Many splice-forms of WT1-AS have been characterized, where defects in the splicing machinery are implicated with acute myeloid leukaemia [ 63].
The validity of these new predictions will need to be confirmed using other techniques, but the fact that many of these novel transcripts and NTRs were observed in multiple samples suggests that many new splice forms of previously annotated genes and new genes have in fact been identified.
Simultaneously, this analysis implies that many alternative splice forms may accumulate to different levels, possibly resulting in accumulation of varying amounts of protein products with different functions.
Our data includes the discovery of many novel splice forms of cancer-associated genes and alternative-splicing patterns in cancer, and it suggests a significant new direction for human cancer research.
Second, models for quantifying full-length isoforms with single-end RNA-Seq data are often not identifiable for genes with many alternative splice forms (Hiller et al., 2009; Lacroix et al., 2008).
Following the initial identification of VEGF (Senger et al, 1983) many splice isoforms were subsequently identified, eventually forming a family of mature peptides – the VEGF xxx family (see Figure 1) (Houck et al, 1991).
First, because the RefSeq database excludes splice forms without enough experimental support, many true NMD targets may well be missed.
As observed for many other integrins [ 17] sequence analysis revealed alternative splice forms of the pre-mRNA.
Isoform selection of alternative splice forms may be involved in the pathogenesis of many human diseases and animal models thereof, including cancer and autoimmune diseases [62] [65].
Most human and mouse genes have many exons (Fig. 1, left) and are annotated with multiple splice forms.
The reciprocal best hit method (rbh) was adapted to account for alternative splice forms that are present in the KOME dataset that would otherwise give many false negatives.
