ArrayMiner statistics

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ArrayMiner specifications

Information


Unique identifier OMICS_01570
Name ArrayMiner
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Medium
Version 5.3
Stability Stable
Maintained Yes

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  • person_outline ArrayMiner Team <>

ArrayMiner in publications

 (7)
PMCID: 3202757
PMID: 22045987
DOI: 10.1128/mBio.00138-11

[…] between variability of gene expression as measured by sd and overall expression levels (data not shown). this demonstrates that the data were not biased., unsupervised clustering was conducted using arrayminer (optimaldesign, inc.). additional calculations were performed in r, version 2.5.0. the linear trend was computed using robust regression ()., citation dittmer dp. 2011. restricted […]

PMCID: 3156770
PMID: 21858131
DOI: 10.1371/journal.pone.0023466

[…] and biological replicates become more comparable, a prerequisite for statistical analysis. between-array-normalised data were then transformed into log2 values and exported into the web-tool arrayminer for statistical analysis. using the empirical bayesian option of arrayminer, 99 genes with a q-value lower than 0.05 were returned, and we consider this to represent significant […]

PMCID: 3022917
PMID: 21167028
DOI: 10.1186/1471-2164-11-709

[…] focused on the as(iii) response in h. arsenicoxydans., to classify the transcripts on the basis of their temporal dynamics after exposure to arsenite, we performed a hierarchical clustering with the arrayminer® software http://www.optimaldesign.com/arrayminer/arrayminer.htm. genes were sorted into groups that exhibited similar transcription kinetics as cells transitioned from a1 to a3 phases. […]

PMCID: 2996331
PMID: 21170361
DOI: 10.1371/journal.pgen.1001231

[…] to identify groups of co-expressed target genes affected through pathway inhibition, we subjected 7,049 genes (corresponding to 9,272 probe sets exhibiting significant hybridization intensities) to arrayminer clustering. this algorithm identified 36 clusters of co-regulated genes in the entire set of pathway interference experiments (, and ). some of the gene clusters reflect cell […]

PMCID: 2663814
PMID: 19381257
DOI: 10.1371/journal.ppat.1000389

[…] to ˆctu6. this yielded dct for each primer/sample combination. the dct were normalized to median for each array and subjected to unsupervised clustering using a correlation metric and the program arrayminer™., our exploratory cluster analysis included all primers and all samples. however, for statistical analysis we excluded primers, which yielded ct <38 for the non-template and reverse […]


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