Table 1. Validation set characteristics, based on data from discovery stage in this study, in addition to data from other gene expression profiling studies.
Entrez GeneID | Gene Symbol | Gene name | Chromosomal location | Fold change | FDR ♯ | Supporting evidence from other studies | Function |
---|---|---|---|---|---|---|---|
539 | ATP5O | ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit | 21q22.1-q22.2 | 2.29 | 8.20E-04 | [4,9,10] | energy metabolism |
6651 | SON | SON DNA binding protein | 21q22.11 | 2.51 | 4.32E-02 | [4,7,9] | regulator of cell-cycle |
6647 | SOD1 | superoxide dismutase 1, soluble | 21q22.11 | 2.29 | 2.52E-05 | [4,7,9,10,20] | involved in ROS metabolism |
6453 | ITSN1 | intersectin 1 (SH3 domain protein) | 21q22.1-q22.2 | 2.11 | 1.79E-02 | [3,7,10] | actin assembly and trafficking |
6612 | SUMO3 | SMT3 suppressor of mif two 3 homolog 3 | 21q22.11 | 2.53 | 4.33E-03 | [3,4,9] | involved in ROS metabolism |
10950 | BTG3 | BTG family, member 3 | 21q21.2 | 2.14 | 4.51E-03 | [3,4,7,9] | role in neurogenesis |
1827 | RCAN1 | regulator of calcineurin 1 | 21q22.12 | 2.33 | 4.58E-02 | [3,7,9,10] | role in neurogenesis |
10600 | USP16 | ubiquitin specific peptidase 16 | 21q22.11 | 3.24 | 4.78E-03 | [4,7,9] | involved in ROS metabolism |
3914 | LAMB3 | laminin, beta 3 | 1q32 | 0.16 | 5.79E-03 | [7]* | laminin is a basement membrane protein |
FDR – stands for “false discovery rate”, proportion of anticipated false discoveries, according to Benjamini-Hochberg method of adjusting for multiple testing
Although LAMB3 was not identified in other studies, we incorporated it into our biomarker set, due to its marked and highly significant down-regulation in TS21 samples. Additionally, its down-regulation was not directly reported in [7], but it could nevertheless be detected in the same processed dataset in the Gene Expression Atlas (http://www.ebi.ac.uk/gxa/)