An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

Table 4 Multiple Comparisons for Score, and Proportion of dominant variants.

MSA	2299 Resistant Isolates w1	2299 Resistant Isolates w2	AZT-3TC-ABC	D4T-3TC-NVP	GENOME DNA All Subtype	GENOME DNA GroupM plus Recombinants	GENOME DNA No Recombinants	POL DNA All Subtypes	POL DNA GroupM plus Recombinants	Pol DNA No recombinants	ZDV-3TC-EFV w1	ZDV-3TC-EFV w2	ZDV-3TC-EFV w3
Assigned letter group	(A)	(B)	(C)	(D)	(E)	(F)	(G)	(H)	(I)	(J)	(K)	(L)	(M)
Mean ^a Score			A B K L	A B K L	A B C D K L M	A B C D K L M	A B C D K L M	A B C D K L M	A B C D K L M	A B C D K L M	A B L		A B K L
^b 0			K	K	K	K	K	K	K	K		K	A B E F G H I J K L
^b 1	M	M			M	M	M	M	M	M	C D E F G H I J L M	M

a. Weighted average of the score was used for multiple comparisons between de MSAs
b. In the comparisons of the proportion of dominant variants, number 1 represents the dominant viral variants while number 0 represents the rest of viral variants (subdominant and infrequent).
For weighted average score, a multiple comparison Student t-test was used to evaluate mean equality between each pair of groups. The MSA was assigned as the segmenting categorical variable and the score was the continuous variable for which the mean was calculated. For the comparison between pairs of proportions of dominant variants, a Z-test was used. The MSA was assigned as the segmenting categorical variable, and the proportion was assigned the categorical variable that revealed the presence or absence of the event of interest. In the second and third rows appear the corresponding letters of the groups that showed significant differences with the MSA of the column. In both cases p values were corrected with Bonferroni-Dunn test with an alpha of 0.05. See Methods, for further understanding on how weighted average scores were calculated.

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