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ArrayMining specifications


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



  • person_outline Enrico Glaab

Publication for ArrayMining

ArrayMining citations


Cancer reversion with oocyte extracts is mediated by cell cycle arrest and induction of tumour dormancy

PMCID: 5882314
PMID: 29662623
DOI: 10.18632/oncotarget.24664
call_split See protocol

[…] 2010.2. 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 wer […]


Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning based early diagnosis and proposes novel diagnostic and prognostic biomarkers

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

[…] ssification 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 is a combinatio […]


HOXC8 regulates self renewal, differentiation and transformation of breast cancer stem cells

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

[…] For the analysis of the Homeobox gene array, hierarchical cluster analysis was performed by using the software ArrayMining ( Venn diagrams were generated with the online tool Venny ( analysis of copy number variation in clinic […]


Construction and evaluation of yeast expression networks by database guided predictions

PMCID: 5348991
PMID: 28357360
DOI: 10.15698/mic2016.06.505

[…] nditions regarding common transcriptional responses . Further tools include functions to facilitate the assembly of data analysis routines such as limma , web servers for microarray analysis, such as ArrayMining and tools to perform technical aspects of the analysis, such as TM4 . Also methods are available to group genes according to their function, regulation or biological processes with Gene S […]


Transcriptome wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos

BMC Genomics
PMCID: 4647491
PMID: 26572793
DOI: 10.1186/s12864-015-2108-x

[…] in-house SVM classifier CodeWise to assess the coding potential of transcripts. Second, additional tools were applied to the set of 2,938 transcripts, including (i) co-expression network analyses by ArrayMining [] and visualization in Cytoscape [], (ii) the depiction of inferred signal transduction pathways in the Beacon Pathway Editor [] based on prior knowledge combined with our data, and (iii) […]


Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling

Genom Data
PMCID: 4584005
PMID: 26484251
DOI: 10.1016/j.gdata.2015.06.016
call_split See protocol

[…] egulated RNA transcripts, we considered differential expression as present if the fold-change was > 2, and the adjusted p-value (false discovery rate) was p < 0.05. A heatmap (see ) was created using ArrayMining . […]


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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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