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Table 4 Shortlist of differentially expressed transcripts annotated as involved in response to water. Transcripts with a known Arabidopsis homolog were selected from a total of 211 DEGs in this category, based on their specificity to a single cluster and higher expression level in a given stage as determined by a stage expression factor (SEFa) higher than 0.85. To have transcripts specific of cluster D in the short list, the stage expression factor considered in this case was 0.57. Expression in each stage is represented as normalized counts

From: Characterization of the cork oak transcriptome dynamics during acorn development

Cluster

Transcript name

At Locus

At homologous

Annotation

counts

SEFa

     

S1

S2

S3S4

S5

S8

 

A

Contig16112

AT2G47000

MDR4, PGP4, ABCB4

Multidrug resistance 4, P-glycoprotein 4, ATP binding cassette subfamily B4

19.8

0

0.6

0.4

0

0.95

A

Qs-dev_rep_c84235

AT3G17000

UBC32

Ubiquitin-conjugating enzyme 32

25

0

1.2

0

1.2

0.91

B

Contig18768

AT3G23920

BAM1

β-Amylase 1

1.2

29.6

0.6

1.2

2.2

0.85

Qs-dev_rep_c76744

0.4

54.2

0.2

8.4

0.8

0.85

C

Qs-dev_rep_c77033

AT5G25610

RD22

Responsive to desiccation 22

0.4

0

34.4

0

3.6

0.90

D

Contig17288

AT3G30775

ERD5, PRODH, ATPOX, ATPDH, PRO1, PDH1

Methylenetetrahydrofolate reductase family protein

0

0

0

22

15

0.59

D

Qs-dev_rep_c76415

AT3G29320

PHS1

Glycosyl transferase

0.4

0.6

0.2

25.4

16.6

0.59

D

Contig19318

AT3G24650

ABI3

AP2/B3-like transcriptional factor family protein

0

0

7.2

66.8

42.2

0.57

E

Contig19981

AT2G41430

ERD15, LSR1, CID1

Dehydration-induced protein (ERD15)

0

2.2

0.6

25.8

37.2

0.96

F

Contig18471

AT5G59320

LTP3

Lipid transfer protein 3

0

0.2

0

5.6

38.6

0.87

F

Contig16935

AT4G15910

DI21

Late embryogenesis abundant protein Lea5; drought-induced 21

1.2

0

3.6

18.8

179.2

0.88

Qs-dev_c42419

0

0

0

0

16.4

1

F

Contig18808

AT5G06760

LEA4-5

Late embryogenesis abundant 4-5

1.2

2.2

0.6

0.4

53

0.92

F

Contig17917

AT3G50980

XERO1

Dehydrin xero1

3

0.8

0.6

3.4

50.8

0.87

F

Contig19993

AT1G05680

UGT74E2

Uridine diphosphate glycosyltransferase 74E2

0

0.8

0

4.2

33.8

0.87

F

Qs-dev_rep_c73281

AT3G15353

MT3

Metallothionein 3

0.4

3

0.2

4.6

75

0.90

Qs-dev_rep_c79475

0.4

0

0.2

0.8

18.8

0.93

  1. a \( Stage\ Expression\ Factor=\frac{normalizedcount{s}_{stageX}}{{\displaystyle \sum } normalizedcount{s}_{allstages}} \)