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Table 1 List of 16 core modules defined by the ensemble.

From: BRNI: Modular analysis of transcriptional regulatory programs

Module Number

Main functions

Expression peak phase

*Transcription peak phase

Number of genes

Member genes that are known cell cycle regulators (TFs in bold)

1

Histones (7/7)

S

M/G1

7

 

2

Cell wall (6/12); glycoproteins (3)

M/G1

M

12

cig2,ams2

3

Metabolism (6/12)

S/G2

G1/S

12

 

4

Cell wall (4/11), cell division (4/11)

M/G1

G2/M

11

ace2, plo1, cdc15, slp1

5

Mixed

S/G2

G1/S

10

 

6

Cytokinesis (2/9);

M/G1

G2/M

9

fkh2

7

Mixed

G1

M

27

 

8

Translation regulation (9/20) (ribosome biogenesis (7/20)); transporters (4/20)

G2

G1/S

20

 

9

Mixed

G2

G1/S

15

 

10

Mixed

Mixed

Mixed

11

 

11

Mixed

G2/M

G2

15

 

12

Mixed

G1

M

15

pmk1

13

Mixed

M/G1

M

18

cdc10, res2, csk1

14

Mixed

G1/S

G1

18

 

15

Cell wall (6/21)

Early G2

S/G2

21

 

16

Mixed

M

G2

27

cdc13, crk1, cdr1, clb1

  1. The 16 gene modules in the unified model. For each enriched function, the number of genes in the module having that function is shown in parentheses. *Transcription rates, as predicted by our pre-processing (see Methods).