Table 1 SVMR 4-level search strategy and results

Theme

Genes that contained highly correlated genes

From the same biological family

Across biological families

Random Walk (all genes)

Sample size

1000

55 RP^a 49 ZFP^b

49

3554

Sample selection criteria

A total of 1000 genes that contained 100 highly correlated genes

all in RP family, all in ZFP family

RP, ZFP, and DEAD^c

The full data set of all 3554 genes

Training size

2 genes per training, 3 trainings

2 to 10 genes

3 genes per training

3 to 20 genes

Training selection criteria

Corr > 0.85, p < 0.001

Randomly from 55 RP genes or from 49 ZFP genes

Only from RP family

Randomly from entire sample

Best training size

2 genes

4–5 genes

3 genes

3–7 genes

Example of training genes

1. 200088_x_at and 200809_x_at (both are different problems for RPL12) (Pearson corr > 0.92 and Spearman corr > 0.90, p < 0.0001)

2. RPL32 and RPS18 (Pearson corr > 0.94, p < 0.0001)

3. DDX3Y and EIF1AY (Pearson corr > 0.9875, p < 0.0001)^d

RPS11

RPS10

RPS3A (201257_x_at)

RPS16

RPS4X

RPS4Y1

RPS5

C1D

ALOX5

ENO2

RERE

Example of captured genes

1. 200088_x_at and 200809_x_at

2. RPL32, RPS15, RPS18, RPS3A, and RPS28

3. DDX3Y and EIF1AY

1. RPL27, RPS3A(2000099_s_at), RPS3A(201257_x_at), RPS29, RPS28

2. RPS15A, RPS18, RPS12, RPS19

3. Similar results were seen among genes with ZFP family

DDX39

DDX3Y

DDX58

DDX26

SCAP1

SGPP1

TGFBR3

CD9

VAMP8