DawnRank statistics

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DawnRank specifications

Information


Unique identifier OMICS_10915
Name DawnRank
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input includes differential gene expression (between tumor and normal) and somatic alteration data (point mutations or CNVs).
Output data The output includes a ranked list of mutated genes according to their DawnRank score. A high DawnRank score for an altered gene in cancer indicates that the gene is more likely to be a driver.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.2
Stability No
Maintained No

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Publication for DawnRank

DawnRank in publications

 (6)
PMCID: 5756345
PMID: 29304754
DOI: 10.1186/s12864-017-4423-x

[…] well-validated computational methods used to identify cancer driver genes, such as activedriver [], dendrix [], mdpfinder [], simon [], netbox [], oncodrivefm [], mutsigcv [], memo [], comdp [], dawnrank [], drivernet [], e-driver [], ipac [], msea [], and oncodriveclust []., we applied driverdb [] to obtain results from all these algorithms and the cancer datasets considered […]

PMCID: 5601632
PMID: 28938536
DOI: 10.18632/oncotarget.19481

[…] using the network or pathway information can be effective in identifying drivers. an example is that hamed and his colleges used the protein interaction network for identifying cancer drivers []. dawnrank, which used pagerank algorithm to detect driver genes [], is an affective module level method. besides, drivernet identifies drivers by estimating their effect on mrna expression []. muffinn […]

PMCID: 5415494
PMID: 28492066
DOI: 10.1016/j.heliyon.2017.e00277

[…] assembles together lists of the top ranked driver genes determined from the use of 15 packages, including activedriver, dendrix, mdpfinder, simon, netbox, oncodrivefm, mutsigcv, memo, comdp, dawnrank, drivernet, e-driver, ipac, msea, and oncodriveclust. lists the cancer types, sample size, and descriptions of the driver genes used, including chromosome location, gene ontology […]

PMCID: 5274523
PMID: 28149674
DOI: 10.7717/peerj.2568

[…] on the quality and size of the pathway interaction network employed, and require a powerful statistical environment for analyses. a number of genomic libraries are available in r. drivernet and dawnrank employ pathway-based methods that use gene interaction graphs in matrix form. we investigated the benefit of combining data from 3 different sources on the prediction outcome of cancer […]

PMCID: 4868730
PMID: 26716509
DOI: 10.18632/oncotarget.6716

[…] 5 (erbb2, pdxk, hdac4, plxna1 and tnfaip2) were also correlated with mutational esnvs (figure )., we distinguished driver mutations from functionally neutral passenger mutations with the dawnrank algorithm, and included prior-identified genes from tcga in the prioritization step. as a result, a gene list containing 1,619 genes was generated for endometrial cancer (figure and ). […]


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DawnRank institution(s)
Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Medical Scholars Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
DawnRank funding source(s)
This work was supported by an award from the Interdisciplinary Innovation Initiative (In3) program at the University of Illinois and an Illinois Distinguished Fellowship.

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