KinomeXplorer statistics

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KinomeXplorer specifications

Information


Unique identifier OMICS_05087
Name KinomeXplorer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C, Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_05087
Name KinomeXplorer
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages C, Python
Computer skills Basic
Stability Stable
Maintained Yes

Publication for KinomeXplorer

KinomeXplorer citations

 (5)
library_books

Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis

2018
Sci Rep
PMCID: 5797227
PMID: 29396449
DOI: 10.1038/s41598-018-20231-5

[…] used to reveal the enriched annotations for biological function and cellular component. GO subgroups that were significantly enriched with p-values below 0.05 were reported.NetworKIN 3.0 (as part of KinomeXplorer) was used to generate kinase-substrate networks. Predictions scoring ≥5 were selected. Predicted kinase-substrate interaction networks were visualized using Cytoscape 3.4.0. Cellular com […]

library_books

Phosphoproteomic insights into processes influenced by the kinase like protein DIA1/C3orf58

2018
PeerJ
PMCID: 5896498
PMID: 29666759
DOI: 10.7717/peerj.4599

[…] y Analysis (IPA) (Qiagen, Redwood City, CA, USA), in particular by generating networks of protein–protein relationships. As background, the set of all proteins detected in the experiment was used.The KinomeXplorer toolset (; ; ) was applied to predict likely kinases causing the observed phosphorylation changes. Two programs were used, NetPhorest, the atlas of consensus phosphorylation site sequenc […]

library_books

Phospho proteomic analyses of B Raf protein complexes reveal new regulatory principles

2016
Oncotarget
PMCID: 5042004
PMID: 27034005
DOI: 10.18632/oncotarget.8427

[…] he HR between CR2 and CR3, and the C-terminus (Figure ). This suggests that these areas reside in less-ordered states allowing easy access for kinases and phosphatases. Using bioinformatic tools like KinomeXplorer, Scansite or PhosphoNET, we list which kinases could be implicated in these phosphorylation events (). […]

library_books

Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress

2015
Mol Syst Biol
PMCID: 4501848
PMID: 26040289
DOI: 10.15252/msb.20156170

[…] ate the minimum centroid distance (minimum distance between two cluster centers produced by c-means clustering) (Schwammle & Jensen, ). Prediction of kinase–substrate relationships was achieved using KinomeXplorer with default thresholding criteria (Horn et al, ) (http://networkin.info/). Gene ontology enrichment analyses were performed against whole S. cerevisiae proteome as background using DAVI […]

library_books

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites

2015
PLoS One
PMCID: 4401752
PMID: 25886273
DOI: 10.1371/journal.pone.0122294

[…] sifier for predicting protein phosphorylation sites [–, ]. Another method Musite is considered for large scale predictions of both non-kinase and kinase-specific phosphorylation sites []. RegPhos and KinomeXplorer are two latest tools, aimed to explore kinase signaling networks [, ]. Recently in 2014, Suo et al. have proposed a method PSEA for predicting kinase specific phosphorylation sites as we […]

Citations

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KinomeXplorer institution(s)
Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark; Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark; Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Molecular Health GmbH, Heidelberg, Germany,Department of Biology, University of Rome Tor Vergata, Rome, Italy; Department of Biology, University of Rome Tor Vergata, Rome, Italy; Istituto Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, Rome, Italy; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark

KinomeXplorer reviews

 (2)
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Anonymous user #5340

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Response to the review on 2015-12-24:

At first, I thought "kinomexplorer.info" was a "blank webpage" too but then my friend pointed out that I have to click on the text "NetworKIN" and "NetPhorest." I haven't actually used it yet, so my 5-star rating is only to balance out the previous review.
Anonymous user #965's avatar image No country

Anonymous user #965

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Yet another "resource/tool" from Linding group which is nothing more than a blank webpage that doesn't allow you to do anything at all.