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ArrayMining specifications

Information


Unique identifier OMICS_05580
Name ArrayMining
Interface Web user interface
Restrictions to use Academic or non-commercial use
Biological technology Illumina, Affymetrix, Agilent Technologies, Luminex
Programming languages Python, R
License Apache License version 2.0
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Enrico Glaab <>

Publication for ArrayMining

ArrayMining in pipeline

2015
PMCID: 4924658
PMID: 26575329
DOI: 10.18632/oncotarget.5876

[…] on r environment (http://www.r-project.org/). to remove the non-biological experiment variation across different microarray individuals, ailun [] platform comparison (http://ailun.stanford.edu/) and arraymining [] cross-study integration (http://www.arraymining.net/) were achieved as our previously described []., as a major challenge for gene signatures identification, limited sample of clusters […]


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ArrayMining in publications

 (11)
PMCID: 5882314
PMID: 29662623
DOI: 10.18632/oncotarget.24664

[…] all analyses reported used the ‘quantile’ normalisation method with background correction within genomestudio., bioinformatics analysis of differentially expressed genes was performed using the arraymining software [] with the empirical bayes moderated t-test method. significant difference in expression was determined by fdr corrected p-value from multiple t-tests < 0.05. microarray data […]

PMCID: 5752532
PMID: 29312619
DOI: 10.18632/oncotarget.22689

[…] was the corresponding value that optimize f1-score at default., ensemble class assignment analyses on the corresponding data sets of the whole transcriptome information were conducted using arraymining online software []. in brief, the data set was introduced to the class assignment module with the settings of the ensemble method for feature selection. the ensemble method […]

PMCID: 5312582
PMID: 28202042
DOI: 10.1186/s12943-017-0605-z

[…] cholera toxin and 10% matrigel for up to 7 days, with medium changed every other day., for the analysis of the homeobox gene array, hierarchical cluster analysis was performed by using the software arraymining (http://www.arraymining.net/). venn diagrams were generated with the online tool venny (http://bioinfogp.cnb.csic.es/tools/venny/index.html)., the analysis of copy number variation […]

PMCID: 5261002
PMID: 27906186
DOI: 10.1038/cddis.2016.382

[…] genes by taking the mean of all probes that corresponds to the same gene. the missing values were eventually replaced using the knn algorithm., bioinformatics analysis was completed by applying arraymining software (http://www.arraymining.net/) and the cytoscape package. the transcriptome analysis for microarrays was carried out using complementary approaches: a david analysis […]

PMCID: 4692059
PMID: 26678268
DOI: 10.1371/journal.pone.0144708

[…] relative values between the cell lines. the sample gene profile file was then annotated using hg18 prior to performing differential gene expression analysis (dgea)., the dgea was performed using arraymining, an online microarray data mining software package []. differential gene expression was conducted using sam analysis to list genes differentially expressed with respect to treatment […]


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ArrayMining institution(s)
School of Computer Science, Nottingham University, Jubilee Campus, Wollaton Road, Nottingham, UK
ArrayMining funding source(s)
Supported by the Marie-Curie Early-Stage-Training programme (grant MEST-CT-2004-007597), by the UK Engineering and Physical Sciences Research Council (EP/E017215/1) and the Biotechnology and Biological Sciences Research Council (BB/F01855X/1).

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