The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
Open accessAbstract
PhosphoSitePlus (http://www.phosphosite.org) is an open, comprehensive, manually curated and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses 1,30,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The interface is designed for clarity and ease of navigation. From the home page, users can launch simple or complex searches and browse high-throughput data sets by disease, tissue or cell line. Searches can be restricted by specific treatments, protein types, domains, cellular components, disease, cell types, cell lines, tissue and sequences or motifs. A few clicks of the mouse will take users to substrate pages or protein pages with sites, sequences, domain diagrams and molecular visualization of side-chains known to be modified; to site pages with information about how the modified site relates to the functions of specific proteins and cellular processes and to curated information pages summarizing the details from one record. PyMOL and Chimera scripts that colorize reactive groups on residues that are modified can be downloaded. Features designed to facilitate proteomic analyses include downloads of modification sites, kinase-substrate data sets, sequence logo generators, a Cytoscape plugin and BioPAX download to enable pathway visualization of the kinase-substrate interactions in PhosphoSitePlus®.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
The Pfam protein families database
Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694
Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · cited 1×
“The Downloadable Data set section provides downloads of six different modi-fication type data sets, an archive of all protein sequences in PSP and the PSP Kinase-Substrate data set in three formats: a tab-delimited text file, a Cytoscape Plugin (36) and a file in BioPAX (37) format.”
MethodSelf-citation
Cited by
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V., & Skrzypek, E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1267 · Cited by 3,411
Self-citationUncovering disease-disease relationships through the incomplete interactome
Menche, J., Sharma, A., Kitsak, M., Ghiassian, S. D., Vidal, M., Loscalzo, J., & Barabási, A.-L. (2015) · Science · doi:10.1126/science.1257601 · Cited by 1,546
Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide
Fischer, E. S., Böhm, K., Lydeard, J. R., Yang, H., Stadler, M. B., Cavadini, S., Nagel, J., Serluca, F., Acker, V., Lingaraju, G. M., et al. (2014) · Nature · doi:10.1038/nature13527 · Cited by 1,141
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Gillette, M. A., Satpathy, S., Cao, S., Dhanasekaran, S. M., Vasaikar, S. V., Krug, K., Petralia, F., Li, Y., Liang, W.-W., Reva, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.013 · Cited by 820
Self-citationmTOR regulates MAPKAPK2 translation to control the senescence-associated secretory phenotype
Herranz, N., Gallage, S., Mellone, M., Wuestefeld, T., Klotz, S., Hanley, C. J., Raguz, S., Acosta, J. C., Innes, A. J., Banito, A., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3225 · Cited by 788
D2P2: database of disordered protein predictions
Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1226 · Cited by 705
Regulation of RAF protein kinases in ERK signalling
Lavoie, H., & Therrien, M. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3979 · Cited by 702
Network-based in silico drug efficacy screening
Guney, E., Menche, J., Vidal, M., & Barábasi, A.-L. (2016) · Nature Communications · doi:10.1038/ncomms10331 · Cited by 625
Therapeutic opportunities within the DNA damage response
Pearl, L. H., Schierz, A. C., Ward, S. E., Al-Lazikani, B., & Pearl, F. M. G. (2015) · Nature Reviews Cancer · doi:10.1038/nrc3891 · Cited by 587
Morris, M., Knudsen, G. M., Maeda, S., Trinidad, J. C., Ioanoviciu, A., Burlingame, A. L., & Mucke, L. (2015) · Nature Neuroscience · doi:10.1038/nn.4067 · Cited by 472
Non-histone protein methylation as a regulator of cellular signalling and function
Biggar, K. K., & Li, S. S.-C. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3915 · Cited by 479
Impact of regulatory variation from RNA to protein
Battle, A., Khan, Z., Wang, S. H., Mitrano, A., Ford, M. J., Pritchard, J. K., & Gilad, Y. (2015) · Science · doi:10.1126/science.1260793 · Cited by 471
Hoffman, N. J., Parker, B. L., Chaudhuri, R., Fisher-Wellman, K. H., Kleinert, M., Humphrey, S. J., Yang, P., Holliday, M., Trefely, S., Fazakerley, D. J., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.09.001 · Cited by 426
Pejaver, V., Hsu, W., Xin, F., Dunker, A. K., Uversky, V. N., & Radivojac, P. (2014) · Protein Science · doi:10.1002/pro.2494 · Cited by 349
SIRT4 is a lysine deacylase that controls leucine metabolism and insulin secretion
Anderson, K. A., Huynh, F. K., Fisher-Wellman, K., Stuart, J. D., Peterson, B. S., Douros, J. D., Wagner, G. R., Thompson, J. W., Madsen, A. S., Green, M. F., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.03.003 · Cited by 326
“Our proteomic analysis of MCCC identified acetylation sites dispersed throughout the a subunit (Figure 4E), consistent with previous findings (Hornbeck et al., 2012).”
ResultThe WAVE regulatory complex links diverse receptors to the actin cytoskeleton
Chen, B., Brinkmann, K., Chen, Z., Pak, C. W., Liao, Y., Shi, S., Henry, L., Grishin, N. V., Bogdan, S., & Rosen, M. K. (2014) · Cell · doi:10.1016/j.cell.2013.11.048 · Cited by 323
Molecular Basis of Tubulin Transport Within the Cilium by IFT74 and IFT81
Bhogaraju, S., Cajanek, L., Fort, C., Blisnick, T., Weber, K., Taschner, M., Mizuno, N., Lamla, S., Bastin, P., Nigg, E. A., et al. (2013) · Science · doi:10.1126/science.1240985 · Cited by 317
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082873 · Cited by 280
Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers
Yugi, K., Kubota, H., Hatano, A., & Kuroda, S. (2016) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.12.013 · Cited by 258
Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling
Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265
Regulation of transcription factor activity by interconnected post-translational modifications
Filtz, T. M., Vogel, W. K., & Leid, M. (2014) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2013.11.005 · Cited by 242
Hafner, M., Mills, C. E., Subramanian, K., Chen, C., Chung, M., Boswell, S. A., Everley, R. A., Liu, C., Walmsley, C. S., Juric, D., et al. (2019) · Cell Chemical Biology · doi:10.1016/j.chembiol.2019.05.005 · Cited by 250
Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures
Khan, Z., Ford, M. J., Cusanovich, D. A., Mitrano, A., Pritchard, J. K., & Gilad, Y. (2013) · Science · doi:10.1126/science.1242379 · Cited by 240
Cavin family proteins and the assembly of caveolae
Kovtun, O., Tillu, V. A., Ariotti, N., Parton, R. G., & Collins, B. M. (2015) · Journal of Cell Science · doi:10.1242/jcs.167866 · Cited by 230
V'kovski, P., Gerber, M., Kelly, J., Pfaender, S., Ebert, N., Braga Lagache, S., Simillion, C., Portmann, J., Stalder, H., Gaschen, V., et al. (2019) · eLife · doi:10.7554/elife.42037 · Cited by 186
Poly-ubiquitination in TNFR1-mediated necroptosis
Dondelinger, Y., Darding, M., Bertrand, M. J. M., & Walczak, H. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2191-4 · Cited by 173
Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
Yang, P., Humphrey, S. J., Cinghu, S., Pathania, R., Oldfield, A. J., Kumar, D., Perera, D., Yang, J. Y. H., James, D. E., Mann, M., et al. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.012 · Cited by 146
Albanese, A., Daly, L. A., Mennerich, D., Kietzmann, T., & Sée, V. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms22010268 · Cited by 136
Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle
Hochegger, H., Hégarat, N., & Pereira-Leal, J. B. (2013) · Open Biology · doi:10.1098/rsob.120185 · Cited by 112
A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells*
Stuart, S. A., Houel, S., Lee, T., Wang, N., Old, W. M., & Ahn, N. G. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047233 · Cited by 116
Site-specific incorporation of phosphotyrosine using an expanded genetic code
Hoppmann, C., Wong, A., Yang, B., Li, S., Hunter, T., Shokat, K. M., & Wang, L. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2406 · Cited by 112
PICALM and Alzheimer’s Disease: An Update and Perspectives
Ando, K., Nagaraj, S., Küçükali, F., de Fisenne, M.-A., Kosa, A.-C., Doeraene, E., Lopez Gutierrez, L., Brion, J.-P., & Leroy, K. (2022) · Cells · doi:10.3390/cells11243994 · Cited by 104
McDermott, J. E., Arshad, O. A., Petyuk, V. A., Fu, Y., Gritsenko, M. A., Clauss, T. R., Moore, R. J., Schepmoes, A. A., Zhao, R., Monroe, M. E., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2020.100004 · Cited by 97
Self-citationPP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis
Wu, C.-G., Chen, H., Guo, F., Yadav, V. K., Mcilwain, S. J., Rowse, M., Choudhary, A., Lin, Z., Li, Y., Gu, T., et al. (2017) · Cell Discovery · doi:10.1038/celldisc.2017.27 · Cited by 85
Motifs of VDAC2 required for mitochondrial Bak import and tBid-induced apoptosis
Naghdi, S., Várnai, P., & Hajnóczky, G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510574112 · Cited by 96
Richter, E., Ventz, K., Harms, M., Mostertz, J., & Hochgräfe, F. (2016) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2016.00021 · Cited by 75
“…number of records in which the modification was determined using site-specific methods or by proteomic discovery-mode mass spectrometry indicating that the enrichment strategy increased the sensitivity of detection of modified kinase-derived peptides with mass spectrometry (Hornbeck et al., 2012).”
MethodResultIKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data
Mischnik, M., Sacco, F., Cox, J., Schneider, H.-C., Schäfer, M., Hendlich, M., Crowther, D., Mann, M., & Klabunde, T. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv699 · Cited by 75
The UPS and downs of cholesterol homeostasis
Sharpe, L. J., Cook, E. C. L., Zelcer, N., & Brown, A. J. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.08.008 · Cited by 74
De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens
He, W., Zhang, L., Villarreal, O. D., Fu, R., Bedford, E., Dou, J., Patel, A. Y., Bedford, M. T., Shi, X., Chen, T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12489-8 · Cited by 69
Footprint-based functional analysis of multiomic data
Dugourd, A., & Saez-Rodriguez, J. (2019) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2019.04.002 · Cited by 53
Kauko, O., Laajala, T. D., Jumppanen, M., Hintsanen, P., Suni, V., Haapaniemi, P., Corthals, G., Aittokallio, T., Westermarck, J., & Imanishi, S. Y. (2015) · Scientific Reports · doi:10.1038/srep13099 · Cited by 61
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer
Narayan, S., Bader, G. D., & Reimand, J. (2016) · Genome Medicine · doi:10.1186/s13073-016-0311-2 · Cited by 54
“Acetylation and ubiquitination sites for human proteins were retrieved from the PhosphoSitePlus database (retrieved 2013-05-23) [22] and filtered to only keep data from peer-reviewed publications.”
MethodA review of small-molecule inhibitors of one-carbon enzymes: SHMT2 and MTHFD2 in the spotlight
Cuthbertson, C. R., Arabzada, Z., Bankhead, A., Kyani, A., & Neamati, N. (2021) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.0c00223 · Cited by 57
Sviderskiy, V. O., Blumenberg, L., Gorodetsky, E., Karakousi, T. R., Hirsh, N., Alvarez, S. W., Terzi, E. M., Kaparos, E., Whiten, G. C., Ssebyala, S., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.10.016 · Cited by 56
Goliath family E3 ligases regulate the recycling endosome pathway via VAMP3 ubiquitylation
Yamazaki, Y., Schönherr, C., Varshney, G. K., Dogru, M., Hallberg, B., & Palmer, R. H. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.1 · Cited by 55
Afroz, S., Giddaluru, J., Vishwakarma, S., Naz, S., Khan, A. A., & Khan, N. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00074 · Cited by 50
Mitochondrial phosphoproteomes are functionally specialized across tissues
Hansen, F. M., Kremer, L. S., Karayel, O., Bludau, I., Larsson, N.-G., Kühl, I., & Mann, M. (2024) · Life Science Alliance · doi:10.26508/lsa.202302147 · Cited by 29
Rechkunova, N. I., Maltseva, E. A., & Lavrik, O. I. (2019) · Biochemistry (Moscow) · doi:10.1134/s0006297919090037 · Cited by 15
Tsumagari, K., Sato, Y., Shimozawa, A., Aoyagi, H., Okano, H., & Kuromitsu, J. (2022) · iScience · doi:10.1016/j.isci.2022.104832 · Cited by 15
Fendler, N. L., Ly, J., Welp, L., Lu, D., Schulte, F., Urlaub, H., & Vos, S. M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1273 · Cited by 12
Crowl, S., Coleman, M. B., Chaphiv, A., Jordan, B. T., & Naegle, K. M. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101318 · Cited by 10
Sittipongpittaya, N., Skinner, K. A., Jeffery, E. D., Watts, E. F., & Sheynkman, G. M. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00978 · Cited by 10
Crowgey, E. L., Matlock, A., Venkatraman, V., Fert-Bober, J., & Van Eyk, J. E. (2017) · Methods in Molecular Biology · doi:10.1007/978-1-4939-6783-4_19 · Cited by 9
Singer, A., Ramos, A., & Keating, A. E. (2024) · Protein Science · doi:10.1002/pro.5094 · Cited by 6
Dhulipala, S., & Uversky, V. N. (2022) · Biomolecules · doi:10.3390/biom12101436 · Cited by 6
Vaparanta, K., Merilahti, J. A. M., Ojala, V. K., & Elenius, K. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100780 · Cited by 3
Metadata
- Authors
- Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B., Latham, V., & Sullivan, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-12-01
- Volume
- 40
- Issue
- D1
- Pages
- D261-D270
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2157658519
- Cited by
- 1,646
- References
- 4
- FWCI
- 59.91
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
