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Methods Enzymol. 2016;574:53-77. doi: 10.1016/bs.mie.2016.02.002. Epub 2016 Mar 2.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

Author information

1
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, United States.
2
Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, United States. Electronic address: scott.rothbart@vai.org.

Abstract

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools.

KEYWORDS:

Array construction; Array quantification; Array visualization; Histone biochemistry; Virtual tools

PMID:
27423857
PMCID:
PMC5353857
DOI:
10.1016/bs.mie.2016.02.002
[Indexed for MEDLINE]
Free PMC Article

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