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\begin{document}

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\title{FELLA v0.3 report}
\author{Sergio Picart-Armada \qquad Alexandre Perera-Lluna \\ B2SLab at UPC}
\maketitle
% 
% <<tableTest, results='asis', echo=FALSE>>=
% test <- data.frame(x = 1:3, y = 1:3)
% print(xtable(test, caption = '\\textbf{Test Table}', label = ''), 
%   caption.placement = getOption("xtable.caption.placement", "top"), size = 'tiny')
% @

\section{Metabolites enrichment using KEGG entries}

\subsection{Original idea}

The user of this tool has completed a case-control experiment. This gives him
data about the \textbf{affected compounds} between control and case populations.
Given the \textbf{KEGG id} of these compounds, FELLA performs an enrichment 
procedure resulting in a straightforward interpretation.

The enrichment method heats up the affected compounds that live in the bottom of
a hierarchical structure. The final temperatures of every entry are compared to the null 
hypothesis, which states that the compounds are chosen at random. The relevant 
subgraph is then extracted and analysed.

\subsection{Generalized enrichment}

The heating technique is strongly oriented to bottom-to-top heat flow. Thus, if 
the user disposes of \textbf{affected enzymes} instead of affected compounds and tries to heat them up, the result loses its clean interpretation. 

To address this, FELLA attempts to solve the reverse problem: \textit{given some affected enzymes, which compounds should be heated up so that the enzymes become 
significant again?} This procedure consists of two steps.

\subsubsection{Solution approximation}

Let $q = q_1, \ldots, q_{nc}$ be the heat generation vector, where $q_i = 1W$ 
if and only if compound $i$ is affected. Otherwise, $q_i = 0$.
Let $e_1, \ldots, e_{ne} \in V(G)$ be the affected enzymes. Let $p_i = p_i(q)$ 
be the p-value for node $i \in V(G)$ given the generation $q$.

We define a cost function that should be minimized:

$$f(q) = \sum_{i \in e_1, \ldots, e_{ne}} p_i$$

We have to find an appropiate logical vector $q$, which is equivalent to determine
whether each compound should generate or not. Notice that adding too many compounds 
will increase $f(q)$ as the significance will eventually drop for all the nodes.

To estimate this minimum, we have computed whether switching bit $q_k$ in $q$ 
improves the cost function. 

$$
J_k f(q) = \sum_{i \in e_1, \ldots, e_{ne}} \Delta _k (p_i) = \sum_{i \in e_1, \ldots, e_{ne}} p'_i(q'_k = ! q_k) - p_i(q)
$$

$$
J f(q) = (J_1 f(q), \ldots, J_{nc} f(q) )
$$

In order to find a first approximation, we start with $q = q^0 = 0$ and take a 
predefined number of steps, say $50$, to catch the most promising compounds. 
Each step can also remove a compound if this implies the largest descent for the 
objective function. Having $q^{50}$, we refine this solution in the second part.

\subsubsection{Solution refinement}

In this step we want a more accurate input. We obtain that by penalizing even more 
the objective function by the number of compounds that are generating. We expect noisy compounds to be removed and only the strongest evidence remains. We define a fitness 
function which evaluates the goodness of a solution $q$:

$$ g(q) = -\log{  \sum_{i = 1}^{nc} q_i }  -  \sum_{i \in e_1, \ldots, e_{ne}} p_i  $$

We maximize this function using a genetic algorithm via \textbf{GA} R package. 
The starting population contains the individual $q^{50}$ and also mutations $\hat{q}$, where 
each bit $\hat{q}_k$ had a $5\%$ chance to negate his value.
Once the algorithm has finished we obtain $q_{final}$. Applying our original method 
on it we obtain a whole subgraph, whose plot may explain the relationships 
between the affected enzymes and the predicted compounds.



\section{Report}

\subsection{Input}

Table \ref{tableInput} contains the items in the input.

% latex table generated in R 3.1.3 by xtable 1.7-4 package
% Tue Mar 17 17:09:41 2015
\begin{table}[ht]
\centering
{\small
\begin{tabular}{ll}
  \hline
Enzyme & Description \\ 
  \hline
3.2.1.24 & alpha-mannosidase; alpha-D-mannosidase; p-nitrophe... \\ 
  2.4.1.1 & glycogen phosphorylase; muscle phosphorylase a and... \\ 
  1.11.1.9 & glutathione peroxidase; GSH peroxidase; selenium-g... \\ 
  5.3.4.1 & protein disulfide-isomerase; S-S rearrangase \\ 
  2.4.1.11 & glycogen(starch) synthase; UDP-glucose---glycogen ... \\ 
  4.2.1.3 & aconitate hydratase; cis-aconitase; aconitase; Acn... \\ 
  3.1.3.5 & 5'-nucleotidase; uridine 5'-nucleotidase; 5'-adeny... \\ 
  5.2.1.8 & peptidylprolyl isomerase; PPIase; cyclophilin (mis... \\ 
  1.1.1.37 & malate dehydrogenase; malic dehydrogenase; L-malat... \\ 
  3.4.16.2 & lysosomal Pro-Xaa carboxypeptidase; angiotensinase... \\ 
  4.1.1.32 & phosphoenolpyruvate carboxykinase (GTP); phosphoen... \\ 
  3.1.1.5 & lysophospholipase; lecithinase B; lysolecithinase;... \\ 
  1.1.1.184 & carbonyl reductase (NADPH); aldehyde reductase 1; ... \\ 
  2.5.1.18 & glutathione transferase; glutathione S-transferase... \\ 
   \hline
\end{tabular}
}
\caption{Enzymes in the input} 
\label{tableInput}
\end{table}
% latex table generated in R 3.1.3 by xtable 1.7-4 package
% Tue Mar 17 17:09:41 2015
\begin{table}[ht]
\centering
{\small
\begin{tabular}{ll}
  \hline
Predicted compound & Description \\ 
  \hline
C00036 & Oxaloacetate; Oxalacetic acid; Oxaloacetic acid; 2... \\ 
  C00417 & cis-Aconitate; cis-Aconitic acid \\ 
  C00127 & Glutathione disulfide; GSSG; Oxiglutatione; Oxidiz... \\ 
  C20237 & alpha-Maltose 1-phosphate \\ 
  C00670 & sn-Glycero-3-phosphocholine; Glycerophosphocholine \\ 
  C14868 & S-(1,2-Dichlorovinyl)glutathione; DCVG \\ 
  C11310 & 1-Methyl-4-phenylpyridinium; N-Methyl-4-phenylpyri... \\ 
  C07593 & Rotenone \\ 
  C01612 & Secondary alcohol; R-CHOH-R' \\ 
  C04540 & N4-(Acetyl-beta-D-glucosaminyl)asparagine; N4-(bet... \\ 
  C02611 & (E,E)-Piperoyl-CoA \\ 
  C03899 & S-(2-Hydroxyacyl)glutathione \\ 
  C03356 & 3-Phospho-D-erythronate \\ 
  C03706 & Lysosomal-enzyme D-mannose \\ 
  C15541 & NDP-glucose; NDP-D-glucose; NDP-alpha-D-glucose \\ 
  C20183 & 7-Methylguanosine 5'-diphosphate \\ 
   \hline
\end{tabular}
}
\caption{Compounds predicted from the input. These compounds are the \textbf{new heat source}} 
\label{tableGuess}
\end{table}



\clearpage

\subsection{Relevant subgraph}

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}

All the relevant nodes are plotted in the graph.
Pathways are red, modules are violet, enzymes are orange, reactions are blue and compounds are green. Generally nodes are circular. If compounds were specified, they appear as a green square. Otherwise, if enzymes were entered, both the \textbf{enzymes at the input} and the \textbf{predicted compounds} are squares.

The following table contains a brief description for each node and its p-value in the solution. Furthermore, in the case where the solution was built from significant enzymes, a \textit{Guess} column highlights if a significant enzyme was already in the original input. 

\subsection{Nodes in the relevant subgraph}




\resizebox{\textwidth}{!}{
% latex table generated in R 3.1.3 by xtable 1.7-4 package
% Tue Mar 17 17:09:41 2015
{\tiny
\begin{tabular}{llllllll}
  \hline
KEGG id & p.value & Description & Guess? & KEGG id & p.value & Description & Guess? \\ 
  \hline
hsa00020 &  6.31e-06 & Citrate cycle (TCA cycle) - Homo sapiens (human) & FALSE & R01309 & $<$2e-16 & phosphatidylcholine acylhydrolase & FALSE \\ 
  hsa00500 &  4.65e-09 & Starch and sucrose metabolism - Homo sapiens (huma... & FALSE & R01447 &  2.79e-02 & (S)-Lactate:oxaloacetate oxidoreductase & FALSE \\ 
  hsa00511 &  7.00e-06 & Other glycan degradation - Homo sapiens (human) & FALSE & R01875 & $<$2e-16 & Thiosulfate:thiol sulfurtransferase & FALSE \\ 
  hsa00620 &  2.06e-08 & Pyruvate metabolism - Homo sapiens (human) & FALSE & R02243 & $<$2e-16 & cis-Aconitate carboxy-lyase & FALSE \\ 
  hsa03018 &  3.21e-07 & RNA degradation - Homo sapiens (human) & FALSE & R02244 & $<$2e-16 & trans-Aconitate delta2-delta3-isomerase & FALSE \\ 
  hsa04142 & $<$2e-16 & Lysosome - Homo sapiens (human) & FALSE & R02277 & $<$2e-16 & Secondary-alcohol:oxygen oxidoreductase & FALSE \\ 
  hsa05012 & $<$2e-16 & Parkinson's disease - Homo sapiens (human) & FALSE & R02591 & $<$2e-16 & sn-Glycero-3-phosphocholine cholinephosphohydrolas... & FALSE \\ 
  M00001 &  1.71e-08 & Glycolysis (Embden-Meyerhof pathway), glucose =$>$ p... & FALSE & R02744 & $<$2e-16 &  & FALSE \\ 
  M00002 & $<$2e-16 & Glycolysis, core module involving three-carbon com... & FALSE & R02745 &  2.68e-12 & 1-(1-Alkenyl)-sn-glycero-3-phosphocholine aldehydo... & FALSE \\ 
  M00003 & $<$2e-16 & Gluconeogenesis, oxaloacetate =$>$ fructose-6P & FALSE & R02746 & $<$2e-16 & 1-Acyl-sn-glycero-3-phosphocholine acylhydrolase & FALSE \\ 
  M00010 & $<$2e-16 & Citrate cycle, first carbon oxidation, oxaloacetat... & FALSE & R02747 & $<$2e-16 & 2-Acyl-sn-glycero-3-phosphocholine acylhydrolase & FALSE \\ 
  M00012 & $<$2e-16 & Glyoxylate cycle & FALSE & R03421 & $<$2e-16 & N4-(beta-N-Acetyl-D-glucosaminyl)-L-asparagine ami... & FALSE \\ 
  M00168 &  1.37e-05 & CAM (Crassulacean acid metabolism), dark & FALSE & R03557 & $<$2e-16 & Secondary alcohol:NADP+ oxidoreductase & FALSE \\ 
  M00172 &  1.80e-05 & C4-dicarboxylic acid cycle, NADP - malic enzyme ty... & FALSE & R03994 & $<$2e-16 & (E,E)-Piperoyl-CoA:piperidine N-piperoyltransferas... & FALSE \\ 
  M00173 &  3.87e-07 & Reductive citrate cycle (Arnon-Buchanan cycle) & FALSE & R04090 & $<$2e-16 & S-(2-Hydroxyacyl)glutathione hydrolase & FALSE \\ 
  M00346 & $<$2e-16 & Formaldehyde assimilation, serine pathway & FALSE & R04206 & $<$2e-16 & 3-Phospho-D-erythronate hydro-lyase & FALSE \\ 
  M00394 & $<$2e-16 & RNA degradosome & FALSE & R04291 & $<$2e-16 & UDP-N-acetyl-D-glucosamine:lysosomal-enzyme N-acet... & FALSE \\ 
  4.2.1.11 & $<$2e-16 & phosphopyruvate hydratase; enolase; 2-phosphoglyce... & FALSE & R05717 &  3.14e-13 & AMP,sulfite:glutathione-disulfide oxidoreductase (... & FALSE \\ 
  4.1.1.32 &  3.36e-16 & phosphoenolpyruvate carboxykinase (GTP); phosphoen... & TRUE & R07100 & $<$2e-16 & trichloroethene:glutathione S-(1,2-dichlorovinyl)t... & FALSE \\ 
  2.3.3.1 &  9.15e-03 & citrate (Si)-synthase; (R)-citric synthase; citrat... & FALSE & R07164 & $<$2e-16 & L-aspartate:NAD+ oxidoreductase (deaminating) & FALSE \\ 
  2.3.3.8 &  9.09e-03 & ATP citrate synthase; ATP-citric lyase; ATP:citrat... & FALSE & R07165 & $<$2e-16 & L-aspartate:NADP+ oxidoreductase (deaminating) & FALSE \\ 
  4.2.1.3 & $<$2e-16 & aconitate hydratase; cis-aconitase; aconitase; Acn... & TRUE & R07256 & $<$2e-16 & NDP-glucose:D-fructose 2-alpha-D-glucosyltransfera... & FALSE \\ 
  6.4.1.1 & $<$2e-16 & pyruvate carboxylase; pyruvic carboxylase & FALSE & R07261 & $<$2e-16 & NDP-glucose:1,4-alpha-D-glucan 4-alpha-D-glucosylt... & FALSE \\ 
  2.5.1.18 &  2.23e-04 & glutathione transferase; glutathione S-transferase... & TRUE & R07291 & $<$2e-16 & 2-lysophosphatidylcholine acylhydrolase & FALSE \\ 
  1.8.1.7 & $<$2e-16 & glutathione-disulfide reductase; glutathione reduc... & FALSE & R07744 & $<$2e-16 &  & FALSE \\ 
  3.5.1.26 & $<$2e-16 & N4-(beta-N-acetylglucosaminyl)-L-asparaginase; asp... & FALSE & R09467 & $<$2e-16 &  & FALSE \\ 
  3.1.1.5 & $<$2e-16 & lysophospholipase; lecithinase B; lysolecithinase;... & TRUE & R09468 & $<$2e-16 &  & FALSE \\ 
  1.1.1.184 & $<$2e-16 & carbonyl reductase (NADPH); aldehyde reductase 1; ... & TRUE & R09663 & $<$2e-16 & NDP-glucose:3-phospho-D-glycerate 2-alpha-D-glucos... & FALSE \\ 
  3.1.2.6 & $<$2e-16 & hydroxyacylglutathione hydrolase; glyoxalase II; S... & FALSE & R09945 & $<$2e-16 & ATP:alpha-maltose 1-phosphotransferase & FALSE \\ 
  1.1.1.38 &  3.26e-03 & malate dehydrogenase (oxaloacetate-decarboxylating... & FALSE & R09994 & $<$2e-16 & alpha-maltose 1-phosphate:(1-$>$4)-alpha-D-glucan 4-... & FALSE \\ 
  2.7.8.17 & $<$2e-16 & UDP-N-acetylglucosamine---lysosomal-enzyme N-acety... & FALSE & R10525 & $<$2e-16 & NDP-alpha-D-glucose:D-glucose 1-alpha-D-glucosyltr... & FALSE \\ 
  4.1.1.49 & $<$2e-16 & phosphoenolpyruvate carboxykinase (ATP); phosphopy... & FALSE & C00036 & $<$2e-16 & Oxaloacetate; Oxalacetic acid; Oxaloacetic acid; 2... & FALSE \\ 
  4.1.1.31 & $<$2e-16 & phosphoenolpyruvate carboxylase; phosphopyruvate (... & FALSE & C00417 & $<$2e-16 & cis-Aconitate; cis-Aconitic acid & FALSE \\ 
  1.1.1.82 &  7.74e-08 & malate dehydrogenase (NADP+); NADP+-malic enzyme; ... & FALSE & C00127 & $<$2e-16 & Glutathione disulfide; GSSG; Oxiglutatione; Oxidiz... & FALSE \\ 
  1.8.3.3 & $<$2e-16 & glutathione oxidase & FALSE & C20237 & $<$2e-16 & alpha-Maltose 1-phosphate & FALSE \\ 
  3.7.1.1 &  4.09e-06 & oxaloacetase; oxalacetic hydrolase & FALSE & C00670 & $<$2e-16 & sn-Glycero-3-phosphocholine; Glycerophosphocholine & FALSE \\ 
  1.1.1.299 &  7.17e-08 & malate dehydrogenase (NAD(P)+); MdH II, NAD(P)+-de... & FALSE & C14868 & $<$2e-16 & S-(1,2-Dichlorovinyl)glutathione; DCVG & FALSE \\ 
  4.1.1.38 & $<$2e-16 & phosphoenolpyruvate carboxykinase (diphosphate); p... & FALSE & C11310 & $<$2e-16 & 1-Methyl-4-phenylpyridinium; N-Methyl-4-phenylpyri... & FALSE \\ 
  2.3.3.3 &  9.15e-03 & citrate (Re)-synthase; (R)-citrate synthase; Re-ci... & FALSE & C07593 & $<$2e-16 & Rotenone & FALSE \\ 
  2.1.3.1 &  2.20e-06 & methylmalonyl-CoA carboxytransferase; transcarboxy... & FALSE & C01612 & $<$2e-16 & Secondary alcohol; R-CHOH-R' & FALSE \\ 
  1.1.3.3 &  7.55e-08 & malate oxidase; FAD-dependent malate oxidase; mali... & FALSE & C04540 & $<$2e-16 & N4-(Acetyl-beta-D-glucosaminyl)asparagine; N4-(bet... & FALSE \\ 
  1.1.5.4 &  1.19e-07 & malate dehydrogenase (quinone); FAD-dependent mala... & FALSE & C02611 & $<$2e-16 & (E,E)-Piperoyl-CoA & FALSE \\ 
  4.1.3.6 &  9.09e-03 & citrate (pro-3S)-lyase; citrase; citratase; citrit... & FALSE & C03899 & $<$2e-16 & S-(2-Hydroxyacyl)glutathione & FALSE \\ 
  2.6.1.35 & $<$2e-16 & glycine---oxaloacetate transaminase; glycine-oxala... & FALSE & C03356 & $<$2e-16 & 3-Phospho-D-erythronate & FALSE \\ 
  2.6.1.12 &  2.39e-08 & alanine---oxo-acid transaminase; L-alanine-alpha-k... & FALSE & C03706 & $<$2e-16 & Lysosomal-enzyme D-mannose & FALSE \\ 
  3.1.3.91 & $<$2e-16 & 7-methylguanosine nucleotidase; cytosolic nucleoti... & FALSE & C15541 & $<$2e-16 & NDP-glucose; NDP-D-glucose; NDP-alpha-D-glucose & FALSE \\ 
  2.6.1.70 &  2.04e-09 & aspartate---phenylpyruvate transaminase; aspartate... & FALSE & C20183 & $<$2e-16 & 7-Methylguanosine 5'-diphosphate & FALSE \\ 
  2.4.1.13 & $<$2e-16 & sucrose synthase; UDPglucose-fructose glucosyltran... & FALSE &  &  &  &  \\ 
  3.1.4.2 & $<$2e-16 & glycerophosphocholine phosphodiesterase; glyceroph... & FALSE &  &  &  &  \\ 
  1.8.5.1 & $<$2e-16 & glutathione dehydrogenase (ascorbate); dehydroasco... & FALSE &  &  &  &  \\ 
  3.2.2.11 & $<$2e-16 & beta-aspartyl-N-acetylglucosaminidase; beta-aspart... & FALSE &  &  &  &  \\ 
  1.1.99.7 &  2.86e-02 & lactate---malate transhydrogenase; malate-lactate ... & FALSE &  &  &  &  \\ 
  2.8.1.3 & $<$2e-16 & thiosulfate---thiol sulfurtransferase; glutathione... & FALSE &  &  &  &  \\ 
  4.1.1.6 & $<$2e-16 & aconitate decarboxylase; cis-aconitic decarboxylas... & FALSE &  &  &  &  \\ 
  5.3.3.7 & $<$2e-16 & aconitate Delta-isomerase; aconitate isomerase & FALSE &  &  &  &  \\ 
  1.1.3.18 & $<$2e-16 & secondary-alcohol oxidase; polyvinyl alcohol oxida... & FALSE &  &  &  &  \\ 
  3.1.4.38 & $<$2e-16 & glycerophosphocholine cholinephosphodiesterase; L-... & FALSE &  &  &  &  \\ 
  3.3.2.2 &  2.71e-12 & alkenylglycerophosphocholine hydrolase; lysoplasma... & FALSE &  &  &  &  \\ 
  2.3.1.145 & $<$2e-16 & piperidine N-piperoyltransferase; piperidine piper... & FALSE &  &  &  &  \\ 
  1.8.4.9 &  3.40e-13 & adenylyl-sulfate reductase (glutathione); 5'-adeny... & FALSE &  &  &  &  \\ 
  2.4.1.242 & $<$2e-16 & NDP-glucose---starch glucosyltransferase; granule-... & FALSE &  &  &  &  \\ 
  2.4.1.245 & $<$2e-16 & alpha,alpha-trehalose synthase; trehalose synthase... & FALSE &  &  &  &  \\ 
  2.4.1.266 & $<$2e-16 & glucosyl-3-phosphoglycerate synthase; GpgS protein... & FALSE &  &  &  &  \\ 
  2.7.1.175 & $<$2e-16 & maltokinase & FALSE &  &  &  &  \\ 
  2.4.99.16 & $<$2e-16 & starch synthase (maltosyl-transferring); alpha1,4-... & FALSE &  &  &  &  \\ 
  1.1.98.5 & $<$2e-16 & secondary-alcohol dehydrogenase (coenzyme-F420); F... & FALSE &  &  &  &  \\ 
  R00431 & $<$2e-16 & GTP:oxaloacetate carboxy-lyase (adding GTP;phospho... & FALSE &  &  &  &  \\ 
  R00726 &  8.48e-07 & ITP:oxaloacetate carboxy-lyase (adding ITP; phosph... & FALSE &  &  &  &  \\ 
  R00341 & $<$2e-16 & ATP:oxaloacetate carboxy-lyase (transphosphorylati... & FALSE &  &  &  &  \\ 
  R00351 &  8.87e-03 & acetyl-CoA:oxaloacetate C-acetyltransferase (thioe... & FALSE &  &  &  &  \\ 
  R01325 & $<$2e-16 & citrate hydro-lyase (cis-aconitate-forming) & FALSE &  &  &  &  \\ 
  R01900 & $<$2e-16 & isocitrate hydro-lyase (cis-aconitate-forming) & FALSE &  &  &  &  \\ 
  R00342 &  6.69e-08 & (S)-malate:NAD+ oxidoreductase & FALSE &  &  &  &  \\ 
  R00345 & $<$2e-16 & phosphate:oxaloacetate carboxy-lyase (adding phosp... & FALSE &  &  &  &  \\ 
  R00355 & $<$2e-16 & L-Aspartate:2-oxoglutarate aminotransferase & FALSE &  &  &  &  \\ 
  R00343 &  6.69e-08 & (S)-malate:NADP+ oxidoreductase & FALSE &  &  &  &  \\ 
  R00344 & $<$2e-16 & Pyruvate:carbon-dioxide ligase (ADP-forming) & FALSE &  &  &  &  \\ 
  R00352 &  8.90e-03 & acetyl-CoA:oxaloacetate C-acetyltransferase ((pro-... & FALSE &  &  &  &  \\ 
  R00094 & $<$2e-16 & glutathione:NAD+ oxidoreductase & FALSE &  &  &  &  \\ 
  R00115 & $<$2e-16 & glutathione:NADP+ oxidoreductase & FALSE &  &  &  &  \\ 
  R00120 & $<$2e-16 & glutathione:oxygen oxidoreductase & FALSE &  &  &  &  \\ 
  R00217 & $<$2e-16 & oxaloacetate carboxy-lyase (pyruvate-forming) & FALSE &  &  &  &  \\ 
  R00274 & $<$2e-16 & glutathione:hydrogen-peroxide oxidoreductase & FALSE &  &  &  &  \\ 
  R00338 &  3.82e-06 & Oxaloacetate acetylhydrolase & FALSE &  &  &  &  \\ 
  R00346 & $<$2e-16 & diphosphate:oxaloacetate carboxy-lyase (transphosp... & FALSE &  &  &  &  \\ 
  R00353 & $<$2e-16 & malonyl-CoA:pyruvate carboxytransferase & FALSE &  &  &  &  \\ 
  R00357 & $<$2e-16 & L-Aspartic acid:oxygen oxidoreductase (deaminating... & FALSE &  &  &  &  \\ 
  R00360 &  7.07e-08 & (S)-Malate:oxygen oxidoreductase & FALSE &  &  &  &  \\ 
  R00361 &  7.46e-08 & (S)-malate:acceptor oxidoreductase & FALSE &  &  &  &  \\ 
  R00362 &  8.90e-03 & citrate oxaloacetate-lyase (forming acetate from t... & FALSE &  &  &  &  \\ 
  R00373 & $<$2e-16 & Glycine:oxaloacetate aminotransferase & FALSE &  &  &  &  \\ 
  R00400 & $<$2e-16 & L-alanine:oxaloacetate aminotransferase & FALSE &  &  &  &  \\ 
  R00493 &  2.93e-03 & L-aspartate:2-oxo acid aminotransferase & FALSE &  &  &  &  \\ 
  R00624 & $<$2e-16 & Secondary\_alcohol:NAD+ oxidoreductase & FALSE &  &  &  &  \\ 
  R00695 &  1.84e-09 & L-Aspartate:phenylpyruvate aminotransferase & FALSE &  &  &  &  \\ 
  R01030 & $<$2e-16 & sn-Glycero-3-phosphocholine glycerophosphohydrolas... & FALSE &  &  &  &  \\ 
  R01108 & $<$2e-16 & glutathione:dehydroascorbate oxidoreductase & FALSE &  &  &  &  \\ 
  R01113 &  3.23e-02 & Glutathione:L-cystine oxidoreductase & FALSE &  &  &  &  \\ 
  R01257 &  4.30e-07 & (S)-Malate:(acceptor) oxidoreductase & FALSE &  &  &  &  \\ 
  R01266 & $<$2e-16 & 1-beta-Aspartyl-N-acetyl-D-glucosaminylamine L-asp... & FALSE &  &  &  &  \\ 
   \hline
\end{tabular}
}

}

\resizebox{\textwidth}{!}{
% latex table generated in R 3.1.3 by xtable 1.7-4 package
% Tue Mar 17 17:09:41 2015
{\tiny
\begin{tabular}{llllllll}
  \hline
KEGG id & p.value & Description & Guess? & KEGG id & p.value & Description & Guess? \\ 
  \hline
 &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
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   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
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   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  &  &  &  &  \\ 
   &  &  &  & C20183 & $<$2e-16 & 7-Methylguanosine 5'-diphosphate & FALSE \\ 
   &  &  &  &  &  &  &  \\ 
   \hline
\end{tabular}
}

}

\end{document}
