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Table 3 Genes that were found most stably up or down-regulated in Arabidopsis wild type across 11 studies in a total of 14 transcriptomic comparisons between -Fe and  +Fe

From: Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks

Symbol

AGI

1

2

3

4

5

6a

6b

6c

7

8

9a

9b

10

11

VIRT

Genes that are most stably up-regulated under iron deficiency

 Kelch repeat family protein

AT3G07720

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1.00

 MTPA2

AT3G58810

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1.00

 IRT1

AT4G19690

1

1

1

1

1

1

1

1

1

1

1

1

1

0

0.93

 2OG

AT3G12900

1

1

1

1

1

1

1

1

1

1

1

1

1

0

0.93

 unknown

AT3G61930

1

1

1

1

1

1

1

1

1

1

1

1

1

0

0.93

 GLP5

AT1G09560

1

1

1

1

1

1

1

1

1

1

1

1

0

0

0.86

 Unknown

AT3G06890

1

1

1

1

1

1

1

1

0

1

1

1

1

0

0.86

 COPT2

AT3G46900

1

1

0

1

1

1

1

1

1

1

1

1

1

0

0.86

 UGT72E1

AT3G50740

1

1

1

1

1

1

1

1

0

0

1

1

1

1

0.86

 bHLH039

AT3G56980

1

1

1

1

1

1

1

1

0

1

1

1

0

1

0.86

 MYB72

AT1G56160

1

1

0

1

1

1

1

1

1

1

1

1

1

0

0.86

 Cation efflux family protein

AT3G58060

1

1

1

1

1

1

1

1

0

1

1

1

1

0

0.86

Genes that are most stably down-regulated under iron deficiency

 FER1

AT5G01600

-1

0

-1

-1

-1

-1

-1

-1

 

-1

-1

-1

 

0

-0.83

 ATABC1

AT4G04770

-1

0

-1

-1

-1

-1

-1

-1

 

0

-1

-1

 

0

-0.75

 unknown

AT2G36885

-1

0

0

0

-1

-1

-1

-1

 

-1

-1

-1

 

0

-0.67

 PSAF

AT1G31330

-1

0

-1

-1

0

-1

-1

0

 

0

-1

-1

 

0

-0.58

 uncharacterized protein family (UPF0016)

AT1G68650

-1

0

0

0

-1

-1

-1

-1

 

-1

0

-1

 

0

-0.58

 PER21

AT2G37130

-1

0

-1

-1

0

-1

-1

0

 

0

-1

-1

 

0

-0.58

 FER4

AT2G40300

-1

0

0

-1

-1

-1

-1

-1

 

-1

0

0

 

0

-0.58

 LAC7

AT3G09220

-1

-1

0

0

-1

-1

-1

0

 

0

-1

-1

 

0

-0.58

 SAPX

AT4G08390

-1

0

-1

-1

0

-1

-1

0

 

0

-1

-1

 

0

-0.58

 unknown

AT5G59400

-1

0

-1

-1

-1

-1

-1

-1

 

0

0

0

 

0

-0.58

 HEMA1

AT1G58290

0

0

0

0

-1

-1

-1

-1

 

0

-1

-1

 

0

-0.50

 FSD1

AT4G25100

-1

-1

0

-1

-1

0

0

-1

 

0

0

0

 

-1

-0.50

 peroxidase, putative

AT5G64100

0

-1

0

-1

0

-1

-1

0

 

0

-1

-1

 

0

-0.50

  1. Up-regulated genes are represented by the value 1. Down-regulated genes are represented by the value -1. Genes with no significant regulation or with regulation below the threshold of the respective study are represented by the value 0. The genes with the highest VIRT absolute value are regarded as most stably up- or down-regulated, respectively. 1: This study (seedlings). 2: This study (roots). 3: Bauer and Blondet, 2011 [63]. 4: Ivanov et al., 2012 [13]. 5: Yang et al., 2010 [19]. 6a: Long et al., 2010. 48 h [25]. 6b: Long et al., 2010. 72 h [25]. 6c: Long et al., 2010. 24 h (WT vs. pye) [25]. 7: Garcia et al., 2010 [20]. 8: Buckhout et al., 2009 [24]. 9a: Dinneny et al., 2008. 48 h [64]. 9b: Dinneny et al., 2008. 72 h [64]. 10: Colangelo and Guerinot, 2004 [11]. 11: Schuler et al., 2011 [65]. For the down-regulated genes, the analyses 7 [20] and 10 [11] were excluded in the calculation of the VIRT value since these only contained genes that were induced upon iron deficiency