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Table 3 Differentially accumulated transcripts between LoPro and HiPro identified by Affymetrix® Soy GeneChip

From: Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

#

Affymetrix® ID

LoPro

HiPro

Ratio of Means

LoPro/HiPro

Pvalue

FDR

Ch

Start

Stop

Uniprot Desc.

E-value

1

Gma.7719.1.A1_at

7705

401

19.22

2.43 × 10-15

9.16 × 10-11

20

26511887

26511422

Mov34/MPN/PAD-1

1 × 10-19

 

GmaAffx.74372.1.S1_at

2478

502

4.94

2.63 × 10-12

1.98 × 10-08

20

26512404

26511978

"

"

2

Gma.1680.1.S1_x_at

289926

63810

4.54

5.51 × 10-15

1.04 × 10-10

20

32331958

32332062

Hypothetical protein

6 × 10-24

 

Gma.1680.1.S1_at

134237

30039

4.47

1.05 × 10-14

1.32 × 10-10

20

32331999

32332062

"

"

3

GmaAffx.49130.1.S1_at

10163

842

12.06

4.38 × 10-13

4.12 × 10-09

20

30182754

30182479

na

na

 

GmaAffx.67113.1.S1_at

8643

1438

6.01

2.19 × 10-10

9.17 × 10-07

20

30182353

30181939

"

"

4

GmaAffx.65278.1.A1_at

2695

5039

0.53

5.95 × 10-12

3.74 × 10-08

20

31053180

31054158

na

na

5

Gma.926.1.A1_at

2047

1031

1.99

2.99 × 10-11

1.61 × 10-07

20

31812657

31812894

na

na

6

GmaAffx.55722.1.S1_at

12024

5126

2.35

1.01 × 10-10

4.74 × 10-07

20

26515177

26514175

Hypothetical protein

2 × 10-27

7

GmaAffx.69807.1.A1_at

8369

13209

0.63

8.08 × 10-07

2.42 × 10-03

17

1020953

1020579

Hypothetical protein

3 × 10-23

8

Gma.10034.1.A1_at

1563

2548

0.61

8.35 × 10-07

2.42 × 10-03

18

13340405

13340201

na

na

9

GmaAffx.42487.1.S1_at

9513

5786

1.64

1.51 × 10-06

3.79 × 10-03

18

12183748

12183617

na

na

10

GmaAffx.47978.1.S1_at

3007

1378

2.18

2.31 × 10-05

4.58 × 10-02

7

897321

897126

Putative phosphatase

3 × 10-75

  1. Each Affymetrix® probeset identifier (ID) is shown with corresponding normalized expression values for LoPro and HiPro and the ratio of mean LoPro divided by mean HiPro values. Criteria for the list: FDR < 0.05 and fold-change > 1.5. The Uniprot description for each Affymetrix® ID is accompanied by the E-value for the alignment; na = not applicable, no significant alignment.