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Table 1 Illustration of the sign inference process

From: Inferring the role of transcription factors in regulatory networks

Experiments used

Qualitative system

Replacing values from experiments

Consistent solutions (S BA ,S CA )

Inferred signs (identical in all solutions)

{e1}

x A 1 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabigdaXaaaaaa@2F76@

(+) ≈ S BA × (+) + S CA × (+)

(+, +)

(+, -)

(-, +)

∅

{e1, e2}

x A 1 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabigdaXaaaaaa@2F76@

(+) ≈ S BA × (+) + S CA × (+)

(+,+)

{S BA = +}

 

x A 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabikdaYaaaaaa@2F78@

(+) ≈ S BA × (+) + S CA × (-)

(+, -)

 

{e1, e2, e3}

x A 1 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabigdaXaaaaaa@2F76@

(+) ≈ S BA × (+) + S CA × (+)

(+, +)

{S BA = +, S CA = +}

 

x A 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabikdaYaaaaaa@2F78@

(+) ≈ S BA × (+) + S CA × (-)

  
 

x A 3 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemiEaG3aa0baaSqaaiabdgeabbqaaiabiodaZaaaaaa@2F7A@

(-) ≈ S BA × (+) + S CA × (-)

  
  1. In this example the variables are only the roles of regulations (signs) in the interaction graph. Variations of the species in the graph are obtained from six experiments. Using different sets of experiments we infer different roles of regulation. Using experiments {e1, e2, e3}, for example, our qualitative system will have three constraints and not all valuations of variables S BA and S CA satisfy this system according to the sign algebra rules. As we obtain unique values for these variables in the solution of the system, we consider them as inferred (predicted).
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BMC Bioinformatics

ISSN: 1471-2105

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