Table 2.
Positional candidate genes for the Fatq2a and Fatq2b QTL
| mm9 | Symbol | HG2D microarray p-value 1 & (tissue) 2 | SNP 3 | Sift 4 | KO Models 5 | |||
|---|---|---|---|---|---|---|---|---|
| Chr | Location (Mb) | Prediction | Score | KO | P | |||
| 2 | 170.56 | Dok5 | -- | -- | -- | -- | -- | -- |
| 2 | 172.07 | Mc3r | -- | -- | -- | -- | 3 | Bh, G/S, Ob, S |
| 2 | 172.2 | Cstf1 | -- | rs27646875 | deleterious | 0 | -- | -- |
| 2 | 172.69 | Bmp7 | -- | -- | -- | -- | 3 | S, G/S, Eg, M/A |
| 2 | 172.98 | Pck1 | -- | -- | -- | -- | 4 | Ob, M/A, G/S |
| 2 | 173.03 | Zbp1 | -- | -- | -- | -- | 1 | -- |
| 2 | 173.34 | 1700021F07Rik | 0.0220(A) | -- | -- | -- | -- | -- |
| 2 | 173.44 | Ppp4r1l-ps | 0.0035(B) | -- | -- | -- | -- | -- |
| 2 | 173.51 | Rab22a | ≤0.0001(ABL) | -- | -- | -- | -- | -- |
| 2 | 173.59 | Vapb | ≤0.017(BL) | -- | -- | -- | -- | -- |
| 2 | 173.91 | Stx16 | -- | -- | -- | -- | -- | -- |
| 2 | 173.94 | Npepl1 | ≤0.0050(BL) | -- | -- | -- | -- | -- |
| 2 | 174.11 | Nespas** | -- | -- | -- | -- | 1 | PL, G/S, Bh |
| 2 | 174.14 | Gnas | ≤0.0037(AB) | rs28297630 | deleterious | 0.03 | 12 | EL, PL, G/S, Mt, Ob, DA |
| rs28297631 | deleterious | 0.01 | ||||||
| rs28297633 | deleterious | 0 | ||||||
| rs6313545 | deleterious | 0.02 | ||||||
| rs6314659 | deleterious | 0 | ||||||
| 2 | 174.25 | Th1l | -- | -- | -- | -- | -- | -- |
| 2 | 174.26 | Ctsz | 0.0020(B) | rs16789971 | deleterious | 0.02 | 3 | Tm |
| 2 | 174.28 | Tubb1 | -- | -- | -- | -- | -- | |
| 2 | 174.29 | Atp5e | ≤ 0.0021(ABL) | rs28261286 | deleterious | 0.01 | -- | -- |
| 2 | 174.29 | Slmo2 | 0.0800(B) | -- | -- | -- | -- | -- |
| 2 | 177.75 | Etohi1 | -- | -- | -- | -- | -- | -- |
**Antisense gene selected from MGI.
1P-values correspond to a comparison between HG2D Cast/Cast vs HG2D B6/B6 littermates (GSE22042) . The highest p-value is shown if multiple tissues were selected.
2Tissue: A = Gonadal White Adipose; B: Whole Brain; L: Liver. Genes without p-value had p > 0.1.
3SNP from dbSNP 128 contained in each gene with a deleterious Sift Prediction.
4SIFT prediction output from the ENSEMBL 76 Variation data set. Input variants were the 17,310 and 14,920 SNP variants contained between the CI interval of Fatq2a (170.5 to 173.03) and Fatq2b (173.3 and 175.6), BioMart settings were set to filter variants containing a tolerated and deleterious prediction between CAST/EiJ and C57BL/6J.
5KO = Number of Knockout Models; P = Phenotype; Bh = Behaviour; G/S = Growth and Size; Ob = Obesity related phenotype; S = Skeletal phenotype, Eg = Embriogenesis; M/A = Mortality/Aging; PL = Postnatal Lethality; EL = Embryonic Lethality; Mt = Metabolism; DA = Developmental Abnormalities; Tm – Tumorigenesis. Phenotype information and number of KO was obtained from MGI (revised March 2010).