Table 4. Summary of transcript isoforms detected by BWA/ANOVA and TopHat/Cufflinks workflows.

Analysis	BWA/ANOVA	TopHat/Cufflinks
Total detected transcripts	16,014	34,115
mRNA	15,142	32,001
mRNA DETs	1,422	3,258

The BWA workflow employed refflat.txt annotation for mouse build mm9 from UCSC genome browser. The TopHat workflow employed GTF annotation for mouse build mm9 from the Ensembl database. After FPKM filtering (see Materials and Methods), transcribed features were classified as protein coding mRNAs and non-coding (nc) RNAs. The features classified as protein-coding mRNAs were further filtered based on fold change (≥1.5) and p-value (<0.05) to be considered significantly differentially expressed transcripts (DETs).