Table IV.
Summary of XCI analysis results for genes thought to escape XCI with strong evidence of undergoing XCI (PP<0.10) from XCI in at least one ovarian tumor sample.
| Gene | Cytoband (Ensembl)a | Total number of tumors evaluated | Escaping XCI (PPjg>0.5) | Subject to XCI (PPjg<0.5) | Proportion of samples undergoing XCI (N undergoing/N total)b | Consensus State[Balaton, Cotton, & Brown 2015] | Known Oncogene or Tumor Suppressor (reference) |
|---|---|---|---|---|---|---|---|
| ARSD | Xp22.33 | 25 | 11 | 3 | 21% (3/14) | Mostly Ec | |
| KAL1 | Xp22.31 | 14 | 1 | 6 | 86% (6/7) | Mostly E | Tumor suppressor[Liu, Cao, Chen, Xu, & Zhang 2015; Tanaka, et al. 2015] |
| NLGN4X | Xp22.31 | 19 | 8 | 2 | 20% (2/10) | Mostly E | |
| CTPS2 | Xp22.2 | 9 | 0 | 9 | 100% (9/9) | Mostly E | Platinum sensitivity[Gamazon, et al. 2011] |
| GEMIN8 | Xp22.2 | 11 | 1 | 4 | 80% (4/5) | Mostly E | |
| GPM6B | Xp22.2 | 12 | 3 | 7 | 70% (7/10) | Mostly E | |
| OFD1 | Xp22.2 | 4 | 0 | 1 | 100% (1/1) | Mostly E | |
| RBBP7 | Xp22.2 | 2 | 0 | 2 | 100% (2/2) | Mostly E | Tumor suppressor[Li, et al. 2016] [Chaligne, et al. 2015] |
| TCEANC | Xp22.2 | 9 | 0 | 7 | 100% (7/7) | Mostly E | Tumor suppressor with BRCA1[Hill, et al. 2014] |
| TRAPPC2 | Xp22.2 | 23 | 10 | 3 | 23% (3/13) | Mostly E | Tumor suppressor[Tokunaga, et al. 2013] |
| TXLNG | Xp22.2 | 16 | 8 | 1 | 11% (1/9) | Ed | |
| EIF1AX | Xp22.12 | 21 | 4 | 11 | 73% (11/15) | E | |
| EIF2S3 | Xp22.11 | 18 | 1 | 4 | 80% (4/5) | E | |
| CXorf38 | Xp11.4 | 12 | 1 | 8 | 89% (8/9) | E | |
| DDX3X | Xp11.4 | 17 | 9 | 1 | 10% (1/10) | E | Tumor suppressor[Bol, Xie, & Raman 2015; Dunford, et al. 2016] |
| USP9X | Xp11.4 | 23 | 3 | 6 | 67% (6/9) | Mostly E | Tumor suppressor[Jo, Kim, Yoo, & Lee 2016; Perez-Mancera, et al. 2012] |
| IQSEC2 | Xp11.22 | 3 | 1 | 2 | 67% (2/3) | Mostly E | |
| KDM5C | Xp11.22 | 8 | 0 | 8 | 100% (8/8) | Mostly E | Tumor suppressor[Dalgliesh, et al. 2010; Dunford, et al. 2016] |
| RPS4X | Xq13.1 | 13 | 10 | 1 | 9% (1/11) | Mostly E | Prognostic marker[Tsofack, et al. 2013] |
| NAP1L3 | Xq21.32 | 3 | 0 | 2 | 100% (2/2) | Mostly E |
a
as denoted by Ensembl GRCh38
b
Tumors are defined as escaping XCI if PPjg>0.90, subject to XCI if PPjg<0.10, or otherwise were not called.
c
Consensus state defined by previous literature suggests these genes escape XCI in almost all tissues
d
Consensus state defined by previous literature suggests these genes escape XCI in most tissue