motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs

Wang, Shisheng; Cai, Yuanqiang; Cheng, Jingqiu; Li, Wenxue; Liu, Yansheng; Yang, Hao

doi:10.1002/pmic.201900245

Cited by 29 publications

(33 citation statements)

References 20 publications

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“…a relative fold change of 1.5 folds) were considered to be differentially expressed. The PTM motif enrichment analysis of differentially regulated phosphosites was performed with motifeR ( 72 ), using the comparison between first three samples (according their actual acquisition time which is random in each group) and the ‘Gold Standard’ result.…”

Section: Methodsmentioning

confidence: 99%

NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses

Wang

et al. 2020

Nucleic Acids Research

Self Cite

102

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Mass spectrometry (MS)-based quantitative proteomics experiments frequently generate data with missing values, which may profoundly affect downstream analyses. A wide variety of imputation methods have been established to deal with the missing-value issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for proteomics community. Herein, we developed a user-friendly and powerful stand-alone software, NAguideR, to enable implementation and evaluation of different missing value methods offered by 23 widely used missing-value imputation algorithms. NAguideR further evaluates data imputation results through classic computational criteria and, unprecedentedly, proteomic empirical criteria, such as quantitative consistency between different charge-states of the same peptide, different peptides belonging to the same proteins, and individual proteins participating protein complexes and functional interactions. We applied NAguideR into three label-free proteomic datasets featuring peptide-level, protein-level, and phosphoproteomic variables respectively, all generated by data independent acquisition mass spectrometry (DIA-MS) with substantial biological replicates. The results indicate that NAguideR is able to discriminate the optimal imputation methods that are facilitating DIA-MS experiments over those sub-optimal and low-performance algorithms. NAguideR further provides downloadable tables and figures supporting flexible data analysis and interpretation. NAguideR is freely available at http://www.omicsolution.org/wukong/NAguideR/ and the source code: https://github.com/wangshisheng/NAguideR/.

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Section: Methodsmentioning

confidence: 99%

NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses

Wang

et al. 2020

Nucleic Acids Research

Self Cite

102

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“…Motif analyses. Motif enrichment was performed in R using the motifeR package (55). We used default settings including a 14 amino acid window size for the analysis.…”

Section: Methodsmentioning

confidence: 99%

Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states

Song

Olatunji

Montes

et al. 2021

Preprint

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Protein activity, abundance, and stability can be regulated by posttranslational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function and yet we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich peptides containing the di-glycine (diGly) remnant of ubiquitin and coupled that with isobaric labeling to enable quantification, from up to 16-multiplexed samples, for plant tissues. Collectively, we identified 7,130 diGly-modified lysine residues sites arising from 3,178 proteins in Arabidopsis primary roots. These data include ubiquitin proteasome dependent ubiquitination events as well as ubiquitination events associated with auxin treatment. Gene Ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and root morphogenesis. We determined the ubiquitinated lysine residues that directly regulate the stability of the transcription factors CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY (STOP1) using site directed mutagenesis and in vivo degradation assays. These comprehensive site-level ubiquitinome profiles provide a wealth of data for future studies related to modulation of biological processes mediated by this posttranslational modification in plants.

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“…Motif enrichment was performed using the motifeR R package (Wang et al, 2019) with default settings, serine or threonine as the central residues, a p-value threshold of 0.001, and TAIR10 protein annotation as background reference. Enrichment p-value was calculated using hypergeometric testing.…”

Section: Methodsmentioning

confidence: 99%

Interplay between brassinosteroids and TORC signaling in Arabidopsis revealed by integrated multi-dimensional analysis

Montes

Liao

Nolan

et al. 2021

Preprint

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Brassinosteroids (BR) and Target of Rapamycin Complex (TORC) are two major processes coordinating plant growth and stress responses. BRs function through a signaling pathway to extensively regulate gene expression and TORC is known to regulate translation and autophagy. Recent studies revealed that these two pathways crosstalk, but a system-wide view of their interplay is still missing. Thus, we performed transcriptome, proteome, and phosphoproteome profiling of Arabidopsis mutants with altered levels of either BIN2 or RAPTOR1B, two key players in BR and TORC signaling, respectively. We found that perturbation of BIN2 or RAPTOR1B levels affects a common set of gene-products involved in growth and stress responses. Additionally, we performed Multiplexed Assay for Kinase Specificity (MAKS), which provided a system-wide view of direct BIN2 substrates. Furthermore, phosphoproteomic data was used to reconstruct a kinase-signaling network and to identify novel proteins dependent on BR and/or TORC signaling pathways. Loss of function mutants of many of these proteins led to an altered BR response and/or modulated autophagy activity. Altogether, these results provide genome-wide evidence for crosstalk between BR and TORC signaling and established a kinase signaling network that defines the molecular mechanisms of BR and TORC interactions in the regulation of plant growth/stress balance.

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motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs

Cited by 29 publications

References 20 publications

NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses

NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses

Quantitative proteomics reveals extensive lysine ubiquitination in the Arabidopsis root proteome and uncovers novel transcription factor stability states

Interplay between brassinosteroids and TORC signaling in Arabidopsis revealed by integrated multi-dimensional analysis

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