A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
iPTMnet: an integrated resource for protein post-translational modification network discovery
2017
Nucleic Acids Research
Preserved Fulltext
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]
2019
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2017
Msphere
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2020
Frontiers in Cell and Developmental Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2015
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Database: The Journal of Biological Databases and Curation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2021
Current Issues in Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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 (https://research.bioinformatics.udel.edu/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
2020
JCO Clinical Cancer Informatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2020
Cellular and Molecular Life Sciences (CMLS)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2020
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 18 results