Many tools have been developed to allow users to perform a bulk query of GO using a list of gene, protein or probe identifiers, that have been identified from proteomics or other high-throughput experiments [4,23].
Bayesian binary regression performed in MatLab identified the top gene probe identifiers used in separating resistant from sensitive cell lines, and those probes are reported in Table S2.
Probe identifiers were mapped to HGNC gene names through EnsEMBL BioMart.
Agilent probe identifiers were mapped to their corresponding gene objects in the Ingenuity Pathways Knowledge Base.
Briefly, each signature, containing probe identifiers and LogRatio values, were uploaded into the application.
All differential expression or co-expression analysis here are performed on individual probe identifiers, while transcription factor overrepresentation are performed based on the target genes identifiers.
With these criteria, 1192 probe identifiers were up-regulated and 1003 were down-regulated in the dicamba treated plants.
or relating probe identifiers to public database identifiers.
Affymetrix probe identifiers were converted to SWISS-PROT identifiers (Boeckmann et al., 2003); data without corresponding identifiers were discarded.
The correspondence between probe identifiers and gene identifiers was obtained from http://genomes.cribi.unipd.it/.it/
