Analysis of microarray data

Raw data were processed using Feature Extraction software Version 9.5 (Agilent Technologies) as previously described [9]. Spot data identified by the software as greater than the background were used for additional analyses. The resulting MIAME compliant microarray data were submitted to the NCBI Gene Expression Omnibus database repository (http://www.ncbi.nlm.nih.gov/geo/) under the accession number {"type":"entrez-geo","attrs":{"text":"GSE97711","term_id":"97711"}}GSE97711.

Gene expression profiles were analyzed with Subio Basic-Plug-in software (Subio Inc., Kagoshima, Japan). Differentially expressed genes (DEGs) between LWDL and LWDM pigs were defined as a >2.0-fold expression difference with a false discovery ratio (FDR) of < 0.05 by the Benjamini-Hochberg procedure [28], as determined using a student’s t-test. Functional annotations of DEGs were investigated with the Gene Ontology Biological Process (GOBP) and with the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 [29, 30]. Any statistically significant GOBP terms and KEGG pathways (EASE-score, a modified Fisher’s exact P-value < 0.01) we found were selected for further analysis.