Reliable analysis of the catabolic gene landscape and transcriptome for pollutant degradation using a custom open source microarray with internal calibration

ABSTRACT: Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval o

ORGANISM(S): Pseudomonas putida F1

SUBMITTER: Robert Geffers 

PROVIDER: E-GEOD-30303 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress