Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes

Table 3 Proteome and Transcriptome Alignments Summary

		Detected Viral Genes (Tallies)				Aligned%
Transcripts		+	+	-	-	T% ^§
Proteins		-	+	+	-		P%
*KSHV*
BCBL-1	Latent	34	53	3	7	*68%*	*95%*
	* Lytic	31	56	3	7	*	*95%*
BC-1	Latent	28	10	10	49	*31%*	*50%*
	Lytic	45	37	5	10	*51%*	*88%*
*EBV*
BC-1	Latent	21	2	12	58	*11%*	*14%*
	Lytic	18	13	28	34	*46%*	*32%*

+/- Column: # viral genes detected at only the transcript level
+/+ Column: # viral genes detected at both transcript and protein levels (indicated in bold)
-/+ Column: # viral genes detected at only the protein level
-/- Column: # viral genes not detected at either level
Total Transcripts Possible: KSHV = 97; EBV = 93 (row totals)
Detected Transcripts (+) ≥1.25-fold over reference sample
Undetected Transcripts (-) <1.25-fold over reference sample
Total Proteins Possible: KSHV = 86; EBV = 86
Detected Proteins (+): spectra are observed with the protein
Undetected Proteins (-): spectra are not observed with the protein
Aligned%= 100% × +/+ column ÷ total detected transcripts (T%) or total detected proteins (P%)
^§Transcript-to-protein alignments (%) were adjusted to remove non-coding RNAs from the denominator.
* BCBL-1 latent transcripts were aligned to lytic proteins (no transcript analysis was performed with lytic BCBL-1).

ISSN: 1471-2164