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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 citations
(9)Cancer reversion with oocyte extracts is mediated by cell cycle arrest and induction of tumour dormancy
[…] 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
[…] 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
[…] 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 in clinic […]
Construction and evaluation of yeast expression networks by database guided predictions
[…] 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
[…] 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
[…] 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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