Table 1 The input/output relationships in the Snf1 pathway

From: Network reconstruction and validation of the Snf1/AMPK pathway in baker’s yeast based on a comprehensive literature review

Input

Output

Recon 0

Recon I

Recon II

Recon III

Expected behaviour

Reference PMID

Glucose−

[Snf1Degradation]

Fail

Pass

Pass

Pass

OFF

21628526

 

[Rod1Degradation]

Fail

Fail

Fail

Pass

OFF

22249293

 

[Mig1Transcription]

Fail

Fail

Pass

Pass

ON

2167835, 14871952, 2002006, 1541392, 17178716

 

[Nrg1Transcription]

Fail

Fail

Pass

Pass

ON

12024013

 

[Nrg2Transcription]

Fail

Fail

Pass

Pass

ON

12024013

 

[CSRETranscription]

Fail

Fail

Pass

Pass

ON

9111319, 15121831

 

[Rds2Transcription]

Fail

Fail

Pass

Pass

ON

17875938

 

[STRETranscription]

Fail

Pass

Pass

Pass

ON

12093809

pH 8

[Mig1Transcription]

Fail

Fail

Pass

Pass

ON

22372618

 

[Nrg1Transcription]

Fail

Fail

Pass

Pass

ON

12509465, 17023428

 

[STRETranscription]

Fail

Pass

Pass

Pass

ON

21749328

Nitrogen−

[GATATranscription]

Fail

Fail

Pass

Pass

ON

11809814, 12062797

NaCl+

[STRETranscription]

Fail

Pass

Pass

Pass

ON

8641288

  1. For each input condition, the table lists the expected state of each outputs, as well as the observed output in the simulation of (0) the initial network reconstruction (NR1), (1) after the first round of refinement, (2) after the second round of refinement and (3) in the final model (NR2). The PMIDs indicate references to experimental observations of these input/output relationships. The reference condition is the presence of glucose and the absence of any stress (Supplementary File 9), and entries are only given when they have been reported to differ from the reference condition.
Back to article page