Human genes escaping X-inactivation revealed by single cell expression data

BMC Genomics

Table 2 Escapees from 25 clonal single cell lymphoblasts

Gene symbol^a	Gene Type	Total iSNPs	iSNPs Ratio^b	# cells with any observation	# cells with paternal observation^c	Total Reads	Paternal reads	Paternal Ratio^d	Evidence poor^e
SLC25A6	PAR	34	0.882	18	16	9182	4887	0.532
ZFX		48	0.438	21	12	11,697	2221	0.190
CD99	PAR	38	0.605	17	10	5205	2027	0.389
DDX3X		13	0.846	12	10	1003	367	0.366
XIST	ncRNA	20	0.950	10	10	1652	1640	0.993
JPX	ncRNA	19	0.579	10	8	1931	1039	0.538
EIF2S3		10	0.600	10	6	1322	706	0.534
DHRSX	PAR	17	0.471	8	5	2379	1815	0.763
SMC1A		9	0.556	9	5	807	511	0.633
TRAPPC2		19	0.211	12	4	4427	790	0.178
DMD		11	0.364	6	4	1533	160	0.104
AKAP17A	PAR	7	0.429	7	3	722	438	0.607
AP1S2		3	1.000	3	3	99	54	0.545
XIAP		19	0.158	6	3	1944	437	0.225
P2RY8	PAR	13	0.308	5	2	843	454	0.539
TMSB4X		5	0.400	5	2	372	70	0.188
FAAH2		2	1.000	2	2	35	35	1.000
DIAPH2		12	0.167	7	2	835	83	0.099
CSF2RA	PAR	3	1.000	1	1	58	56	0.966
IL3RA	PAR	13	0.231	6	1	837	120	0.143
PRKX		2	1.000	1	1	36	36	1.000	*
FRMPD4		3	1.000	1	1	119	118	0.992
SYAP1		3	0.333	2	1	190	57	0.300
TXLNG		6	1.000	1	1	197	170	0.863
OTC		4	1.000	1	1	44	44	1.000	*
KIF4A		3	0.333	3	1	265	27	0.102	*
TEX11		4	0.250	3	1	244	84	0.344	*
FTX	ncRNA	8	0.125	3	1	716	35	0.049	*
BRWD3		4	0.500	3	1	88	48	0.545	*
ZCCHC16		2	0.500	1	1	57	32	0.561	*

^aOnly 30 genes that are supported by iSNP-based and read-based methods are listed. A full list of all genes (49) is available in Additional file 3: Table S4
^bFraction of iSNP supporting the paternal or biallelic observations out of total recorded iSNPs for a gene, for example in ZCCHC16 there were overall 2 iSNPs, one of them was paternal so the iSNPs ratio is 0.5
^cAn underline indicates that the single paternal observation originated from the outlier cell (SRR764803)
^dFraction of parental reads out of total read for a gene
^eEvidence poor apply for genes with a cell-based inconsistency or having < 50 paternal reads with only one supporting cell indicated by an asterisk

ISSN: 1471-2164