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iPTMnet: an integrated resource for protein post-translational modification network discovery

Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
2017 Nucleic Acids Research  
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function.  ...  Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby  ...  ACKNOWLEDGEMENTS We would like to thank all data sources in iPTMnet for providing such valuable data to our resource.  ... 
doi:10.1093/nar/gkx1104 pmid:29145615 pmcid:PMC5753337 fatcat:37boketufrdphgpohb4wmqzily

piNET: a versatile web platform for downstream analysis and visualization of proteomics data [article]

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Dusica Vidovic, Vagisha Sharma, Juozas Vasiliauskas (+8 others)
2019 bioRxiv   pre-print
Computational methods and tools to identify and quantify peptides, proteins and post-translational modifications (PTMs) that are captured in modern mass spectrometers have matured over the years.  ...  Building on our experience with large scale analysis of gene and protein expression profiles as part of the Library of Integrated Network Cellular Signatures (LINCS) project, piNET has been designed as  ...  As illustrated in Figure 1 , piNET integrates iPTMnet (Protein Information Resource), PhosphositePlus, SIGNOR, and other proteomic resources with pathway and PTM network analysis, while making use of  ... 
doi:10.1101/607432 fatcat:d5yluyxpyfbpzoqksczhun3zwe

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Liang-Chin Huang, Karen E. Ross, Timothy R. Baffi, Harold Drabkin, Krzysztof J. Kochut, Zheng Ruan, Peter D'Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A. Natale, Cynthia Smith (+4 others)
2018 Scientific Reports  
Natarajan, "Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources." (2018).  ...  the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies.  ...  This work was funded by grants from the National Institutes of Health (U01GM120953 for iPTMnet and R01GM080646 for PRO) and R35 GM122523 (ACN).  ... 
doi:10.1038/s41598-018-24457-1 pmid:29695735 pmcid:PMC5916945 fatcat:bxzho6wisfckfhrza5vaabisya

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.  ...  In section 3, we discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in Big Data era.  ...  The user can also download PeptideProphet [168] results and ProteinProphet [169] [120] is an integrated resource for protein post-translational modification network discovery which combines text  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945 [article]

Mauro Rosales, Arielis Rodriguez-Ulloa, Vladimir Besada, Ailyn C. Ramon, George V. Perez, Yassel Ramos, Osmany Guirola, Luis J. Gonzalez, Katharina Zettl, Jacek R. Wisniewski, Yasser Perera, Silvio E. Perea
2021 bioRxiv   pre-print
behind the pharmacologic blockade of protein kinase CK2 for AML targeted therapy.  ...  Particularly, in acute myeloid leukemia (AML) CK2 has been pointed as an attractive therapeutic target and prognostic marker.  ...  Acknowledgments: We thank Igor Parón for the support in mass spectrometry analysis.  ... 
doi:10.1101/2021.01.04.425248 fatcat:7wqm5eiqxjazraap77uhyypf3q

PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification

Di Peng, Huiqin Li, Bosu Hu, Hongwan Zhang, Li Chen, Shaofeng Lin, Zhixiang Zuo, Yu Xue, Jian Ren, Yubin Xie
2020 Frontiers in Cell and Developmental Biology  
Combining functional features such as protein post-translational modification (PTM) with genetic mutations is an effective way to predict such alterations.  ...  A total of 4,11,574 modification sites from 33 different types of PTMs and 1,776,848 somatic mutations from TCGA across 33 different cancer types are integrated into the web server, enabling identification  ...  Combining functional features such as protein post-translational modification (PTM) with genetic mutations is an effective way to predict such alterations.  ... 
doi:10.3389/fcell.2020.593661 pmid:33240890 pmcid:PMC7683509 fatcat:qofib3nfdveflkb7zbdiuqsspi

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  ...  This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant  ...  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

Bioinformatics Knowledge Map for Analysis of Beta-Catenin Function in Cancer

İrem Çelen, Karen E. Ross, Cecilia N. Arighi, Cathy H. Wu, Min Zhao
2015 PLoS ONE  
The knowledge map includes post-translational modifications (PTMs), protein-protein interactions, disease-associated mutations, and transcription factors coactivated by beta-catenin and their targets and  ...  Given the wealth of bioinformatics resources and the growing complexity of biological information, it is valuable to integrate data from disparate sources to gain insight into the role of genes/proteins  ...  Acknowledgments We thank Oana Tudor for assistance with the figures and Hongzhan Huang for assistance with the heatmap.  ... 
doi:10.1371/journal.pone.0141773 pmid:26509276 pmcid:PMC4624812 fatcat:y5fnyyr3avbyjkyl3ikubjvgnq

Global proteome and phosphoproteome alterations in third generation EGFR TKI resistance reveal drug targets to circumvent resistance [article]

Xu Zhang, Tapan Maity, Karen Ross, Yue Qi, Constance Cultraro, Shaojian Gao, Khoa Dang Nguyen, Julie Cowart, Fatos Kirkali, Cathy Wu, Udayan Guha
2020 bioRxiv   pre-print
Furthermore, we performed anticorrelation analyses of this phosphoproteomic dataset with the published drug-induced P100 phosphoproteomic datasets from the Library of Integrated Network-Based Cellular  ...  To our knowledge, this is the most comprehensive proteomic dataset resource to date to investigate 3rd generation EGFR TKI resistance in lung adenocarcinoma.  ...  U.G. is currently an employee of Bristol Myers Squibb. The other authors have no conflicts of interest to report.  ... 
doi:10.1101/2020.07.04.187617 fatcat:m27znkobiffbtjjywmsztutpgm

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature

Jia Ren, Gang Li, Karen Ross, Cecilia Arighi, Peter McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K Vijay-Shanker, Cathy H Wu
2018 Database: The Journal of Biological Databases and Curation  
The website allows users to browse the text evidence and view integrated results for knowledge discovery through a network view.  ...  In this paper, we describe the iTextMine system with an automated workflow to run multiple text-mining tools on large-scale text for knowledge extraction.  ...  For example, in iPTMnet (5) , three different text-mining tools (2, 3, 6) were used to extract and post-process information for protein post-translational modification.  ... 
doi:10.1093/database/bay128 pmid:30576489 pmcid:PMC6301332 fatcat:du7v66ytybhhbdsnhc6lpeeyby

Investigation of Antidepressant Properties of Yohimbine by Employing Structure-Based Computational Assessments

Munazzah Tasleem, Abdulwahed Alrehaily, Tahani M. Almeleebia, Mohammad Y. Alshahrani, Irfan Ahmad, Mohammed Asiri, Nadiyah M. Alabdallah, Mohd Saeed
2021 Current Issues in Molecular Biology  
Yohimbine was found to satisfy all the parameters for drug-likeness and pharmacokinetics analysis.  ...  Protein functions are modulated by post-translational modifications (PTMs), which were detected through iPTMnet ( (accessed on 1 March 2021))-an integrative  ...  . 5 Prediction of post-translational modification sites in5HT1A.  ... 
doi:10.3390/cimb43030127 pmid:34889886 fatcat:uvkeviga4vgtjkqjdr52jnpiei

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

Hayley M. Dingerdissen, Frederic Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi, Amanda Bell, Nikhita Gogate, Samir Gupta, Evan Holmes, Robel Kahsay, Jonathon Keeney, Heather Kincaid, Charles Hadley King (+3 others)
2020 JCO Clinical Cancer Informatics  
RESULTS OncoMX provides integrated data encompassing more than 1,000 unique biomarker entries (939 from the Early Detection Research Network [EDRN] and 96 from the US Food and Drug Administration) mapped  ...  By mapping to and integrating data from several cancer genomics resources, it is hoped that OncoMX will foster a dynamic engagement between bioinformaticians and cancer biomarker researchers.  ...  Of note, extension to a new evidence type, glycan-protein type biomarkers, is actively underway, which should allow for the future extension to other subtypes of the anticipated post-translational modification  ... 
doi:10.1200/cci.19.00117 pmid:32142370 pmcid:PMC7101249 fatcat:qijqv25waffovfheo77vm7meey

Chemoproteomics Maps Glycolytic Targetome in Cancer Cells [article]

Yang Tian, Ning Wan, Ming Ding, Chang Shao, Nian Wang, Qiuyu Bao, Wenjie Lu, Haiyang Hu, Huiyong Sun, Chenxi Yang, Kun Zhou, Shuai Chen (+3 others)
2020 bioRxiv   pre-print
We identified 913 proteins and 2,487 interactions as target candidates for 10 metabolites involved in glycolysis.  ...  The advantages gained by enhanced glycolysis in cancer cells through these distinct mechanisms are innovated by discovering lactate as a ligand for an orphan transcriptional regulator TRIM 28 that promotes  ...  TRPs of the glycolytic targetome with annotation of post-translational modifications (PTMs) based on iPTMnet. (i) PTM category analysis of lysines in quantified peptides vs.  ... 
doi:10.1101/2020.11.18.387670 fatcat:ddmrscu35fhvnootvw7jdarnle

Updating dual-specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2): molecular basis, functions and role in diseases

Alejandro Correa-Sáez, Rafael Jiménez-Izquierdo, Martín Garrido-Rodríguez, Rosario Morrugares, Eduardo Muñoz, Marco A. Calzado
2020 Cellular and Molecular Life Sciences (CMLS)  
According to the post-transcriptional and post-translational modifications, DYRK2 expression greatly differs among human tissues.  ...  Then, here we present an innovative approach to clarify DYRK2 functionality and importance.  ...  Expression, regulation, and post-translational modifications DYRK2 presents an expression pattern that varies across tissues and which depends on the measured biological level.  ... 
doi:10.1007/s00018-020-03556-1 pmid:32462403 fatcat:ayvsa4tijvddbfvkgivlmwxa4y

Differential responses to kinase inhibition in FGFR2-addicted triple negative breast cancer cells: a quantitative phosphoproteomics study

Debbie L. Cunningham, Adil R. Sarhan, Andrew J. Creese, Katherine P. B. Larkins, Hongyan Zhao, Harriet R. Ferguson, Katie Brookes, Anna A. Marusiak, Helen J. Cooper, John K. Heath
2020 Scientific Reports  
Comparative Gene Ontology proteome analysis revealed that SUM52 cells were enriched in proteins associated with cell metabolism and MFM223 cells enriched in proteins associated with cell adhesion and migration  ...  This study expands the known landscape of FGF signalling and identifies many new targets for functional investigation.  ...  HJC is an EPSRC Established Career Fellow (EP/S002979/1).  ... 
doi:10.1038/s41598-020-64534-y pmid:32409632 fatcat:74uh4tjru5fjzcqcinvdnuigxm
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