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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  ...  These two processes are interdependent and together are responsible for the function of the protein in a particular cell state.  ...  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.  ...  Comparison with existing methods further suggests that co-occurrence analysis can be a useful complement to uncover novel functional associations between PTM sites.  ...  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

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 apologize for not being able to cite several relevant papers on this topic due to space constraints. 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

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 describe for the first time a general scenario of PTM types and genetic diseases direct associations, many of them novel, that provides new capacities to understand and diagnose these disorders.  ...  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