scholarly journals PamgeneAnalyzeR open and reproducible pipeline for kinase profiling

2019 ◽  
Author(s):  
Amel Bekkar ◽  
Anita Nasrallah ◽  
Nicolas Guex ◽  
Lluis Fajas ◽  
Ioannis Xenarios ◽  
...  
Keyword(s):  
Protein Kinases ◽  
High Throughput ◽  
Kinase Activity ◽  
Experimental Approach ◽  
R Package ◽  
Activity Measurement ◽  
Post Translational Modification ◽  
Peptide Microarrays ◽  
Disease States ◽  
Downstream Analysis

AbstractProtein phosphorylation - catalyzed by protein kinases - is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here we present “pamgeneAnalyzeR”, an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis.Availability and implementationPamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.

scholarly journals PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling

2020 ◽  
Vol 36 (20) ◽  
pp. 5117-5119 ◽  
Author(s):  
Amel Bekkar ◽  
Anita Nasrallah ◽  
Nicolas Guex ◽  
Lluis Fajas ◽  
Ioannis Xenarios ◽  
...  
Keyword(s):  
Protein Kinases ◽  
High Throughput ◽  
Kinase Activity ◽  
Experimental Approach ◽  
R Package ◽  
Activity Measurement ◽  
Post Translational Modification ◽  
Peptide Microarrays ◽  
Disease States ◽  
Downstream Analysis

Abstract   Protein phosphorylation––catalyzed by protein kinases–is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here, we present ‘pamgeneAnalyzeR’, an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis. Availability and implementation PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.

Glutaredoxin AtGRXC2 catalyses inhibitory glutathionylation of Arabidopsis BRI1-associated receptor-like kinase 1 (BAK1) in vitro

2015 ◽  
Vol 467 (3) ◽  
pp. 399-413 ◽  
Author(s):  
Kyle W. Bender ◽  
Xuejun Wang ◽  
George B. Cheng ◽  
Hyoung Seok Kim ◽  
Raymond E. Zielinski ◽  
...  
Keyword(s):  
Protein Kinases ◽  
Redox Regulation ◽  
Kinase Activity ◽  
Cytoplasmic Domain ◽  
Post Translational Modification ◽  
Cysteine Oxidation ◽  
Receptor Like Kinase ◽  
Reversible Protein Phosphorylation ◽  
Two Hybrid

Reversible protein phosphorylation, catalysed by protein kinases, is the most widely studied post-translational modification (PTM), whereas the analysis of other modifications such as S-thiolation is in its relative infancy. In a yeast-two-hybrid (Y2H) screen, we identified a number of novel putative brassinosteroid insensitive 1 (BR1)-associated receptor-like kinase 1 (BAK1) interacting proteins including several proteins related to redox regulation. Glutaredoxin (GRX) C2 (AtGRXC2) was among candidate proteins identified in the Y2H screen and its interaction with recombinant Flag–BAK1 cytoplasmic domain was confirmed using an in vitro pull-down approach. We show that BAK1 peptide kinase activity is sensitive to the oxidizing agents H2O2 and diamide in vitro, suggesting that cysteine oxidation might contribute to control of BAK1 activity. Furthermore, BAK1 was glutathionylated and this reaction could occur via a thiolate-dependent reaction with GSSG or a H2O2-dependent reaction with GSH and inhibited kinase activity. Surprisingly, both reactions were catalysed by AtGRXC2 at lower concentrations of GSSG or GSH than reacted non-enzymatically. Using MALDI–TOF MS, we identified Cys353, Cys374 and Cys408 as potential sites of glutathionylation on the BAK1 cytoplasmic domain and directed mutagenesis suggests that Cys353 and Cys408 are major sites of GRXC2-mediated glutathionylation. Collectively, these results highlight the potential for redox control of BAK1 and demonstrate the ability of AtGRXC2 to catalyse protein glutathionylation, a function not previously described for any plant GRX. The present work presents a foundation for future studies of glutathionylation of plant receptor-like protein kinases (RLKs) as well as for the analysis of activities of plant GRXs.

scholarly journals BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

2021 ◽  
Author(s):  
Darawan Rinchai ◽  
Jessica Roelands ◽  
Mohammed Toufiq ◽  
Wouter Hendrickx ◽  
Matthew C Altman ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
R Package ◽  
Supplementary Information ◽  
Illustrative Case ◽  
Bioinformatic Tools ◽  
Transcriptional Module ◽  
Wide Range ◽  
Downstream Analysis ◽  
Computing Module ◽  
Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

Accelerating the discovery of energetic melt-castable materials by a high-throughput virtual screening and experimental approach

2021 ◽  
Author(s):  
Siwei Song ◽  
Fang Chen ◽  
Yi Wang ◽  
Kangcai Wang ◽  
Mi Yan ◽  
...  
Keyword(s):  
Machine Learning ◽  
Virtual Screening ◽  
High Throughput ◽  
Experimental Approach ◽  
Chemical Data ◽  
Research Paradigm ◽  
New Materials ◽  
High Throughput Virtual Screening

With the growth of chemical data, computation power and algorithms, machine learning-assisted high-throughput virtual screening (ML-assisted HTVS) is revolutionizing the research paradigm of new materials. Herein, a combined ML-assisted HTVS...

scholarly journals kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xue Lin ◽  
Yingying Hua ◽  
Shuanglin Gu ◽  
Li Lv ◽  
Xingyu Li ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Somatic Mutations ◽  
R Package ◽  
Frequency Of Occurrence ◽  
Link Type ◽  
Genomic Landscape ◽  
One Step ◽  
Flanking Regions

Abstract Background Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations “violent storm”, which is just what the Greek word “kataegis” means. Results There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package “kataegis” to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions. Conclusions The kataegis package is available on Bionconductor/Github (https://github.com/flosalbizziae/kataegis), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.

scholarly journals The kinase activity of human Rio1 is required for final steps of cytoplasmic maturation of 40S subunits

2012 ◽  
Vol 23 (1) ◽  
pp. 22-35 ◽  
Author(s):  
Barbara Widmann ◽  
Franziska Wandrey ◽  
Lukas Badertscher ◽  
Emanuel Wyler ◽  
Jens Pfannstiel ◽  
...  
Keyword(s):  
Rna Interference ◽  
Protein Kinases ◽  
18S Rrna ◽  
Kinase Activity ◽  
Ribosomal Biogenesis ◽  
Ribosomal Subunits ◽  
Binding Partner ◽  
Rrna Maturation ◽  
Cytoplasmic Maturation

RIO proteins form a conserved family of atypical protein kinases. Humans possess three distinct RIO kinases—hRio1, hRio2, and hRio3, of which only hRio2 has been characterized with respect to its role in ribosomal biogenesis. Here we show that both hRio1 and hRio3, like hRio2, are associated with precursors of 40S ribosomal subunits in human cells. Furthermore, we demonstrate that depletion of hRio1 by RNA interference affects the last step of 18S rRNA maturation and causes defects in the recycling of several trans-acting factors (hEnp1, hRio2, hLtv1, hDim2/PNO1, and hNob1) from pre-40S subunits in the cytoplasm. Although the effects of hRio1 and hRio2 depletion are similar, we show that the two kinases are not fully interchangeable. Moreover, rescue experiments with a kinase-dead mutant of hRio1 revealed that the kinase activity of hRio1 is essential for the recycling of the endonuclease hNob1 and its binding partner hDim2 from cytoplasmic pre-40S. Kinase-dead hRio1 is trapped on pre-40S particles containing hDim2 and hNob1 but devoid of hEnp1, hLtv1, and hRio2. These data reveal a role of hRio1 in the final stages of cytoplasmic pre-40S maturation.

Development of a high-throughput AlphaScreen assay measuring full-length LRRK2(G2019S) kinase activity using moesin protein substrate

2010 ◽  
Vol 404 (1) ◽  
pp. 45-51 ◽  
Author(s):  
Liliana Pedro ◽  
Jaime Padrós ◽  
Lucille Beaudet ◽  
Hans-Dieter Schubert ◽  
Frank Gillardon ◽  
...  
Keyword(s):  
High Throughput ◽  
Kinase Activity ◽  
Full Length ◽  
Protein Substrate ◽  
Lrrk2 G2019s

scholarly journals HomoKinase: A Curated Database of Human Protein Kinases

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Suresh Subramani ◽  
Saranya Jayapalan ◽  
Raja Kalpana ◽  
Jeyakumar Natarajan
Keyword(s):  
Gene Ontology ◽  
Protein Kinases ◽  
Kinase Activity ◽  
Query Protein ◽  
Amino Acid Sequences ◽  
Human Protein ◽  
Biological Information ◽  
Functional Domain ◽  
Comprehensive Collection ◽  
Search Tool

HomoKinase database is a comprehensive collection of curated human protein kinases and their relevant biological information. The entries in the database are curated by three criteria: HGNC approval, gene ontology-based biological process (protein phosphorylation), and molecular function (ATP binding and kinase activity). For a given query protein kinase name, the database provides its official symbol, full name, other known aliases, amino acid sequences, functional domain, gene ontology, pathways assignments, and drug compounds. In addition, as a search tool, it enables the retrieval of similar protein kinases with specific family, subfamily, group, and domain combinations and tabulates the information. The present version contains 498 curated human protein kinases and links to other popular databases.

scholarly journals A Novel Cell-Based, High-Content Assay for Phosphorylation of Lats2 by Aurora A

2011 ◽  
Vol 16 (8) ◽  
pp. 925-931 ◽  
Author(s):  
Amy Emery ◽  
David A. Sorrell ◽  
Stacy Lawrence ◽  
Emma Easthope ◽  
Mark Stockdale ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Kinase Activity ◽  
High Content Screening ◽  
Aurora A Kinase ◽  
Aurora A ◽  
Assay Performance ◽  
A Cell ◽  
Significant Addition ◽  
Specific Inhibitors

Aurora A kinase is a key regulator of mitosis, which is upregulated in several human cancers, making it a potential target for anticancer therapeutics. Consequently, robust medium- to high-throughput cell-based assays to measure Aurora A kinase activity are critical for the development of small-molecule inhibitors. Here the authors compare measurement of the phosphorylation of two Aurora A substrates previously used in high-content screening Aurora A assays, Aurora A itself and TACC3, with a novel substrate Lats2. Using antibodies directed against phosphorylated forms of Aurora A (pThr288), P-TACC3 (pSer558), and P-Lats2 (pSer83), the authors investigate their suitability in parallel for development of a cell-based assay using several reference Aurora inhibitors: MLN8054, VX680, and AZD1152-HQPA. They validate a combined assay of target-specific phosphorylation of Lats2 at the centrosome and an increase in mitotic index as a measure of Aurora A activity. The assay is both sensitive and robust and has acceptable assay performance for high-throughput screening or potency estimation from concentration–response assays. It has the advantage that it can be carried out using a commercially available monoclonal antibody against phospho-Lats2 and the widely available Cellomics ArrayScan HCS reader and thus represents a significant addition to the tools available for the identification of Aurora A specific inhibitors.

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