TABLE 2.
Mouse bioinformatic evidence for human GWA genes in LD block
| HDL QTL Crossa | Gene Expression Differencesb | Amino Acid Substitutionc | ||||||
|---|---|---|---|---|---|---|---|---|
| Gene | Strains | Diet | Sex | Fold Change(P) | Amino Acid | Charge/Polarity | Functional? | Conserved? |
| Multiple genes locus on Chr 5 | ||||||||
| Kctd10 | B6xNZB | HF | F | +1.13 (0.828) | None | — | — | — |
| NZBxNZW | HF | F | +1.28 (0.767) | None | — | — | — | |
| NZBxSM | HF | F | +1.23 (0.733) | None | — | — | — | |
| C | F | +1.18 (0.883) | ||||||
| B6x129 | HF | F | +1.05 (0.912) | None | — | — | — | |
| C | F | +1.29 (0.453) | ||||||
| Mmab | B6xNZB | HF | F | −1.22 (0.736) | None | — | — | — |
| NZBxNZW | HF | F | −2.08 (0.001) | None | — | — | — | |
| NZBxSM | HF | F | +1.21 (0.690) | None | — | — | — | |
| C | F | +1.05 (0.998) | ||||||
| B6x129 | HF | F | −1.24 (0.426) | None | — | — | — | |
| C | F | +1.14 (0.769) | ||||||
| Mvk | B6xNZB | HF | F | −1.04 (0.955) | V207IF216Y | NoNo | NoNo | YesYes |
| NZBxNZW | HF | F | −1.35 (0.854) | V207IF216Y | NoNo | NoNo | YesYes | |
| NZBxSM | HF | F | +1.03 (0.912) | V207IF216Y | NoNo | NoNo | YesYes | |
| C | F | +1.27 (0.669) | ||||||
| B6x129 | HF | F | −1.00 (0.989) | F216Y | No | No | Yes | |
| C | F | +1.06 (0.873) | ||||||
| Multiple genes locus on Chr 19 | ||||||||
| Fads1 | BALBxB6 | C | M | +1.66 (0.044) | V163I | No | No | Yes |
| C | F | +1.40 (0.129) | ||||||
| Fads2 | BALBxB6 | C | M | +2.32 (0.025) | ||||
HF, high-fat diet; C, chow diet; M, male; F, female.
Bold indicates the high allele strain.
Gene expression differences between the QTL parental strains. All quantitative PCR performed regarding both loci are reported here. Experiments were performed in liver samples from at least three mice for the most relevant strain/sex/diet combination using β2 microglobulin as the endogenous control. The fold change is indicated as the gene expression of the high allele strain (bold) compared with the low allele strain. Only females were used to verify the microarray results provided in supplementary Table X.
Sequencing results are available in supplementary Tables XIII and XIV. Functionality was determined by using Polyphen and SIFT. Conservation was determined by comparison with mammals at the UCSC website.