroups (LYP and LYK) on the basis of the phylogenetic analysis. The Ka/Ks ratio for the duplicated pair of most FaLysM genes was less than 1, which indicates that the selection pressure was mostly subject to the purifying selection during evolution. The protein model analysis revealed that FaLysM2-10 contain conserved mode of chitin binding, which suggest the potential role of FaLysM2-10 in pathogen perception and plant immunity. The RNA-Seq results showed the differential regulation of 14 FaLysM genes in response to Colletotrichum fructicola infection, implying the complex interaction between C. fructicola and strawberry. Knockout of candidate effector gene CfLysM2, which was previously proved to be highly expressed during C. fructicola infection, resulted in the up-regulation of six FaLysM genes (FaLysM1, FaLysM2, FaLysM3, FaLysM7, FaLysM8, and FaLysM12), indicating the competitive relations between CfLysM2 and FaLysM genes. Overall, this study provides fundamental information on the roles of LysM proteins in octoploid strawberry and its interaction with C. fructicola, laying useful information for further investigation on the C. fructicola-strawberry interaction and strawberry resistance breeding.</p

Table2_Smoking patients with laryngeal cancer screened with a novel immunogenomics-based prognostic signature.XLSX

The immune system greatly affects the prognosis of various malignancies. Studies on differentially expressed immune-related genes (IRGs) in the immune microenvironment of laryngeal squamous cell carcinoma (LSCC) have rarely been reported. In this paper, the prognostic potentials of IRGs were explored in LSCC patients with smoking use. The RNA-seq data containing IRGs and corresponding clinical information of smoking LSCC patients was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed IRGs were identified and functional enrichment analysis was used to reveal the pathway of IRGs. Then, IRGs with prognostic potentials in smoking LSCC patients were screened out by univariate Cox regression analysis. Finally, multivariate Cox regression analysis was conducted to assess the prognostic signature of 5 IRGs after adjustment of clinical factors and patients were classified into two subgroups based on different IRGs expression. The prognostic capacity of the model was verified by another independent cohort from Gene Expression Omnibus (GEO) database. Nomogram including the prognostic signature was established and shown some clinical net benefit. These findings may contribute to the development of potential therapeutic targets and biomarkers for the new-immunotherapy of LSCC patients with smoking use.</p

Table1_Smoking patients with laryngeal cancer screened with a novel immunogenomics-based prognostic signature.XLSX

The immune system greatly affects the prognosis of various malignancies. Studies on differentially expressed immune-related genes (IRGs) in the immune microenvironment of laryngeal squamous cell carcinoma (LSCC) have rarely been reported. In this paper, the prognostic potentials of IRGs were explored in LSCC patients with smoking use. The RNA-seq data containing IRGs and corresponding clinical information of smoking LSCC patients was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed IRGs were identified and functional enrichment analysis was used to reveal the pathway of IRGs. Then, IRGs with prognostic potentials in smoking LSCC patients were screened out by univariate Cox regression analysis. Finally, multivariate Cox regression analysis was conducted to assess the prognostic signature of 5 IRGs after adjustment of clinical factors and patients were classified into two subgroups based on different IRGs expression. The prognostic capacity of the model was verified by another independent cohort from Gene Expression Omnibus (GEO) database. Nomogram including the prognostic signature was established and shown some clinical net benefit. These findings may contribute to the development of potential therapeutic targets and biomarkers for the new-immunotherapy of LSCC patients with smoking use.</p

Table3_Smoking patients with laryngeal cancer screened with a novel immunogenomics-based prognostic signature.XLSX

The immune system greatly affects the prognosis of various malignancies. Studies on differentially expressed immune-related genes (IRGs) in the immune microenvironment of laryngeal squamous cell carcinoma (LSCC) have rarely been reported. In this paper, the prognostic potentials of IRGs were explored in LSCC patients with smoking use. The RNA-seq data containing IRGs and corresponding clinical information of smoking LSCC patients was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed IRGs were identified and functional enrichment analysis was used to reveal the pathway of IRGs. Then, IRGs with prognostic potentials in smoking LSCC patients were screened out by univariate Cox regression analysis. Finally, multivariate Cox regression analysis was conducted to assess the prognostic signature of 5 IRGs after adjustment of clinical factors and patients were classified into two subgroups based on different IRGs expression. The prognostic capacity of the model was verified by another independent cohort from Gene Expression Omnibus (GEO) database. Nomogram including the prognostic signature was established and shown some clinical net benefit. These findings may contribute to the development of potential therapeutic targets and biomarkers for the new-immunotherapy of LSCC patients with smoking use.</p

Additional file 2 of vi-HMM: a novel HMM-based method for sequence variant identification in short-read data

Commands and settings for data simulation by wgsim and variant calling by GATK HaplotypeCaller, FreeBayes, Platypus, SAMtools, and VarScan. (PDF 77 kb

Image1_Smoking patients with laryngeal cancer screened with a novel immunogenomics-based prognostic signature.TIF

The immune system greatly affects the prognosis of various malignancies. Studies on differentially expressed immune-related genes (IRGs) in the immune microenvironment of laryngeal squamous cell carcinoma (LSCC) have rarely been reported. In this paper, the prognostic potentials of IRGs were explored in LSCC patients with smoking use. The RNA-seq data containing IRGs and corresponding clinical information of smoking LSCC patients was obtained from The Cancer Genome Atlas (TCGA). Differentially expressed IRGs were identified and functional enrichment analysis was used to reveal the pathway of IRGs. Then, IRGs with prognostic potentials in smoking LSCC patients were screened out by univariate Cox regression analysis. Finally, multivariate Cox regression analysis was conducted to assess the prognostic signature of 5 IRGs after adjustment of clinical factors and patients were classified into two subgroups based on different IRGs expression. The prognostic capacity of the model was verified by another independent cohort from Gene Expression Omnibus (GEO) database. Nomogram including the prognostic signature was established and shown some clinical net benefit. These findings may contribute to the development of potential therapeutic targets and biomarkers for the new-immunotherapy of LSCC patients with smoking use.</p