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We also found 11 complex trait-associated genetic variants overlapping with our identified PM2.5-associated epigenetic signature (Table  2).

Such a comparison identifies which molecular pathways share a group of genes with our identified gene list, providing a potential insight into involved biological networks.

Out of these 31 genes, 28 were overlapping with our identified differentially expressed genes from our microarray data, of which 8 genes (AARS, PEA15, NQO1, STAT1, IGFBP3, HYOU1, HMGB1 and IGF2R) were also matched genes, previously verified in the TCGA dataset (Table  1; Fig.  3; Additional file 2: Figure S3).

As confirmed mtDNA disease-causing mutations are clearly functional (38 nonsynonymous mutations, supplementary table S3, Supplementary Material online), we calculated their scores using the earlier-mentioned tests (i.e., Conservation Index and SIFT scores) and used them as a reference of functionality to compared with our identified RNMs and SNMs.

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To determine the basic features of pig lincRNAs, we compared our identified lincRNAs with mRNAs identified by Ensembl.

Direct sequencing concurrent with our analysis identified a null mutation in the SGCE gene in affecteds from this family.

To evaluate the potential influence of any novel SNPs on our previous results, we compared the 782 differentially spliced probesets with our newly identified SNP-containing probesets.

In our sample, we therefore investigated these markers and compared the association with the one observed with our newly identified SNPs.

To do this, we started with our previously identified network (i.e., the hORGNet and its two modules, hStemModule and hDiffModule) [ 20].

These results suggested that VSV infection induced a post-translational modification of PTEN and we speculated that this modification might correspond with our previously identified SUMO conjugation.

Stoppard has precluded any chance of our identifying with the character.

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