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Table 1 Trail grouping by reactions and by genes for the reference species S against species S1

From: CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts

\(\mathcal {R}\)

S genes (\(\mathcal {G}\))

S1 genes (\(\mathcal {H}\))

S1 in \(T_{S}^{r}\)

S1 in \(T_{S}^{g}\)

r 2

U

A 1

.

.

r 8

X

X 1

x

x

r 3

V

−

 

.

r 7

W

W 1

x

x

r 6

T

T 1

x

x

\({\mathcal {R}^{\prime }}\)

Neigh. ( \({\boldsymbol{\mathcal {G}}^{\prime }}\) )

Neigh. ( \({\boldsymbol{\mathcal {H}}^{\prime }}\) )

  
  1. Trail grouping by reactions and by genes are represented by the fourth (S1 in \(T_{S}^{r}\)) and fifth (S1 in \(T_{S}^{g}\)) columns, respectively (see text for definitions of the \(T_{S}^{r}\) and \(T_{S}^{g}\) tables). Labels without parentheses in table headers and footers refer to \(T_{S}^{r}\), whereas labels within parentheses refer to \(T_{S}^{g}\). \(\mathcal {R}\) refers to both \(T_{S}^{r}\) and \(T_{S}^{g}\). \(\mathcal {R'}\) refers only to \(T_{S}^{r}\). Entries in bold in columns \(\mathcal {R}\), S genes, and S1 genes respectively designate \(\mathcal {R'}\) and neighboring genes in S and S1 (see table footer) for \(T_{S}^{r}\). For \(T_{S}^{g}\), entries in bold in columns \(\mathcal {G}\) and \(\mathcal {H}\) designate \(\mathcal {G'}\) and \(\mathcal {H'}\), respectively (see table footer). \(\mathcal {R}\) represents a reaction set of S. \(\mathcal {G}\) represents the group of neighboring genes of S whose products catalyze the respective reactions in \(\mathcal {R}\). Symbols in column S1 in \(T_{S}^{r}\) represent conserved metabolic patterns between species S and S1 for reactions in \(\mathcal {R}\). Symbols in column S1 in \(T_{S}^{g}\) represent conserved genomic patterns between species S and S1 for genes in \(\mathcal {G}\). Roughly speaking, \(\mathcal {R'}\) designates a maximal subset of \(\mathcal {R}\) such that genes of S1 involved in reactions in \(\mathcal {R'}\) are neighbors; \(\mathcal {H}\) designates genes in S1 involved in reactions in \(\mathcal {R}\); \(\mathcal {H'}\) designates neighboring genes in \(\mathcal {H}\) involved in reactions in \(\mathcal {R}\). \(\mathcal {H'}\) maximizes the number of genes in \(\mathcal {G'}\), where genes in \(\mathcal {H'}\) and \(\mathcal {G'} \subseteq \mathcal {G}\) are involved in the same reactions in \(\mathcal {R}\) (see text for formal definitions)
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BMC Bioinformatics

ISSN: 1471-2105

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