Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach

BMC Genomics

Table 3 RXE based on annotation

Annotation type	Human liver	Human brain	Human lymphoblast 45, X^m	Human lymphoblast 45, X^p
RefSeq	−0.28	0.16	−0.14	−0.19
RefSeq protein coding	−0.41	−0.11	−0.17	−0.25
Ensemble (gene)	−0.33	−0.09	0.34	0.02
Ensemble (transcript)	−0.12	0.09	0.01	−0.45
UCSC (h19) known genes	0.05	0.08	0.00	−0.66
Gencode	−0.07	0.09	−0.12	−0.38

Variation in relative X-chromosome expression values resulting from different genome annotations used in mapping. All data was log₂-transformed. For each row, the same mapping file was used, but a different annotation was implemented in the program Cufflinks in order to generate FPKM values for each gene.

ISSN: 1471-2164