TABLE 1.
Filtering process of the cis QTL candidates in the hippocampus of BXD
| Steps of the filtering process | No. of probe sets (genes) | Additive effect (B vs. D ratio, %) |
|---|---|---|
| Affymetrix M430 v2.0 array data set | 45,101 (23,080) | 47:53 |
| A. cis QTL (LRS > 20, QTL mapped ± 3 Mb from source) | 3,810 (2,856) | 66:34 |
| cis QTL (LRS > 20, QTL mapped ± 5 Mb from source) | 4,117 (3,064) | 67:33 |
| cis QTL (LRS > 15, QTL mapped ± 3 Mb from source) | 4,416 (3,279) | 61:39 |
| cis QTL (LRS > 15, QTL mapped ± 5 Mb from source) | 4,844 (3,548) | 65:35 |
| B. cis QTL (LRS > 20, QTL mapped ± 3 Mb from source) fold difference between allelic expression >1.7 | 750 (630) | 60:40 |
| C. Probes associated with potentially true cis QTL—filtering out the remaining 440 cis QTL was based on: | 190 (166) | 49:51 |
| Potential SNP overlapping probes (70%) | 308 (302) | 74:23 |
| Alternative 3′-UTR processing (14%) | 62 (62) | 76:24 |
| Alternative splicing (10%) | 44 (44) | 72:28 |
| Other (6%) |
26 (25) |
64:36 |