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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 17:07:29 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 17:07:29 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 17:07:29 2015
{\tiny
\begin{tabular}{llllllll}
  \hline
KEGG id & p.value & Description & Guess? & KEGG id & p.value & Description & Guess? \\ 
  \hline
1.10.2.2 & $<$2e-16 & quinol---cytochrome-c reductase; ubiquinol---cytoc... & FALSE & hsa04612 &  4.72e-08 & Antigen processing and presentation - Homo sapiens... & FALSE \\ 
  1.11.1.9 &  2.47e-02 & glutathione peroxidase; GSH peroxidase; selenium-g... & TRUE & hsa04932 &  1.05e-13 & Non-alcoholic fatty liver disease (NAFLD) - Homo s... & FALSE \\ 
  1.1.3.18 & $<$2e-16 & secondary-alcohol oxidase; polyvinyl alcohol oxida... & FALSE & hsa05012 & $<$2e-16 & Parkinson's disease - Homo sapiens (human) & FALSE \\ 
  1.14.13.52 &  2.20e-09 & isoflavone 3'-hydroxylase; isoflavone 3'-monooxyge... & FALSE & hsa05016 &  3.85e-02 & Huntington's disease - Homo sapiens (human) & FALSE \\ 
  1.14.16.2 &  8.00e-07 & tyrosine 3-monooxygenase; L-tyrosine hydroxylase; ... & FALSE & hsa05416 &  1.08e-03 & Viral myocarditis - Homo sapiens (human) & FALSE \\ 
  1.14.21.8 &  9.56e-04 & pseudobaptigenin synthase & FALSE & M00001 &  2.97e-03 & Glycolysis (Embden-Meyerhof pathway), glucose =$>$ p... & FALSE \\ 
  1.1.98.5 & $<$2e-16 & secondary-alcohol dehydrogenase (coenzyme-F420); F... & FALSE & M00002 &  7.05e-08 & Glycolysis, core module involving three-carbon com... & FALSE \\ 
  1.3.5.1 & $<$2e-16 & succinate dehydrogenase (ubiquinone); succinic deh... & FALSE & M00003 &  4.42e-10 & Gluconeogenesis, oxaloacetate =$>$ fructose-6P & FALSE \\ 
  1.6.5.3 & $<$2e-16 & NADH:ubiquinone reductase (H+-translocating); ubiq... & FALSE & M00010 &  1.58e-02 & Citrate cycle, first carbon oxidation, oxaloacetat... & FALSE \\ 
  1.6.99.3 & $<$2e-16 & NADH dehydrogenase; cytochrome c reductase; type 1... & FALSE & M00012 &  9.27e-05 & Glyoxylate cycle & FALSE \\ 
  1.8.1.7 &  1.18e-06 & glutathione-disulfide reductase; glutathione reduc... & FALSE & M00142 &  2.23e-10 & NADH:ubiquinone oxidoreductase, mitochondria & FALSE \\ 
  1.8.3.3 &  1.80e-07 & glutathione oxidase & FALSE & M00143 & $<$2e-16 & NADH dehydrogenase (ubiquinone) Fe-S protein/flavo... & FALSE \\ 
  1.8.4.9 &  2.03e-03 & adenylyl-sulfate reductase (glutathione); 5'-adeny... & FALSE & M00144 &  2.23e-10 & NADH:quinone oxidoreductase, prokaryotes & FALSE \\ 
  1.8.5.1 &  4.50e-02 & glutathione dehydrogenase (ascorbate); dehydroasco... & FALSE & M00145 &  2.23e-10 & NAD(P)H:quinone oxidoreductase, chloroplasts and c... & FALSE \\ 
  1.9.3.1 &  2.42e-14 & cytochrome-c oxidase; cytochrome oxidase; cytochro... & FALSE & M00146 & $<$2e-16 & NADH dehydrogenase (ubiquinone) 1 alpha subcomplex & FALSE \\ 
  2.3.1.145 & $<$2e-16 & piperidine N-piperoyltransferase; piperidine piper... & FALSE & M00147 & $<$2e-16 & NADH dehydrogenase (ubiquinone) 1 beta subcomplex & FALSE \\ 
  2.3.3.1 &  6.72e-03 & citrate (Si)-synthase; (R)-citric synthase; citrat... & FALSE & M00148 &  8.75e-13 & Succinate dehydrogenase (ubiquinone) & FALSE \\ 
  2.3.3.3 &  1.94e-03 & citrate (Re)-synthase; (R)-citrate synthase; Re-ci... & FALSE & M00151 &  6.17e-16 & Cytochrome bc1 complex respiratory unit & FALSE \\ 
  2.4.1.13 &  4.08e-13 & sucrose synthase; UDPglucose-fructose glucosyltran... & FALSE & M00152 &  6.17e-16 & Cytochrome bc1 complex & FALSE \\ 
  2.4.1.18 &  4.26e-02 & 1,4-alpha-glucan branching enzyme; branching enzym... & FALSE & M00153 &  9.25e-04 & Cytochrome d ubiquinol oxidase & FALSE \\ 
  2.4.1.242 & $<$2e-16 & NDP-glucose---starch glucosyltransferase; granule-... & FALSE & M00154 &  7.57e-10 & Cytochrome c oxidase & FALSE \\ 
  2.4.1.245 & $<$2e-16 & alpha,alpha-trehalose synthase; trehalose synthase... & FALSE & M00155 &  7.57e-10 & Cytochrome c oxidase, prokaryotes & FALSE \\ 
  2.4.1.25 &  1.28e-02 & 4-alpha-glucanotransferase; disproportionating enz... & FALSE & M00156 &  7.57e-10 & Cytochrome c oxidase, cbb3-type & FALSE \\ 
  2.4.1.266 & $<$2e-16 & glucosyl-3-phosphoglycerate synthase; GpgS protein... & FALSE & M00157 &  5.42e-07 & F-type ATPase, prokaryotes and chloroplasts & FALSE \\ 
  2.4.1.4 &  4.18e-02 & amylosucrase; sucrose---glucan glucosyltransferase... & FALSE & M00158 &  5.42e-07 & F-type ATPase, eukaryotes & FALSE \\ 
  2.4.99.16 & $<$2e-16 & starch synthase (maltosyl-transferring); alpha1,4-... & FALSE & M00159 &  5.42e-07 & V-type ATPase, prokaryotes & FALSE \\ 
  2.5.1.18 &  2.92e-02 & glutathione transferase; glutathione S-transferase... & TRUE & M00160 &  5.42e-07 & V-type ATPase, eukaryotes & FALSE \\ 
  2.6.1.35 &  1.88e-03 & glycine---oxaloacetate transaminase; glycine-oxala... & FALSE & M00332 &  2.18e-05 & Type III secretion system & FALSE \\ 
  2.7.1.175 & $<$2e-16 & maltokinase & FALSE & M00346 &  4.78e-07 & Formaldehyde assimilation, serine pathway & FALSE \\ 
  2.7.8.17 & $<$2e-16 & UDP-N-acetylglucosamine---lysosomal-enzyme N-acety... & FALSE & M00390 &  3.56e-06 & Exosome, archaea & FALSE \\ 
  2.8.1.3 &  1.88e-03 & thiosulfate---thiol sulfurtransferase; glutathione... & FALSE & M00391 &  3.56e-06 & Exosome, eukaryotes & FALSE \\ 
  3.1.13.4 &  3.56e-06 & poly(A)-specific ribonuclease; 3'-exoribonuclease;... & FALSE & M00392 &  3.56e-06 & Ski complex & FALSE \\ 
  3.1.1.5 &  2.60e-08 & lysophospholipase; lecithinase B; lysolecithinase;... & TRUE & M00394 & $<$2e-16 & RNA degradosome & FALSE \\ 
  3.1.22.1 &  1.05e-12 & deoxyribonuclease II; DNase II; pancreatic DNase I... & FALSE & M00395 &  6.43e-03 & Decapping complex & FALSE \\ 
  3.1.2.6 & $<$2e-16 & hydroxyacylglutathione hydrolase; glyoxalase II; S... & FALSE & M00397 &  3.56e-06 & Lsm 1-7 complex & FALSE \\ 
  3.1.26.12 & $<$2e-16 & ribonuclease E; endoribonuclease E; RNase E; Rne p... & FALSE & M00417 &  9.25e-04 & Cytochrome o ubiquinol oxidase & FALSE \\ 
  3.1.3.5 &  2.12e-02 & 5'-nucleotidase; uridine 5'-nucleotidase; 5'-adeny... & TRUE & M00542 &  9.96e-04 & EHEC/EPEC pathogenicity signature, T3SS and effect... & FALSE \\ 
  3.1.3.91 & $<$2e-16 & 7-methylguanosine nucleotidase; cytosolic nucleoti... & FALSE & R00094 &  9.15e-09 & glutathione:NAD+ oxidoreductase & FALSE \\ 
  3.1.4.2 &  2.76e-06 & glycerophosphocholine phosphodiesterase; glyceroph... & FALSE & R00115 &  9.15e-09 & glutathione:NADP+ oxidoreductase & FALSE \\ 
  3.1.4.38 & $<$2e-16 & glycerophosphocholine cholinephosphodiesterase; L-... & FALSE & R00120 &  1.26e-11 & glutathione:oxygen oxidoreductase & FALSE \\ 
  3.2.1.96 &  1.38e-07 & mannosyl-glycoprotein endo-beta-N-acetylglucosamin... & FALSE & R00274 &  6.86e-12 & glutathione:hydrogen-peroxide oxidoreductase & FALSE \\ 
  3.2.2.11 & $<$2e-16 & beta-aspartyl-N-acetylglucosaminidase; beta-aspart... & FALSE & R00351 &  1.94e-03 & acetyl-CoA:oxaloacetate C-acetyltransferase (thioe... & FALSE \\ 
  3.3.2.2 &  1.45e-09 & alkenylglycerophosphocholine hydrolase; lysoplasma... & FALSE & R00352 &  3.46e-02 & acetyl-CoA:oxaloacetate C-acetyltransferase ((pro-... & FALSE \\ 
  3.4.14.1 &  1.05e-12 & dipeptidyl-peptidase I; cathepsin C; dipeptidyl am... & FALSE & R00360 &  4.80e-02 & (S)-Malate:oxygen oxidoreductase & FALSE \\ 
  3.4.14.9 &  1.05e-12 & tripeptidyl-peptidase I; tripeptidyl aminopeptidas... & FALSE & R00362 &  1.58e-05 & citrate oxaloacetate-lyase (forming acetate from t... & FALSE \\ 
  3.4.18.1 &  1.05e-12 & cathepsin X; cathepsin B2; cysteine-type carboxype... & FALSE & R00373 &  1.88e-03 & Glycine:oxaloacetate aminotransferase & FALSE \\ 
  3.4.19.12 & $<$2e-16 & ubiquitinyl hydrolase 1; ubiquitin C-terminal hydr... & FALSE & R00400 &  1.09e-02 & L-alanine:oxaloacetate aminotransferase & FALSE \\ 
  3.4.21.108 & $<$2e-16 & HtrA2 peptidase; high temperature requirement prot... & FALSE & R00511 & $<$2e-16 & cytidine-5'-monophosphate phosphohydrolase & FALSE \\ 
  3.4.22.1 &  7.52e-13 & cathepsin B; cathepsin B1 (obsolete); cathepsin II & FALSE & R00624 & $<$2e-16 & Secondary\_alcohol:NAD+ oxidoreductase & FALSE \\ 
  3.4.22.16 &  1.05e-12 & cathepsin H; cathepsin B3; benzoylarginine-naphthy... & FALSE & R00658 &  5.19e-07 & 2-phospho-D-glycerate hydro-lyase (phosphoenolpyru... & FALSE \\ 
  3.4.22.34 &  7.52e-13 & legumain; asparaginyl endopeptidase; citvac; prote... & FALSE & R01030 & $<$2e-16 & sn-Glycero-3-phosphocholine glycerophosphohydrolas... & FALSE \\ 
  3.4.22.41 &  1.05e-12 & cathepsin F & FALSE & R01108 &  2.51e-07 & glutathione:dehydroascorbate oxidoreductase & FALSE \\ 
  3.4.22.42 &  1.05e-12 & cathepsin O & FALSE & R01113 &  4.08e-04 & Glutathione:L-cystine oxidoreductase & FALSE \\ 
  3.4.22.43 &  1.05e-12 & cathepsin V; Cathepsin L2; cathepsin U & FALSE & R01266 & $<$2e-16 & 1-beta-Aspartyl-N-acetyl-D-glucosaminylamine L-asp... & FALSE \\ 
  3.4.22.56 &  2.63e-05 & caspase-3; CPP32; apopain; yama protein & FALSE & R01309 & $<$2e-16 & phosphatidylcholine acylhydrolase & FALSE \\ 
  3.4.22.62 &  2.96e-10 & caspase-9; CASP-9; ICE-like apoptotic protease 6; ... & FALSE & R01324 &  7.70e-06 & citrate hydroxymutase & FALSE \\ 
  3.4.23.34 &  1.05e-12 & cathepsin E; slow-moving proteinase; erythrocyte m... & FALSE & R01325 & $<$2e-16 & citrate hydro-lyase (cis-aconitate-forming) & FALSE \\ 
  3.5.1.26 & $<$2e-16 & N4-(beta-N-acetylglucosaminyl)-L-asparaginase; asp... & FALSE & R01736 &  8.20e-12 & (R)-S-Lactoylglutathione hydrolase & FALSE \\ 
  3.6.3.14 &  2.18e-05 & H+-transporting two-sector ATPase; ATP synthase; F... & FALSE & R01821 &  2.29e-03 & 1,4-alpha-D-Glucan:orthophosphate alpha-D-glucosyl... & FALSE \\ 
  4.1.1.6 & $<$2e-16 & aconitate decarboxylase; cis-aconitic decarboxylas... & FALSE & R01823 &  7.98e-03 & Sucrose:1,4-alpha-D-glucan 4-alpha-D-glucosyltrans... & FALSE \\ 
  4.1.3.6 &  2.19e-05 & citrate (pro-3S)-lyase; citrase; citratase; citrit... & FALSE & R01875 &  2.02e-04 & Thiosulfate:thiol sulfurtransferase & FALSE \\ 
  4.2.1.11 & $<$2e-16 & phosphopyruvate hydratase; enolase; 2-phosphoglyce... & FALSE & R01900 & $<$2e-16 & isocitrate hydro-lyase (cis-aconitate-forming) & FALSE \\ 
  4.2.1.3 & $<$2e-16 & aconitate hydratase; cis-aconitase; aconitase; Acn... & TRUE & R02110 &  2.72e-02 & 1,4-alpha-D-Glucan:1,4-alpha-D-glucan 6-alpha-D-(1... & FALSE \\ 
  5.3.3.7 & $<$2e-16 & aconitate Delta-isomerase; aconitate isomerase & FALSE & R02243 & $<$2e-16 & cis-Aconitate carboxy-lyase & FALSE \\ 
  5.4.2.11 &  2.39e-02 & phosphoglycerate mutase (2,3-diphosphoglycerate-de... & FALSE & R02244 & $<$2e-16 & trans-Aconitate delta2-delta3-isomerase & FALSE \\ 
  C00036 & $<$2e-16 & Oxaloacetate; Oxalacetic acid; Oxaloacetic acid; 2... & FALSE & R02277 & $<$2e-16 & Secondary-alcohol:oxygen oxidoreductase & FALSE \\ 
  C00051 &  1.60e-06 & Glutathione; 5-L-Glutamyl-L-cysteinylglycine; N-(N... & FALSE & R02421 &  2.05e-02 & ADP-glucose:1,4-alpha-D-glucan 4-alpha-D-glucosylt... & FALSE \\ 
  C00105 &  8.24e-03 & UMP; Uridylic acid; Uridine monophosphate; Uridine... & FALSE & R02591 & $<$2e-16 & sn-Glycero-3-phosphocholine cholinephosphohydrolas... & FALSE \\ 
  C00127 & $<$2e-16 & Glutathione disulfide; GSSG; Oxiglutatione; Oxidiz... & FALSE & R02744 & $<$2e-16 &  & FALSE \\ 
  C00417 & $<$2e-16 & cis-Aconitate; cis-Aconitic acid & FALSE & R02745 &  3.80e-11 & 1-(1-Alkenyl)-sn-glycero-3-phosphocholine aldehydo... & FALSE \\ 
  C00454 &  2.52e-07 & NDP; Nucleoside diphosphate; Nucleoside 5'-diphosp... & FALSE & R02746 & $<$2e-16 & 1-Acyl-sn-glycero-3-phosphocholine acylhydrolase & FALSE \\ 
  C00670 & $<$2e-16 & sn-Glycero-3-phosphocholine; Glycerophosphocholine & FALSE & R02747 & $<$2e-16 & 2-Acyl-sn-glycero-3-phosphocholine acylhydrolase & FALSE \\ 
  C00718 &  1.18e-04 & Amylose; Amylose chain; (1,4-alpha-D-Glucosyl)n; (... & FALSE & R03006 & $<$2e-16 & formononetin,NADPH:oxygen oxidoreductase (3'-hydro... & FALSE \\ 
  C01450 &  2.85e-04 & Ketone; R-CO-R' & FALSE & R03421 & $<$2e-16 & N4-(beta-N-Acetyl-D-glucosaminyl)-L-asparagine ami... & FALSE \\ 
  C01562 & $<$2e-16 & Calycosin & FALSE & R03557 & $<$2e-16 & Secondary alcohol:NADP+ oxidoreductase & FALSE \\ 
  C01612 & $<$2e-16 & Secondary alcohol; R-CHOH-R' & FALSE & R03994 & $<$2e-16 & (E,E)-Piperoyl-CoA:piperidine N-piperoyltransferas... & FALSE \\ 
  C01746 &  3.93e-16 & Piperidine; Azacyclohexane; Hexahydropyridine & FALSE & R04090 & $<$2e-16 & S-(2-Hydroxyacyl)glutathione hydrolase & FALSE \\ 
  C02341 &  2.39e-02 & trans-Aconitate; trans-Aconitic acid & FALSE & R04206 & $<$2e-16 & 3-Phospho-D-erythronate hydro-lyase & FALSE \\ 
  C02611 & $<$2e-16 & (E,E)-Piperoyl-CoA & FALSE & R04291 & $<$2e-16 & UDP-N-acetyl-D-glucosamine:lysosomal-enzyme N-acet... & FALSE \\ 
  C02929 &  1.91e-07 & 2-Hydroxy carboxylate & FALSE & R05196 &  6.95e-05 & 1,4-alpha-D-Glucan:1,4-alpha-D-glucan 4-alpha-D-gl... & FALSE \\ 
  C03356 & $<$2e-16 & 3-Phospho-D-erythronate & FALSE & R05717 &  1.18e-06 & AMP,sulfite:glutathione-disulfide oxidoreductase (... & FALSE \\ 
  C03706 & $<$2e-16 & Lysosomal-enzyme D-mannose & FALSE & R06036 &  6.04e-05 & UDP-glucose:D-fructose 2-alpha-D-glucosyltransfera... & FALSE \\ 
  C03882 &  6.76e-14 & Piperine; N-((E,E)-Piperoyl)piperidine; 1-Piperoyl... & FALSE & R06186 &  4.26e-02 &  & FALSE \\ 
  C03899 & $<$2e-16 & S-(2-Hydroxyacyl)glutathione & FALSE & R07100 & $<$2e-16 & trichloroethene:glutathione S-(1,2-dichlorovinyl)t... & FALSE \\ 
  C04309 &  7.16e-11 & Phosphoenol-4-deoxy-3-tetrulosonate & FALSE & R07256 & $<$2e-16 & NDP-glucose:D-fructose 2-alpha-D-glucosyltransfera... & FALSE \\ 
  C04540 & $<$2e-16 & N4-(Acetyl-beta-D-glucosaminyl)asparagine; N4-(bet... & FALSE & R07261 & $<$2e-16 & NDP-glucose:1,4-alpha-D-glucan 4-alpha-D-glucosylt... & FALSE \\ 
  C04789 &  1.96e-08 & Lysosomal-enzyme N-acetyl-D-glucosaminyl-phospho-D... & FALSE & R07282 &  2.56e-02 & polyribonucleotide:phosphate nucleotidyltransferas... & FALSE \\ 
  C06790 &  4.22e-04 & Trichloroethene; Trichloroethylene; TCE & FALSE & R07291 & $<$2e-16 & 2-lysophosphatidylcholine acylhydrolase & FALSE \\ 
  C07593 & $<$2e-16 & Rotenone & FALSE & R07744 & $<$2e-16 &  & FALSE \\ 
  C11310 & $<$2e-16 & 1-Methyl-4-phenylpyridinium; N-Methyl-4-phenylpyri... & FALSE & R07745 &  1.01e-14 & calycosin,NADPH:oxygen oxidoreductase (methylenedi... & FALSE \\ 
  C14868 & $<$2e-16 & S-(1,2-Dichlorovinyl)glutathione; DCVG & FALSE & R09052 &  4.27e-13 &  & FALSE \\ 
  C15541 & $<$2e-16 & NDP-glucose; NDP-D-glucose; NDP-alpha-D-glucose & FALSE & R09467 & $<$2e-16 &  & FALSE \\ 
  C20183 & $<$2e-16 & 7-Methylguanosine 5'-diphosphate & FALSE & R09468 & $<$2e-16 &  & FALSE \\ 
  C20237 & $<$2e-16 & alpha-Maltose 1-phosphate & FALSE & R09663 & $<$2e-16 & NDP-glucose:3-phospho-D-glycerate 2-alpha-D-glucos... & FALSE \\ 
  hsa00190 &  9.25e-04 & Oxidative phosphorylation - Homo sapiens (human) & FALSE & R09945 & $<$2e-16 & ATP:alpha-maltose 1-phosphotransferase & FALSE \\ 
  hsa00511 &  1.38e-07 & Other glycan degradation - Homo sapiens (human) & FALSE & R09994 & $<$2e-16 & alpha-maltose 1-phosphate:(1-$>$4)-alpha-D-glucan 4-... & FALSE \\ 
  hsa03018 &  3.56e-06 & RNA degradation - Homo sapiens (human) & FALSE & R10525 & $<$2e-16 & NDP-alpha-D-glucose:D-glucose 1-alpha-D-glucosyltr... & FALSE \\ 
  hsa04066 &  1.79e-02 & HIF-1 signaling pathway - Homo sapiens (human) & FALSE & R10546 &  5.90e-15 & N7-methyl-GMP phosphohydrolase & FALSE \\ 
  hsa04142 &  1.05e-12 & Lysosome - Homo sapiens (human) & FALSE &  &  &  &  \\ 
  hsa04260 &  4.80e-03 & Cardiac muscle contraction - Homo sapiens (human) & FALSE &  &  &  &  \\ 
   \hline
\end{tabular}
}

}

\resizebox{\textwidth}{!}{
% latex table generated in R 3.1.3 by xtable 1.7-4 package
% Tue Mar 17 17:07:29 2015
{\tiny
\begin{tabular}{llllllll}
  \hline
KEGG id & p.value & Description & Guess? & KEGG id & p.value & Description & Guess? \\ 
  \hline
 &  &  &  &  &  &  &  \\ 
   &  &  &  & R10546 &  5.90e-15 & N7-methyl-GMP phosphohydrolase & FALSE \\ 
   \hline
\end{tabular}
}

}

\end{document}
