{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T09:38:26Z","timestamp":1777455506916,"version":"3.51.4"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,18]],"date-time":"2019-07-18T00:00:00Z","timestamp":1563408000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University","award":["RA61\/103"],"award-info":[{"award-number":["RA61\/103"]}]},{"name":"Division of Intramural Research of the NHLBI"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["HL-001285"],"award-info":[{"award-number":["HL-001285"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["HL-006129"],"award-info":[{"award-number":["HL-006129"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ratchadapisek Somphot Fund for Postdoctoral Fellowship"},{"DOI":"10.13039\/501100002873","name":"Chulalongkorn University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002873","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chulalongkorn Academic Advancement into Its 2nd Century (CUAASC) Project"},{"DOI":"10.13039\/501100004396","name":"Thailand Research Fund","doi-asserted-by":"publisher","award":["RSA6280026"],"award-info":[{"award-number":["RSA6280026"]}],"id":[{"id":"10.13039\/501100004396","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized \u2018background\u2019 set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences (\u2018logos\u2019) based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PTM-Logo is freely available online at http:\/\/sysbio.chula.ac.th\/PTMLogo\/ or https:\/\/hpcwebapps.cit.nih.gov\/PTMLogo\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz568","type":"journal-article","created":{"date-parts":[[2019,7,16]],"date-time":"2019-07-16T11:09:23Z","timestamp":1563275363000},"page":"5313-5314","source":"Crossref","is-referenced-by-count":14,"title":["PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities"],"prefix":"10.1093","volume":"35","author":[{"given":"Thammakorn","family":"Saethang","sequence":"first","affiliation":[{"name":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"},{"name":"Department of Computer Science, Kasetsart University , Bangkok, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth","family":"Hodge","sequence":"additional","affiliation":[{"name":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chin-Rang","family":"Yang","sequence":"additional","affiliation":[{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Zhao","sequence":"additional","affiliation":[{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingorn","family":"Kimkong","sequence":"additional","affiliation":[{"name":"Department of Microbiology , Faculty of Science, Kasetsart University, Bangkok, Thailand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark A","family":"Knepper","sequence":"additional","affiliation":[{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Trairak","family":"Pisitkun","sequence":"additional","affiliation":[{"name":"Center of Excellence in Systems Biology , Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"},{"name":"Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health , Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,18]]},"reference":[{"key":"2023013108384659300_btz568-B1","doi-asserted-by":"crossref","first-page":"e82655","DOI":"10.1371\/journal.pone.0082655","article-title":"Endogenous carbamylation of renal medullary proteins","volume":"8","author":"Claxton","year":"2013","journal-title":"PLoS One"},{"key":"2023013108384659300_btz568-B2","doi-asserted-by":"crossref","first-page":"C715","DOI":"10.1152\/ajpcell.00166.2012","article-title":"Identifying protein kinase target preferences using mass spectrometry","volume":"303","author":"Douglass","year":"2012","journal-title":"Am. 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