Table 1

20 most significantly deregulated genes after transfection of GFP siRNA.

downregulated

HELA

HEK


#

name

RefSeq

molecular function

MX

p§

BS

MX

p§

BS


1

SOAT1

NM_003101

sterol O-acyltransferase activity

-2.28

8.72E-14

32.76

-0.83

8.18E-07

14.15

2

Q96HQ8

~

unknown

-1.95

8.72E-14

32.87

-1.52

7.71E-12

27.43

3

CASP8

NM_033356

signal transducer activity;caspase activity

-1.56

5.35E-13

30.32

-0.88

6.42E-09

20.37

4

C10orf56

NM_153367

nucleic acid binding;zinc ion binding

-1.62

6.03E-13

30.12

-0.49

1.35E-05

10.51

5

NUDT3

NM_006703

magnesium ion binding;hydrolase activity

-1.45

1.74E-12

28.78

-0.42

6.64E-05

8.35

6

RAB21

NM_014999

nucleotide binding;GTP binding

-1.55

1.89E-12

28.60

-0.76

1.51E-07

16.52

7

HMGCS1

NM_002130

hydroxymethylglutaryl-CoA synthase activity

-1.48

2.73E-12

28.09

-0.45

6.05E-05

8.47

8

PAICS

NM_006452

catalytic activity;ATP binding

-1.37

3.72E-12

27.62

-0.66

3.61E-07

15.39

9

TM16F

NM_001025356

integral to membrane

-1.59

4.96E-12

27.25

-0.45

2.18E-04

6.68

10

GOSR1

NM_004871

v-SNARE activity

-1.47

5.13E-12

27.13

-0.46

6.89E-05

8.29

11

PSF1

NM_021067.3

protein binding

-2.18

5.44E-12

27.01

-1.55

5.47E-09

20.81

12

CYLD

NM_015247

NFkB pathway

-1.39

6.75E-12

26.74

-0.60

2.91E-06

12.56

13

CXorf34

NM_024917

methyltransferase activity

-1.68

1.11E-11

26.08

-0.67

1.08E-05

10.82

14

SKP2

NM_005983

protein binding

-1.18

1.80E-11

25.33

-0.74

7.49E-08

17.28

15

IL6ST

NM_002184

interleukin-6 receptor activity;protein binding

-1.20

2.92E-11

24.72

-0.57

3.49E-06

12.27

16

C10orf119

NM_024834

hypothetical protein

-1.14

3.13E-11

24.63

-0.26

5.18E-03

2.29

17

LARS2

NM_015340

leucine-tRNA ligase activity;ATP binding

-1.18

5.29E-11

23.85

-0.49

2.65E-05

9.59

18

NR1D2

NM_005126

transcription factor activity

-1.12

5.63E-11

23.71

-0.32

1.36E-03

4.11

19

ACSL4

NM_022977

long-chain-fatty-acid-CoA ligase activity

-1.22

6.44E-11

23.51

-0.47

7.21E-05

8.21

20

CCD25

NP_060716

unknown

-1.09

1.72E-10

22.18

-0.33

1.67E-03

3.83


upregulated

HELA

HEK


#

name

RefSeq

molecular function

MX

p§

BS

MX

p§

BS


1

ANXA3

NM_005139

diphosphoinositol-polyphosphate phosphatase

2.75

1.13E-15

37.54

0.47

3.89E-05

9.08

2

LOC51149

NM_016175

hypothetical protein

1.29

3.48E-11

24.46

0.29

8.79E-03

1.61

3

DDAH1

NM_012137

hydrolase activity

1.02

1.87E-10

22.07

0.35

5.88E-04

5.27

4

UBP18

NM_017414.2

ubiquitin thiolesterase activity

1.00

1.99E-10

21.99

0.54

4.64E-06

11.91

5

IL15RA

NM_002189

interleukin receptor activity

1.01

2.06E-10

21.94

0.30

2.38E-03

3.34

6

SPHK1

NM_021972

calmodulin binding;transferase activity

1.01

2.16E-10

21.88

0.42

9.44E-05

7.85

7

HIST1H2AC

NM_003512.3

DNA binding

1.27

2.49E-10

21.68

0.54

7.94E-05

8.08

8

MAG1

NM_032717

acyltransferase activity

0.95

2.70E-10

21.53

0.40

1.21E-04

7.53

9

SAT1

NM_002970

acyltransferase activity

1.08

3.21E-10

21.24

0.45

1.46E-04

7.25

10

PTGS2

NM_000963

peroxidase activity;oxidoreductase activity

1.25

4.65E-10

20.78

0.38

3.44E-03

2.84

11

HDHD1A

NM_012080

catalytic activity

0.95

8.31E-10

20.03

0.35

8.84E-04

4.67

12

STAMBPL1

NM_020799

ubiquitin thiolesterase activity

0.80

9.32E-10

19.90

0.30

8.23E-04

4.78

13

PIGL

NM_004278

hydrolase activity

0.83

1.17E-09

19.61

0.36

2.10E-04

6.73

14

CLPB

NM_030813

nucleoside-triphosphatase activity

0.81

2.28E-09

18.74

0.28

3.67E-03

2.75

15

SMPDL3B

NM_014474

hydrolase activity, acting on glycosyl bonds

0.88

2.40E-09

18.67

0.33

1.45E-03

4.02

16

HERC6

NM_017912

ubiquitin-protein ligase activity;GEF activity

0.81

2.69E-09

18.52

0.43

5.32E-05

8.62

17

GLRB

NM_000824

inhibitory glycine receptor,CNS

0.79

4.31E-09

17.90

0.28

3.47E-03

2.82

18

HHLA3

NM_007071

unknown

0.73

5.02E-09

17.71

0.36

1.86E-04

6.89

19

GNPDA1

NM_005471

hydrolase activity

0.63

2.46E-08

15.68

0.36

1.54E-04

7.17

20

PLEKHA7

NM_175058

unknown

0.63

3.29E-08

15.32

0.28

1.97E-03

3.59


X log2 expression ratio, § adjusted p value, S B statistics (for details see Methods and Additional file 5)

Tschuch et al. BMC Molecular Biology 2008 9:60   doi:10.1186/1471-2199-9-60

Open Data