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Table 2.

Microarray results for genes whose mRNA accumulation is affected at least 1.8-fold (P<0.05, corrected z test) in deps-1 germ lines

Genes downregulated in deps-1 relative to wild type
 
 
 

 

 

 
WormBase ID (gene name)
 
Gene family*
 
Primer pair
 
wt/deps-1 ratio
 
Chr
 
rde-3regulation(wt/rde-3 ratio)
 
F54H12.6  F54H12.6 10.7 III  
Y65B4BL.2 (deps-1 Y65B4B_13.B 6.5  
T21G5.3 (glh-1T21G5.3 3.3  
T20G5.11 (rde-4 T20G5.11 3.2 III  
Y19D10A.12 Y19D10A.L 2.7  
F54H12.1 (aco-2 F54H12.1 2.5 III  
Y19D10A.4 Y19D10A.D 2.4  
Y19D10A.16 Y19D10A.N 2.2  
C01B4.6 C01B4.6 2.0  
C01B4.7 C01B4.7 2.0 Down(2.5) 
F55G1.8 (plk-3 F55G1.8 1.9 IV  
T20G5.2 (cts-1 T20G5.2 1.9 III  
Y116A8C.30
 

 
Y116A8C.30
 
1.9
 
IV
 

 
Genes upregulated in deps-1 relative to wild type
 
 
 

 

 

 
WormBase ID (gene name)
 
Gene family*
 
Primer pair
 
deps-1/wt ratio
 
Chr
 
rde-3regulation(rde-3/wt ratio)
 
W09B7.2 W09B7.B 11.6 Up(39.1) 
Y43F4A.3  Y43F4A.3 8.4 III  
F11A6.2  F11A6.2 6.5  
C38D9.2 C38D9.2 5.7 Up (45.6) 
C07G3.9 (ugt-64 C07G3.9 4.7  
W09B7.1 W09B7.C 4.4  
W03G1.3 W03G1.3 4.1 IV  
C40A11.8  C40A11.8 3.3 II  
K02B7.2 K02B7.2 3.2 II Up (9.2) 
K02B7.1§ K02B7.1 3.2 II  
C18D4.6  C18D4.6 3.1  
K02E7.2 K02E7.2 2.9 II  
F41G4.7 10 F41G4.6 2.6 Up (3.9) 
T23G5.6  T23G5.6 2.6 III Up (2.2) 
F15D4.5 F15D4.5 2.4 II Up (50.9) 
K07E8.10 K07E8.10 2.3 II  
C04C3.5 (dyf-3 C04C3.5 2.3 IV  
ZC15.3 10 ZC15.3 2.2  
K08D10.5  K08D10.5 2.1 IV  
C33H5.4 (klp-1011 C33H5.4 2.0 IV  
D2045.2 12 D2045.2 2.0 III  
T24B8.7  F37B12.4 2.0 II  
H04D03.3 12 H04D03.3 1.9 III  
R03G8.2**  R03G8.2 1.9  
Y39A3CL.6 (pvf-1 Y39A3C_84.B 1.9 II  
C13B9.1  C13B9.1 1.8 III  
C04F12.9 (rnh-1.3 C04F12.9 1.8 Up (17.2) 
F30B5.4  F30B5.4 1.8 IV  
Y55H10B.1** 13 Y55H10B.D 1.8 IV Up (5.2) 
F57G4.3** 13 F57G4.3 1.8 Up (5.0) 
T03D3.5  T03D3.5 1.8  
B0511.11  B0511.11 1.8  
Genes downregulated in deps-1 relative to wild type
 
 
 

 

 

 
WormBase ID (gene name)
 
Gene family*
 
Primer pair
 
wt/deps-1 ratio
 
Chr
 
rde-3regulation(wt/rde-3 ratio)
 
F54H12.6  F54H12.6 10.7 III  
Y65B4BL.2 (deps-1 Y65B4B_13.B 6.5  
T21G5.3 (glh-1T21G5.3 3.3  
T20G5.11 (rde-4 T20G5.11 3.2 III  
Y19D10A.12 Y19D10A.L 2.7  
F54H12.1 (aco-2 F54H12.1 2.5 III  
Y19D10A.4 Y19D10A.D 2.4  
Y19D10A.16 Y19D10A.N 2.2  
C01B4.6 C01B4.6 2.0  
C01B4.7 C01B4.7 2.0 Down(2.5) 
F55G1.8 (plk-3 F55G1.8 1.9 IV  
T20G5.2 (cts-1 T20G5.2 1.9 III  
Y116A8C.30
 

 
Y116A8C.30
 
1.9
 
IV
 

 
Genes upregulated in deps-1 relative to wild type
 
 
 

 

 

 
WormBase ID (gene name)
 
Gene family*
 
Primer pair
 
deps-1/wt ratio
 
Chr
 
rde-3regulation(rde-3/wt ratio)
 
W09B7.2 W09B7.B 11.6 Up(39.1) 
Y43F4A.3  Y43F4A.3 8.4 III  
F11A6.2  F11A6.2 6.5  
C38D9.2 C38D9.2 5.7 Up (45.6) 
C07G3.9 (ugt-64 C07G3.9 4.7  
W09B7.1 W09B7.C 4.4  
W03G1.3 W03G1.3 4.1 IV  
C40A11.8  C40A11.8 3.3 II  
K02B7.2 K02B7.2 3.2 II Up (9.2) 
K02B7.1§ K02B7.1 3.2 II  
C18D4.6  C18D4.6 3.1  
K02E7.2 K02E7.2 2.9 II  
F41G4.7 10 F41G4.6 2.6 Up (3.9) 
T23G5.6  T23G5.6 2.6 III Up (2.2) 
F15D4.5 F15D4.5 2.4 II Up (50.9) 
K07E8.10 K07E8.10 2.3 II  
C04C3.5 (dyf-3 C04C3.5 2.3 IV  
ZC15.3 10 ZC15.3 2.2  
K08D10.5  K08D10.5 2.1 IV  
C33H5.4 (klp-1011 C33H5.4 2.0 IV  
D2045.2 12 D2045.2 2.0 III  
T24B8.7  F37B12.4 2.0 II  
H04D03.3 12 H04D03.3 1.9 III  
R03G8.2**  R03G8.2 1.9  
Y39A3CL.6 (pvf-1 Y39A3C_84.B 1.9 II  
C13B9.1  C13B9.1 1.8 III  
C04F12.9 (rnh-1.3 C04F12.9 1.8 Up (17.2) 
F30B5.4  F30B5.4 1.8 IV  
Y55H10B.1** 13 Y55H10B.D 1.8 IV Up (5.2) 
F57G4.3** 13 F57G4.3 1.8 Up (5.0) 
T03D3.5  T03D3.5 1.8  
B0511.11  B0511.11 1.8  
*

Numbers indicate different gene families. Members of each family are listed in Table 3.

All rde-3(ne298) regulation data are from Table S1 in Lee et al.(Lee et al., 2006).

Oligos on rde-3 arrays are not specific for this gene family member; some or all detect multiple gene family members.

§

99% identical to R09E12.6, which is upregulated 20.88-fold in rde-3(ne298) mutants.

F41G4.6 is upregulated; F41G4.6 was recently merged into F41G4.7.

**

Possible transposon (WormBase release WS172).

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