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Table 3 Candidate genes significantly regulated within the RNA-Seq experiment (FDR < 0.05) and validated by RT-PCR

From: Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17

Gene Position Function1 Accession2 Comp. 1 Comp. 2 Comp. 3 Comp. 4
(log2FC) (log2FC) (log2FC) (log2FC)3
GRMZM2G350312 1:65657063-65660290 bHLH transcription factor AT3G47640.1(PYE)/LOC_Os03g26210.2/B8A2P8 sig. (1.81)    sig. (3.07)
GRMZM2G106980 1:203647045-203653762 Putative BURP-domain protein, uncharacterized protein AT5G25610.1(ATRD22,RD22)/LOC_Os06g19800.1/B8A121 sig. (-3.80) sig. (-4.25)   
GRMZM2G059465 1:209119390-209120903 O-methyl transferase, uncharacterized protein AT4G35160.1/LOC_Os06g16960.1/B8A095     sig. (-2.49)
GRMZM2G055802 1:293997055-290998873 NA LOC_Os03g60840.1    sig. (2.53)  
GRMZM2G132678 3:20795800-20806607 Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase AT5G48930.1(HCT)/LOC_Os08g43040.1 sig. (5.35) sig. (4.50)   
GRMZM2G057413 3:148031451-148062994 bHLH transcription factor AT3G56970.1(BHLH038,ORG2)/LOC_Os01g72370.1     sig. (3.77)
GRMZM2G400602 3:174361241-174363882 Putative oligopeptide transporter, uncharacterized protein AT1G22540.1/LOC_Os01g65100.1/C0HEP6     sig. (3.29)
GRMZM5G896496 3:211872426-211879044 Putative chaperone ClpC1, uncharacterized protein C0HH28 sig. (-5.10) sig. (-5.00)   
GRMZM2G574782 4:18676198-18682894 Probable bifunctional methylribose-1-phosphate dehydratase/enolase phosphatase E1 AT5G53850.2/LOC_Os11g29370.1/B4G0F3 sig. (1.74)    sig. (1.92)
GRMZM2G096958 4:219581607-219585123 Nicotinamine aminotransferase1, uncharacterized protein AT5G36160.1/LOC_Os02g20360.1/B4FEZ7 sig. (1.71)    sig. (1.98)
GRMZM2G010280 4:240232549-240234575 High affinity nitrate transporter AT5G60770.1(ATNRT2.4,NRT2.4/LOC_Os02g02170.1)/Q53CL7     sig. (-3.12)
GRMZM2G010251 4:240243499-240245403 High affinnity nitrate transporter, uncharacterized protein AT1G08090.1(ACH1,ATNRT2.1)/LOC_Os02g02170.1/B4FSV9     sig. (-2.58)
GRMZM2G089836 567508591-67511890 Glycosyl hydrolase, Invertase AT1G62660.1/LOC_Os02g01590.1/B6T0A9     sig. (-2.61)
GRMZM2G041980 5:148304652-148307020 Putative aquaporin protein, NIP1-1 AT4G18910.1(ATNLM2,NIP1)/LOC_Os05g11560.1/Q9ATN4 sig. (3.46)   sig. (-2.41)  
GRMZM2G465226 7:3483731-3484794 Pathogenesis related protein 1 (PR-1), uncharacterized protein AT5G57625.1: CAP/LOC_Os07g03710.1/B4FVP5   sig. (3.71) sig. (1.83)  
GRMZM2G099049 7:120764735-120766193 Auxin/Dormancy related protein AT1G56220.2/LOC_Os09g26620.1     sig. (-2.60)
GRMZM2G336694 8:10989824-10990619 NA NA sig. (3.67) sig. (3.38)   
GRMZM2G153977 8:70995815-70998984 Eukaryotic aspartyl protease AT1G62290.1/LOC_Os05g49200.1   sig. (-4.24)   
GRMZM2G096029 8:104279085-104281118 Obtusifoliol 14α demethylase AT1G11680.1(CYP51)/LOC_Os05g34325.1     sig. (-2.91)
GRMZM2G135536 10:893975-895713 Putative cytochrome P450 AT1G64940.1(CYP89A6)/LOC_Os10g05020.1 sig. (3.51) sig. (4.24)   
GRMZM2G133721 10:111856375-111861824 Putative enolase NA sig. (7.65) sig. (6.36)   
  1. 1Annotations from http://www.maizegdb.org.
  2. 2Accession number for the homologous sequences from Arabidopsis thaliana, Oryza sativa (database information from http://www.maizegdb.org), and UniProtKB/TrEMBL.
  3. 3log2FC for the corresponding comparison in which the gene was identified as being differentially expressed (significant at FDR < 0.05) positive log2FCs reflect higher expression values in Condition2 whilst negative log2FC refer to higher expression in Condition 1 of specific comparisons (cf Table 1).