SnapShot: Phosphoregulation of Mitosis

Burgess, Andrew; Vuong, Jenny; Rogers, Samuel; Malumbres, Marcos; O’Donoghue, Seán I.

doi:10.1016/j.cell.2017.06.003

Cited by 13 publications

(13 citation statements)

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“…Minardo can encode up to eight dimensions of data, including continuous time, subcellular location of proteins and complexes, phosphorylated residues, annotation of cellular functions, timing of reuptake and secretion of pathway products, association and disassociation of protein complexes, phosphorylation and dephosphorylation, and 2D thumbnails of protein structure. This approach has been applied to time-resolved phosphoproteomics data, providing clear and focused snapshots of dynamic signal transduction (197,198). Broad exploratory visualization of phosphoproteomics data is also a challenge, which is particularly important considering the need to explore the dark phosphoproteome.…”

Section: Visualizing the Phosphoproteomementioning

confidence: 99%

Illuminating the dark phosphoproteome

et al. 2019

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Protein phosphorylation is a major regulator of protein function and biological outcomes. This was first recognized through functional biochemical experiments, and in the past decade, major technological advances in mass spectrometry have enabled the study of protein phosphorylation on a global scale. This rapidly growing field of phosphoproteomics has revealed that more than 100,000 distinct phosphorylation events occur in human cells, which likely affect the function of every protein. Phosphoproteomics has improved the understanding of the function of even the most well-characterized protein kinases by revealing new downstream substrates and biology. However, current biochemical and bioinformatic approaches have only identified kinases for less than 5% of the phosphoproteome, and functional assignments of phosphosites are almost negligible. Notably, our understanding of the relationship between kinases and their substrates follows a power law distribution, with almost 90% of phosphorylation sites currently assigned to the top 20% of kinases. In addition, more than 150 kinases do not have a single known substrate. Despite a small group of kinases dominating biomedical research, the number of substrates assigned to a kinase does not correlate with disease relevance as determined by pathogenic human mutation prevalence and mouse model phenotypes. Improving our understanding of the substrates targeted by all kinases and functionally annotating the phosphoproteome will be broadly beneficial. Advances in phosphoproteomics technologies, combined with functional screening approaches, should make it feasible to illuminate the connectivity and functionality of the entire phosphoproteome, providing enormous opportunities for discovering new biology, therapeutic targets, and possibly diagnostics.

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Section: Visualizing the Phosphoproteomementioning

confidence: 99%

Illuminating the dark phosphoproteome

et al. 2019

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“…M phase can be further divided into prophase, metaphase, anaphase, telophase and cytokinesis [ 6 ]. For a visual review of mitotic regulation see [ 7 ]. Cells that are not actively dividing are said to be in G 0 , a resting or quiescent phase.…”

Section: Cell Divisionmentioning

confidence: 99%

Protein arginine methylation: an emerging regulator of the cell cycle

Raposo¹,

Piller²

2018

Cell Div

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Protein arginine methylation is a common post-translational modification where a methyl group is added onto arginine residues of a protein to alter detection by its binding partners or regulate its activity. It is known to be involved in many biological processes, such as regulation of signal transduction, transcription, facilitation of protein–protein interactions, RNA splicing and transport. The enzymes responsible for arginine methylation, protein arginine methyltransferases (PRMTs), have been shown to methylate or associate with important regulatory proteins of the cell cycle and DNA damage repair pathways, such as cyclin D1, p53, p21 and the retinoblastoma protein. Overexpression of PRMTs resulting in aberrant methylation patterns in cancers often correlates with poor recovery prognosis. This indicates that protein arginine methylation is also an important regulator of the cell cycle, and consequently a target for cancer regulation. The effect of protein arginine methylation on the cell cycle and how this emerging key player of cell cycle regulation may be used in therapeutic strategies for cancer are the focus of this review.

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“…Proteins are represented as tracks and phospho-events are positioned by time and subcellular location -two key variables in these experiments. This layout facilitates spatial reasoning about causal relationships, helping researchers use these complex datasets to gain insight into cellular processes, such as insulin response (83) or mitosis (84).…”

Section: Systems Biologymentioning

confidence: 99%

“…Texture is used show context, such as membranes. The online version has further interactive features (e.g., informative popups, motion, highlighting upon hover) that help researchers use these complex datasets to gain insight into cellular processes, such as insulin response (83) or mitosis (84). Image a was redrawn from http://biochemical-pathways.com/ (70), b-d were made using STRING (141), Matplotlib (115), and Minardo (https://minardo.org, 84), respectively, and modified using Illustrator.…”

Section: Figurementioning

confidence: 99%

Visualization of Biomedical Data

O’Donoghue

Baldi

Clark

et al. 2018

Preprint

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The rapid increase in volume and complexity of biomedical data requires changes in research, communication, training, and clinical practices. This includes learning how to effectively integrate automated analysis with high-data-density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including: 3D genomics, single-cell RNA-seq, the protein structure universe, phosphoproteomics, augmented-reality surgery, and metagenomics. While specific areas need highly tailored visualization tools, there are common visualization challenges that can be addressed with general methods and strategies. Unfortunately, poor visualization practices are also common; however, there are good prospects for improvements and innovations that will revolutionize how we see and think about our data. We outline initiatives aimed at fostering these improvements via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers.

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SnapShot: Phosphoregulation of Mitosis

Cited by 13 publications

References 0 publications

Illuminating the dark phosphoproteome

Illuminating the dark phosphoproteome

Protein arginine methylation: an emerging regulator of the cell cycle

Visualization of Biomedical Data

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