Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with s... more Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite ...
Background Natural variation in protein expression is common in all organisms and contributes to ... more Background Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. Results By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and identified four common inheritance patterns, including 1,133 dominant, 980 additive, 63 over- and 62 under-dominant expression. We further applied the proteogenomic approach to det...
Metabolomics is increasingly important for biomedical research, but large-scale metabolite identi... more Metabolomics is increasingly important for biomedical research, but large-scale metabolite identification in untargeted metabolomics is still challenging. Here, we present Jumbo Mass spectrometry-based Program of Metabolomics (JUMPm) software, a streamlined software tool for identifying potential metabolite formulas and structures in mass spectrometry. During database search, the false discovery rate is evaluated by a target-decoy strategy, where the decoys are produced by breaking the octet rule of chemistry. We illustrated the utility of JUMPm by detecting metabolite formulas and structures from liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses of unlabeled and stable-isotope labeled yeast samples. We also benchmarked the performance of JUMPm by analyzing a mixed sample from a commercially available metabolite library in both hydrophilic and hydrophobic LC-MS/MS. These analyses confirm that metabolite identification can be significantly improved by estimat...
Personalized cancer therapy targeting somatic mutations in patient tumors is increasingly being i... more Personalized cancer therapy targeting somatic mutations in patient tumors is increasingly being incorporated into practice. Other therapeutic vulnerabilities resulting from changes in gene expression due to tumor specific epigenetic perturbations are progressively being recognized. These genomic and epigenomic changes are ultimately manifest in the tumor proteome and phosphoproteome. We integrated transcriptomic, epigenomic, and proteomic/phosphoproteomic data to elucidate the cellular origins and therapeutic vulnerabilities of rhabdomyosarcoma (RMS). We discovered that alveolar RMS occurs further along the developmental program than embryonal RMS. We also identified deregulation of the RAS/MEK/ERK/CDK4/6, G/M, and unfolded protein response pathways through our integrated analysis. Comprehensive preclinical testing revealed that targeting the WEE1 kinase in the G/M pathway is the most effective approach in vivo for high-risk RMS.
Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However... more Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. We report a novel method for estimating the false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis and was also evaluated with two other metabolomics tools, mzMatch and MZmine 2. The reliability of FDR calculation was examined by false data sets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled to the target-decoy strategy to process unlabeled and stable-isotope-labeled metabolomic data sets. The results demonstrate that the target-decoy strategy is a simple and effective method for evalu...
Although the link between stress and alcohol is well recognized, the underlying mechanisms of how... more Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (R...
Journal of visualized experiments : JoVE, Jan 15, 2017
Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particu... more Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an extensive LC/LC-MS/MS platform, and post-MS computational interference correction to accurately quantitate whole proteomes. This protocol includes the following main steps: protein extraction and digestion, TMT labeling, 2-dimensional (2D) LC, high-resolution mass spectrometry, and computational data processing. Quality control steps are included for troubleshooting and evaluating experimental variation. More than 10,000 proteins in mammalian samples can be confidently quantitated with this protocol. This protocol can also be applied to the quantitation of post translational modifications with minor changes. This multiplexed, robu...
N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of... more N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions; hence, this modification may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation-dependent interaction between an E2 conjugating enzyme (UBE2M or UBC12) and DCN1 (DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl-amide-binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress anchorage-independent growth of a cell line with DCN1 amplification. Overall, our data demonstrate that N-te...
【Objective】Attempt to use bioinformatic tools to predict snoRNAs presence in the silkworm genome,... more 【Objective】Attempt to use bioinformatic tools to predict snoRNAs presence in the silkworm genome,and acquire its structure and distribution information【.Method】The tool SNOSCAN and our developed script were performed for prediction of Box C/D snoRNA,and the preliminary results were manually verified.【Result】70 candidate snoRNAs were identified,which were considered to guide 56 sites for methylation.Analysis of the snoRNAs’ distribution indicated that there are few snoRNA gene clusters scattered through the whole genome.Functional structures of snoRNA have also been annotated,and we found the D' boxes and terminal stems were not conserved.Moreover,it suggested that intronic snoRNAs lack canonical terminal stems(possibly compensated with the flanking sequences).Comparison of the sequences complementary to rRNAs showed the possibility that Box C/D snoRNAs contain similar complementary sequences.These guide methylation for the same type rRNAs.In addition,the homology analysis of the 70 Box C/D snoRNAs and those reported in Drosophilia melanogaster genome indicated the diversity on primary structure between the two species of animals.【Conclusion】 It is effective to predict the snoRNAs in silkworm genome based on structure feature,however,homology searching seems less helpful because of the high diversity.
The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering ... more The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering the in-depth understanding of human disease. However, sample mix-up is a pervasive problem in proteogenomics because of the complexity of sample processing. Here, we present a pipeline for Sample Matching in Proteogenomics (SMAP) to verify sample identity and ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulated data indicates that SMAP is capable of uniquely matching proteomic and genomic samples when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale dataset generated by the PsychENCODE BrainGVEX project, 54 samples (19%) were corrected. The correction was further confirmed by ribosome profiling and chromatin sequencing (ATAC-seq) data from the same set of sa...
2005 International Conference on Neural Networks and Brain, 2005
Electric arc furnaces (EAFs) represent one of the most disturbing loads in the subtransmission or... more Electric arc furnaces (EAFs) represent one of the most disturbing loads in the subtransmission or transmission electric power systems. Therefore, it is necessary to build a practical model to described the behavior of EAF in the simulation of power system for power quality issues. This EAF operation, the seemingly random arc paper deals with the modeling of EAF based on
IEEE Power Engineering Society General Meeting, 2005, 2005
DC electric arc furnace is an important nonlinear time-varying load in power system. Due to the a... more DC electric arc furnace is an important nonlinear time-varying load in power system. Due to the adverse effects produced by the operation of arc furnace, it is important to build a practical model to described the behavior of electric arc furnace. The electrical fluctuations in the arc furnace voltage have proven to be chaotic in nature. Therefore, this paper deals
Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with s... more Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite ...
Background Natural variation in protein expression is common in all organisms and contributes to ... more Background Natural variation in protein expression is common in all organisms and contributes to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. Results By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and identified four common inheritance patterns, including 1,133 dominant, 980 additive, 63 over- and 62 under-dominant expression. We further applied the proteogenomic approach to det...
Metabolomics is increasingly important for biomedical research, but large-scale metabolite identi... more Metabolomics is increasingly important for biomedical research, but large-scale metabolite identification in untargeted metabolomics is still challenging. Here, we present Jumbo Mass spectrometry-based Program of Metabolomics (JUMPm) software, a streamlined software tool for identifying potential metabolite formulas and structures in mass spectrometry. During database search, the false discovery rate is evaluated by a target-decoy strategy, where the decoys are produced by breaking the octet rule of chemistry. We illustrated the utility of JUMPm by detecting metabolite formulas and structures from liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses of unlabeled and stable-isotope labeled yeast samples. We also benchmarked the performance of JUMPm by analyzing a mixed sample from a commercially available metabolite library in both hydrophilic and hydrophobic LC-MS/MS. These analyses confirm that metabolite identification can be significantly improved by estimat...
Personalized cancer therapy targeting somatic mutations in patient tumors is increasingly being i... more Personalized cancer therapy targeting somatic mutations in patient tumors is increasingly being incorporated into practice. Other therapeutic vulnerabilities resulting from changes in gene expression due to tumor specific epigenetic perturbations are progressively being recognized. These genomic and epigenomic changes are ultimately manifest in the tumor proteome and phosphoproteome. We integrated transcriptomic, epigenomic, and proteomic/phosphoproteomic data to elucidate the cellular origins and therapeutic vulnerabilities of rhabdomyosarcoma (RMS). We discovered that alveolar RMS occurs further along the developmental program than embryonal RMS. We also identified deregulation of the RAS/MEK/ERK/CDK4/6, G/M, and unfolded protein response pathways through our integrated analysis. Comprehensive preclinical testing revealed that targeting the WEE1 kinase in the G/M pathway is the most effective approach in vivo for high-risk RMS.
Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However... more Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. We report a novel method for estimating the false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis and was also evaluated with two other metabolomics tools, mzMatch and MZmine 2. The reliability of FDR calculation was examined by false data sets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled to the target-decoy strategy to process unlabeled and stable-isotope-labeled metabolomic data sets. The results demonstrate that the target-decoy strategy is a simple and effective method for evalu...
Although the link between stress and alcohol is well recognized, the underlying mechanisms of how... more Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (R...
Journal of visualized experiments : JoVE, Jan 15, 2017
Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particu... more Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an extensive LC/LC-MS/MS platform, and post-MS computational interference correction to accurately quantitate whole proteomes. This protocol includes the following main steps: protein extraction and digestion, TMT labeling, 2-dimensional (2D) LC, high-resolution mass spectrometry, and computational data processing. Quality control steps are included for troubleshooting and evaluating experimental variation. More than 10,000 proteins in mammalian samples can be confidently quantitated with this protocol. This protocol can also be applied to the quantitation of post translational modifications with minor changes. This multiplexed, robu...
N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of... more N-terminal acetylation is an abundant modification influencing protein functions. Because ∼80% of mammalian cytosolic proteins are N-terminally acetylated, this modification is potentially an untapped target for chemical control of their functions. Structural studies have revealed that, like lysine acetylation, N-terminal acetylation converts a positively charged amine into a hydrophobic handle that mediates protein interactions; hence, this modification may be a druggable target. We report the development of chemical probes targeting the N-terminal acetylation-dependent interaction between an E2 conjugating enzyme (UBE2M or UBC12) and DCN1 (DCUN1D1), a subunit of a multiprotein E3 ligase for the ubiquitin-like protein NEDD8. The inhibitors are highly selective with respect to other protein acetyl-amide-binding sites, inhibit NEDD8 ligation in vitro and in cells, and suppress anchorage-independent growth of a cell line with DCN1 amplification. Overall, our data demonstrate that N-te...
【Objective】Attempt to use bioinformatic tools to predict snoRNAs presence in the silkworm genome,... more 【Objective】Attempt to use bioinformatic tools to predict snoRNAs presence in the silkworm genome,and acquire its structure and distribution information【.Method】The tool SNOSCAN and our developed script were performed for prediction of Box C/D snoRNA,and the preliminary results were manually verified.【Result】70 candidate snoRNAs were identified,which were considered to guide 56 sites for methylation.Analysis of the snoRNAs’ distribution indicated that there are few snoRNA gene clusters scattered through the whole genome.Functional structures of snoRNA have also been annotated,and we found the D' boxes and terminal stems were not conserved.Moreover,it suggested that intronic snoRNAs lack canonical terminal stems(possibly compensated with the flanking sequences).Comparison of the sequences complementary to rRNAs showed the possibility that Box C/D snoRNAs contain similar complementary sequences.These guide methylation for the same type rRNAs.In addition,the homology analysis of the 70 Box C/D snoRNAs and those reported in Drosophilia melanogaster genome indicated the diversity on primary structure between the two species of animals.【Conclusion】 It is effective to predict the snoRNAs in silkworm genome based on structure feature,however,homology searching seems less helpful because of the high diversity.
The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering ... more The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering the in-depth understanding of human disease. However, sample mix-up is a pervasive problem in proteogenomics because of the complexity of sample processing. Here, we present a pipeline for Sample Matching in Proteogenomics (SMAP) to verify sample identity and ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulated data indicates that SMAP is capable of uniquely matching proteomic and genomic samples when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale dataset generated by the PsychENCODE BrainGVEX project, 54 samples (19%) were corrected. The correction was further confirmed by ribosome profiling and chromatin sequencing (ATAC-seq) data from the same set of sa...
2005 International Conference on Neural Networks and Brain, 2005
Electric arc furnaces (EAFs) represent one of the most disturbing loads in the subtransmission or... more Electric arc furnaces (EAFs) represent one of the most disturbing loads in the subtransmission or transmission electric power systems. Therefore, it is necessary to build a practical model to described the behavior of EAF in the simulation of power system for power quality issues. This EAF operation, the seemingly random arc paper deals with the modeling of EAF based on
IEEE Power Engineering Society General Meeting, 2005, 2005
DC electric arc furnace is an important nonlinear time-varying load in power system. Due to the a... more DC electric arc furnace is an important nonlinear time-varying load in power system. Due to the adverse effects produced by the operation of arc furnace, it is important to build a practical model to described the behavior of electric arc furnace. The electrical fluctuations in the arc furnace voltage have proven to be chaotic in nature. Therefore, this paper deals
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Papers by Xusheng Wang