Determination of Included and Excluded Exons To determine whether alternative exons were included or excluded in the transcripts produced, previously described RNA-seq data used for determining expressed genes was analyzed with MISO (Katz et al., 2010 ).
To determine whether alternative exons were included or excluded in the transcripts produced, previously described RNA-seq data used for determining expressed genes was analyzed with MISO (Katz et al., 2010).
Sequence analyses of the affected transcripts show that the longest intron is either partially retained or excluded in the alternative transcripts.
The exons in a splicing module can belong to different genes, but they exhibit correlated splicing patterns (in terms of being included or excluded in their respective transcripts) across different conditions, thus form an exon co-splicing cluster.
The 15-nucleotide sequence of exon 9 was excluded in 98 % of the transcripts in the brain, with slightly higher inclusion levels in the other tissues (25 27 %).
This list was obtained by comparing profiles of genes detected by the three treatments, excluding duplicate transcripts, unknown transcripts and transcripts not detected in one or two of the treatments.
We divided this set of transcripts into groups that use the same TSSs, and counted the number of transcripts in which the exon was included, and the number of transcripts in which the exon was excluded in each TSS group.
Moreover, we included all C. elegans rRNA transcripts as filter sequences, while the 5.8S (156-nt) and 5S (121-nt) rRNA transcripts were excluded in human.
To determine differential transcript expression, low-abundance transcripts with less than 10 reads in two libraries were first excluded then the remaining transcripts were analyzed with EdgeR with classical analysis parameters.
By excluding the annotated transcripts in RAP and the MSU rice gene models (http://rice.plantbiology.msu.edu/), we were able to detect a total of 8,590 transcripts from the root and 8,193 transcripts from the shoot which have not yet been previously annotated.
