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Functional analyses were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (http://david.abcc.ncifcrf.gov/) [ 20, 21].
Functional analyses were performed using the Cluster of Orthologous Gene classification (COG) [25].
All functional analyses were performed using the Blast2GO software [ 51].
Gene ontology, functional enrichment, and canonical pathways analyses were performed using Ingenuity Pathway Analysis (IPA) [12],[21] (www.ingenuity.com).com
Functional term enrichment analyses were performed using DAVID [ 123] and Ontologizer [ 124].
All preprocessing and analyses were performed using the software suite Analysis of Functional NeuroImages (AFNI)[ 53, 54].
34 Gene-centric functional and canonical pathway enrichment analyses were performed using the ToppGene Suite.
Gene ontology analyses were performed using the functional annotation clustering function of DAVID (http://david.abcc.ncifcrf.gov/).abcc.ncifcrf.gov/
Phylogenetic analyses were performed using nucleotide sequences, unless otherwise indicated, of functional (and ORF) TRDV and TRDJ genes.
Statistical analyses were performed using R and GraphPad Prism.
Statistical analyses were performed using built-in functions in Origin.
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