Functional analysis tools for post‐translational modification: a post‐translational modification database for analysis of proteins and metabolic pathways

Plant Journal - Tập 99 Số 5 - Trang 1003-1013 - 2019
Edward R. Cruz1, Hung Nguyen2, Tin Nguyen2, Ian S. Wallace1,3
1Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, USA
2Department of Computer Science and Engineering, University of Nevada, Reno, Reno, NV, 89557 USA
3Department of Chemistry University of Nevada, Reno Reno NV 89557 USA

Tóm tắt

Summary

Post‐translational modifications (PTMs) are critical regulators of protein function, and nearly 200 different types of PTM have been identified. Advances in high‐resolution mass spectrometry have led to the identification of an unprecedented number of PTM sites in numerous organisms, potentially facilitating a more complete understanding of how PTMs regulate cellular behavior. While databases have been created to house the resulting data, most of these resources focus on individual types of PTM, do not consider quantitative PTM analyses or do not provide tools for the visualization and analysis of PTM data. Here, we describe the Functional Analysis Tools for Post‐Translational Modifications (FAT‐PTM) database (https://bioinformatics.cse.unr.edu/fat-ptm/), which currently supports eight different types of PTM and over 49 000 PTM sites identified in large‐scale proteomic surveys of the model organism Arabidopsis thaliana. The FAT‐PTM database currently supports tools to visualize protein‐centric PTM networks, quantitative phosphorylation site data from over 10 different quantitative phosphoproteomic studies, PTM information displayed in protein‐centric metabolic pathways and groups of proteins that are co‐modified by multiple PTMs. Overall, the FAT‐PTM database provides users with a robust platform to share and visualize experimentally supported PTM data, develop hypotheses related to target proteins or identify emergent patterns in PTM data for signaling and metabolic pathways.

Từ khóa


Tài liệu tham khảo

10.1016/j.pbi.2018.06.006

10.1038/nbt.4150

Bateman A., 2018, The Pfam protein families database in 2019, Nucleic Acids Res., 47, D427

10.1002/msb.201304521

10.1074/mcp.M600429-MCP200

10.1002/dvg.22877

10.1105/tpc.16.00847

Breitkreutz B.‐J., 2013, The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update, Database, 2013, bat026

10.1104/pp.15.01486

10.1093/jxb/erw107

10.1104/pp.15.00364

10.1073/pnas.0503189102

10.1002/pmic.200300777

10.1038/nature24644

10.1093/nar/gkq1159

10.1002/anie.200802336

10.1111/nph.12077

10.1104/pp.15.00026

10.1021/pr4003883

10.1093/nar/gkx1104

10.1104/pp.16.00619

Kao H.‐J., 2015, dbPTM 2016: 10‐year anniversary of a resource for post‐translational modification of proteins, Nucleic Acids Res., 44, D435

10.1016/j.molcel.2011.08.025

10.1105/tpc.112.108613

10.1038/nature17946

10.1105/tpc.18.00155

10.1016/j.plantsci.2016.04.012

10.1111/febs.14491

10.1074/mcp.T500007-MCP200

10.1074/mcp.RA117.000530

10.1105/tpc.17.00523

10.1073/pnas.1004181107

10.1074/mcp.M112.025056

10.1074/mcp.M114.043307

10.1021/pr200893k

10.1104/pp.102.017236

10.1111/j.1365-313X.2007.03192.x

10.1038/ncomms9130

10.1074/mcp.M114.040352

Rosen B.D., 2014, Araport: the Arabidopsis information portal, Nucleic Acids Res., 43, D1003

10.1038/nbt.4137

10.1105/tpc.17.00993

10.1104/pp.16.01942

10.1093/glycob/cww023

10.1074/mcp.M113.036269

10.1128/MCB.00426-18

10.1038/nbt1168

10.1016/j.pbi.2017.07.007

Via A., 2010, Phospho.ELM: a database of phosphorylation sites—update 2011, Nucleic Acids Res., 39, D261

10.1105/tpc.15.00878

10.1073/pnas.1814006115

10.1016/j.pbi.2017.05.004

10.1038/nbt.1654

10.1074/mcp.M115.056101

10.1073/pnas.1610452114

10.1093/nar/gkt1135

10.1074/mcp.RA117.000165

10.1074/mcp.M112.021220

10.1111/ppl.12763

10.1093/nar/gks1081

Thông tin
Thông tin xuất bản

Plant Journal

Tập 99 Số 5

1003-1013

Thông tin tác giả