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Table 3 Categories of DE transcripts between NILs based on predicted function

From: Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat

Category

number of transcripts

Adjusted p-value

5A/not 5A

NIL with higher expression: 5A−/5A+

non-coding RNA

15

0.141

10/5

6/9

transposon-associated

14

0.008

4/10

5/9

ubiquitin

12**

0.008

10/2

8/4

cell cycle

5

–

5/0

2/3

histone-related

5

–

3/2

3/2

heat shock

5

–

3/2

2/3

protease

4

–

3/1

3/1

transport

4

–

3/1

2/2

metabolism

5

–

5/0

4/1

homeobox

4

0.001

3/1

1/3

cell wall

3

–

2/1

2/1

transcription

3

–

2/1

0/3

non-translating

2

–

0/2

1/1

peroxisome

2

–

0/2

0/2

other*

20

–

14/6

11/9

No annotation

8

–

4/4

5/3

  1. Adjusted p-values displayed are based on an enrichment test of the functional categories relative to all expressed transcripts. - indicates that an enrichment test was not performed as categories were based on bespoke annotations
  2. *includes transcripts with annotations that could not be grouped by function with other transcripts
  3. **only the 7 transcripts that were annotated as ubiquitin-related in the TGAC annotation were used in the enrichment test (see methods)
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BMC Plant Biology

ISSN: 1471-2229

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