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X2K specifications

Information


Unique identifier OMICS_17637
Name X2K
Alternative names Expression2Kinases, X2K Web
Software type Package/Module
Interface Command line interface, Graphical user interface
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.6.1207
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Additional information


Previous version: http://www.maayanlab.net/X2K/

Information


Unique identifier OMICS_17637
Name X2K
Alternative names Expression2Kinases, X2K Web
Interface Web user interface
Restrictions to use None
Input data Some lists of differentially expressed genes.
Output data Some interactive downloadable vector graphic network images, bar graphs and downloadable tables.
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Download


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Documentation


Additional information


Previous version: http://www.maayanlab.net/X2K/

Publications for Expression2Kinases

X2K citations

 (10)
library_books

Broad Spectrum Regulation of Nonreceptor Tyrosine Kinases by the Bacterial ADP Ribosyltransferase EspJ

2018
MBio
PMCID: 5893879
PMID: 29636436
DOI: 10.1128/mBio.00170-18

[…] We used the kinase enrichment analysis (KEA) function within the Expression2Kinases (X2K) software to predict upstream regulatory kinases from the group of 457 proteins repressed by EspJ (). KEA draws from kinase perturbation studies within numerous protein and gen […]

library_books

Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis

2018
Front Genet
PMCID: 5820528
PMID: 29503661
DOI: 10.3389/fgene.2018.00042

[…] Upstream regulators and protein kinases associated with DEGs were recognized by submitting the list of shared DEGs to Expression2Kinases (X2K) web interface (https://amp.pharm.mssm.edu/X2K/; Chen et al., ). X2K identifies the enriched transcription factors (TFs) from the upstream of the shared DEGs using a ChEA datab […]

library_books

Time Course Expression Analysis of 1[2 cyano 3,12 dioxooleana 1,9(11) dien 28 oyl]imidazole Induction of Cytoprotection in Human Endothelial Cells

2017
PMCID: 5398299
PMID: 28469413
DOI: 10.1177/1177625017701106

[…] le for the cytoprotective effect., In addition, analysis with Expression2Kinases (X2K) was used to identify transcription factors, kinases, and complexes that drive changes in global gene expression. Expression2Kinases integrates chromatin immunoprecipitation (ChIP)-seq/chip and position weight matrix data, protein-protein interactions, and kinase-substrate phosphorylation reactions to better iden […]

library_books

cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool

2017
eLife
PMCID: 5745079
PMID: 29239726
DOI: 10.7554/eLife.29750.032

[…] s the activity of three different transcription factors: CREB1, CREM and ATF1. The Ma’ayan laboratory has posted analyzed data online from both the ChEA and ENCODE projects (http://amp.pharm.mssm.edu/X2K/#downloads). To find genes potentially regulated by these three transcription factors, we used the ENCODE 2015 and ChEA 2015 databases (; ). Experiments using rat cells are uncommon in these datab […]

library_books

Comprehensive Gene expression meta analysis and integrated bioinformatic approaches reveal shared signatures between thrombosis and myeloproliferative disorders

2016
Sci Rep
PMCID: 5125005
PMID: 27892526
DOI: 10.1038/srep37099

[…] d in other hematologic disorders. Briefly to understand the association of the DEGs list to the most significant kinases and transcription factors, we conducted regulatory gene network analysis using X2K software. The mitogen-activated protein (MAP) kinases MAPK1, MAPK3, MAPK14 were amongst the most significant kinases associated with the DEGs. Besides other cells, MAP kinases are present in plate […]

library_books

L1000CDS2: LINCS L1000 characteristic direction signatures search engine

2016
NPJ Syst Biol Appl
PMCID: 5389891
PMID: 28413689
DOI: 10.1038/npjsba.2016.15

[…] (). At the 30-min time point, substrates of CDK1 and CDK2 are also highly enriched together with GSK3B. These observation are consistent with our prediction of kenpaullone as the top mimicking drug. X2K analysis also confirms the potential involvement of GSK3B, CDK1 and CDK2 through the transcription factors beta-catenin, Smad3 and estrogen receptor 2 (). Smad3 activity was recently shown to be i […]

Citations

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X2K institution(s)
DBD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Knowledge Management Center for the Illuminating the Druggable Genome, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
X2K funding source(s)
Supported by NIH [U54-HL127624, U24-CA224260, OT3-OD025467].

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