Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures

BMC Genomics

Table 2 Protein structure disruptions in mammalian messenger RNA transcripts

Type of initial frame disruption*	Alignment verification**	Protein structure disruption***
		Observed [nondisrupting : disrupting]	Expected [nondisrupting : disrupting]	Significance
Frameshift	All cases	293 : 54	272.7 : 74.3	††
	Cases with verifying alignments	230 : 51	211.3 : 69.7	†††
Stop codon	All cases	68 : 5	55.6 : 17.4	†††
	Cases with verifying alignments	34 : 5	27.4 : 11.6	†
Frameshift or stop codon	All cases	360 : 59	327.5 : 91.5	†††
	Cases with verifying alignments	268 : 57	242.2 : 82.8	††
	Cases with verifying alignments (excluding probable UTR features)	174 : 35	153.6 : 55.4	†††

* For the last row, those with frameshifts and stop codons are pooled together.
** Verifiying alignments are significant alignments to a rodent or non-mammalian vertebrate protein, as detailed in Methods.
*** The ratio stands for 'the number of frame disruptions not disrupting a protein structure domain assignment versus the number that do'. A margin for ascertaining overlap with a protein domain assignment of 15 nucleotides was used in the calculations. The expectations for the statistical tests (χ²) are calculated by adding up the total amount of coding sequence that can be assigned to a SCOP protein structure domain for the sample of transcripts analysed in each row of the table. † stands for P < 0.05, †† for P < 0.01 and ††† for P < 0.001. The significant results remain significant to at least P < 0.05 when margins for calculating overlap with protein domains of 0, 5, 10, 20 or 25 nucleotides are also used.

ISSN: 1471-2164