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PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Pablo Minguez, Ivica Letunic, Luca Parca, Peer Bork
2012 Nucleic Acids Research  
Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins.  ...  In its first release, PTMcode provides PTM functional associations of 13 different PTM types within proteins in 8 eukaryotes.  ...  ACKNOWLEDGEMENTS We thank Yan Yuan for all his help and support on all technical and infrastructure issues we encountered during this project.  ... 
doi:10.1093/nar/gks1230 pmid:23193284 pmcid:PMC3531129 fatcat:xh5bppkb5jgubiknp37u47izzq

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Pablo Minguez, Ivica Letunic, Luca Parca, Luz Garcia-Alonso, Joaquin Dopazo, Jaime Huerta-Cepas, Peer Bork
2014 Nucleic Acids Research  
We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting  ...  Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein posttranslational modifications (PTMs), however, there  ...  ACKNOWLEDGEMENT We thank Yan Yuan for all his help and support on all technical and infrastructure issues we encountered during this project.  ... 
doi:10.1093/nar/gku1081 pmid:25361965 pmcid:PMC4383916 fatcat:43c5ecunjrb5lnztwjyqeqcglm

Co-occurring protein phosphorylation are functionally associated

Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li, Predrag Radivojac
2017 PLoS Computational Biology  
Post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions.  ...  Co-occurring phosphorylation occurs significantly more frequently than randomly expected and include many known examples of cross-talk or functional connections.  ...  Torsten Juelich (Peking University, China) for critical reading and editing the draft version of this manuscript. Visualization: YL XZ. Writing -original draft: TL YL XZ.  ... 
doi:10.1371/journal.pcbi.1005502 pmid:28459814 pmcid:PMC5432191 fatcat:ovcvlmfjmjhknjupa35f22o34i

Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases

Suruchi Aggarwal, Sanjay K. Banerjee, Narayan Chandra Talukdar, Amit Kumar Yadav
2020 Frontiers in Genetics  
The protein post-translational modifications (PTMs) are known to crosstalk among each other to bring about complex phenotypic outcomes.  ...  We observed that a large proportion of disease-associated sequence variants were found in PTM motifs of CVD proteins.  ...  FIGURE 6 | 6 Post-translational modification and crosstalk hotspots in sirtuin interactors. (A) Frequency of proteins in each hotspot bin.  ... 
doi:10.3389/fgene.2020.00356 pmid:32425973 pmcid:PMC7204943 fatcat:7h4n3lyl65h37bpglpjux6q4c4

Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer [article]

Marzieh Ayati, Mark R Chance, Mehmet Koyuturk
2020 biorxiv/medrxiv   pre-print
Motivation: Protein phosphorylation is a ubiquitous mechanism of post-translational modification that plays a central role in cellular signaling.  ...  For this purpose, we integrate prior knowledge on evolutionary, structural, and functional association of phosphosites, kinase-substrate associations, and protein-protein interactions with the correlation  ...  Funding This work was supported in part by US National Institute of Health (NIH) awards R01-LM012980, R01-GM117208 and P30CA043703.  ... 
doi:10.1101/2020.05.04.073148 fatcat:n4uhcja4xrhczoa6fozhfbveie

ProteomeScout: a repository and analysis resource for post-translational modifications and proteins

Matthew K. Matlock, Alex S. Holehouse, Kristen M. Naegle
2014 Nucleic Acids Research  
ProteomeScout (https://proteomescout.wustl.edu) is a resource for the study of proteins and their posttranslational modifications (PTMs) consisting of a database of PTMs, a repository for experimental  ...  These annotations are available in the database download, in the analysis tools and in the protein viewer.  ...  ProteomeScout relies entirely on open-source software and publicly available data. We are immensely grateful to the design, maintenance and distribution of these projects and data.  ... 
doi:10.1093/nar/gku1154 pmid:25414335 pmcid:PMC4383955 fatcat:n7plui5sgnc2nf2dsywwyx463y

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
a primary repository for smallangle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular  ...  The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

SysPTM 2.0: an updated systematic resource for post-translational modification

J. Li, J. Jia, H. Li, J. Yu, H. Sun, Y. He, D. Lv, X. Yang, M. O. Glocker, L. Ma, J. Yang, L. Li (+5 others)
2014 Database: The Journal of Biological Databases and Curation  
Post-translational modifications (PTMs) of proteins play essential roles in almost all cellular processes, and are closely related to physiological activity and disease development of living organisms.  ...  SysPTM 2.0: an updated systematic resource for post-translational modification.  ...  Acknowledgements The authors would like to acknowledge all the developers of databases mentioned and referenced, thanks to their previous work and sharing their data.  ... 
doi:10.1093/database/bau025 pmid:24705204 pmcid:PMC3975108 fatcat:bhiaq7f275fjvjqp6jmyc6ahoy

PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis

Payman Nickchi, Mohieddin Jafari, Shiva Kalantari
2015 Database: The Journal of Biological Databases and Curation  
Conventional proteomics has discovered a wide gap between protein sequences and biological functions. The third generation of proteomics was provoked to bridge this gap.  ...  Targeted and untargeted post-translational modification (PTM) studies are the most important parts of today's proteomics.  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/bav037 pmid:25911152 pmcid:PMC4408379 fatcat:tuk3pzhvbfd2howlfupczhmjhq

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
2018 International Journal of Molecular Sciences  
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation  ...  PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques  ...  The authors would like to thank Alison Rodger for the critical reviewing and editing of the manuscript. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms20010016 fatcat:3m4rsyjl4zgwtprkz65ydbrhpa

Dysregulation of USP18/FTO/PYCR1 signaling network promotes bladder cancer development and progression

Wei Song, Ke Yang, Jianjun Luo, Zhiyong Gao, Yunliang Gao
2021 Aging  
In this study, we demonstrated that the post-translational deubiquitination by USP18 up-regulates the protein but not mRNA of FTO in bladder cancer tissues and cells.  ...  N6-methyladenosine refers to a methylation of adenosine base at the 6th nitrogen position, which is the dominant methylation modification in both message and non-coding RNAs.  ...  USP-18 promotes FTO protein stability by inhibiting proteasomal degradation An increase in protein but not mRNA level was reminiscent of post-translational modification of FTO in bladder tumors.  ... 
doi:10.18632/aging.202359 pmid:33461172 pmcid:PMC7906198 fatcat:3kaha3c4sfddbhvdw47gxxkmym

Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk

Yuanhua Huang, Bosen Xu, Xueya Zhou, Ying Li, Ming Lu, Rui Jiang, Tingting Li
2015 Molecular & Cellular Proteomics  
Post-translational modification (PTM) 1 plays an important role in regulating the functions of proteins.  ...  PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM crosstalk.  ...  Pedro Beltrao and Dr. Oliver Stegle for fruitful discussions and useful comments in developing the methods. Furthermore, we express our gratitude to Justin Chu, Dr. Xi Wang, Dr.  ... 
doi:10.1074/mcp.m114.037994 pmid:25605461 pmcid:PMC4349993 fatcat:hw5jfqodf5ajdposyefedvx2vy

Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer

Natasha S. Latysheva, Matt E. Oates, Louis Maddox, Tilman Flock, Julian Gough, Marija Buljan, Robert J. Weatheritt, M. Madan Babu
2016 Molecular Cell  
Fusion often results in the loss of these parental features and the depletion of regulatory sites such as post-translational modifications.  ...  We suggest that the deregulation of central, interaction-prone proteins may represent a widespread mechanism by which fusion proteins alter the topology of cellular signaling pathways and promote cancer  ...  We have extensively discussed a number of important papers in Latysheva and Babu (2016) .  ... 
doi:10.1016/j.molcel.2016.07.008 pmid:27540857 pmcid:PMC5003813 fatcat:gs4uwqm7ybdzvdkldcyke2ihq4

Advances on Plant Ubiquitylome—From Mechanism to Application

Dongli He, Rebecca Njeri Damaris, Ming Li, Imran Khan, Pingfang Yang
2020 International Journal of Molecular Sciences  
Post-translational modifications (PTMs) of proteins enable modulation of their structure, function, localization and turnover.  ...  This obtained information on a large number of ubiquitylated proteins/sites helps crack the mechanism of ubiquitylation in plants.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms21217909 pmid:33114409 fatcat:zlhoe7zttfds3d7dzsyrlndj6e

A global map of the impact of deletion of Post-Translational Modification sites in genetic diseases [article]

Perceval Vellosillo, Pablo Minguez
2020 bioRxiv   pre-print
There are >200 protein post-translational modifications (PTMs) types described in eukaryotes, having diverse species conservation levels, proteome coverage, number of high-throughput experiments and functional  ...  We report >1.74M PTM-variant concurrences in >16,500 proteins that an enrichment analysis distributed in 217 pairwise significant associations between 18 PTM types and 150 genetic diseases.  ...  We also thank IIS-FJD and ISCIII for their support and the RAREGenomics network for providing a forum of discussion. Funding  ... 
doi:10.1101/2020.12.20.423666 fatcat:usoyxwj3cjdq7krapliwqeoeni
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