Table 1 Symbol Definitions

n

Total number of genes with potential AE sites in a transcriptome.

k, k _i

Total number of AE cleavage sites within the transcripts of a gene (or gene i).

${k^{\prime }}_i$

Total number of AE cleavage sites within the coding region of gene i.

p

Global cleavage efficiency of the AE.

m _i

The frequency of mRNA for the i^th gene in the transcriptome. ${\displaystyle {\sum }_{i=1}^n{m}_i}=1$.

$\overrightarrow{m}$

{m₁, m₂, ..., m _n }

${\widehat{m}}_i$

mRNA frequency of gene i the joint posterior mode.

${\tilde{m}}_i$

mRNA frequency of gene i at the marginal posterior mode.

θ _i

The frequency of the observed tags for the i^th gene in the total tag pool, ${\displaystyle {\sum }_{i=1}^n{\theta }_i}=1$.

$\overrightarrow{\theta }$

{θ₁, θ₂, ..., θ _n }

${\widehat{\theta }}_i$

Tag frequency of gene i the joint posterior mode.

φ _i

Tag formation probability of gene i. Note this varies by experiment.

$\overline{\Phi }$

Mean tag formation progbability which is the sum of φ _i m _i across all genes.

T _i , T _{i, k}

Number of observed tags (at the j^th AE site) within the i^th gene's transcript.

$\overrightarrow{T}$

{T₁, T₂, ..., T _n }

T ₀

Total number of observed informative tags, which is ∑ _i ∑ _j T_{i, j}

α _i

Parameter for the prior of m _i .

$\overrightarrow{\alpha }$

{α₁, α₂, ..., α _n }

α ₀

Sum of all prior parameters, i.e. ∑ _i α _i .

β _i

Sum of prior parameters for genes other than i, i.e. α₀ - α _i .