\documentclass[a4paper,11pt]{article} 
\usepackage[margin=1.0in]{geometry}
%\addtolength{\oddsidemargin}{-.875in}
%\addtolength{\evensidemargin}{-.875in}
%\addtolength{\textwidth}{1.75in}

%\addtolength{\topmargin}{-.875in}
%\addtolength{\textheight}{1.75in}
\usepackage[controls]{animate}
\usepackage[colorlinks=true,urlcolor=orange]{hyperref}
\usepackage{attachfile}
\usepackage{multirow}
\title{Networks}
\author{Tota Juliusdottir}
\usepackage{Sweave}
\begin{document}
 %applies to all chunks after this statement, sets the default for all code chunks
\setlength{\parindent}{0pt}
\maketitle

%To make the R code prettier, limit the line length and get rid of "+" 
%sweave customisation for R output
%\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em}
%\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em}
%\DefineVerbatimEnvironment{Scode}{Verbatim}{xleftmargin=2em}
\fvset{listparameters={\setlength{\topsep}{0pt}}}
\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}


\section{Data Overview}\label{overview}
All relevant in- and output files are in \textbf{MUS:/data/www/networks/} 

\begin{description}
\item[A modules]: @MUS:/data/www/networks/\textbf{modules/A}\\
The first set of Jon's modules:
  \begin{itemize}
    \item hippo 
    \item lung
    \item liver
    \end{itemize}


\item[B modules]: @MUS:/data/www/networks/\textbf{modules/B} \\
The second set of Jon's modules (the most recent ones):
  \begin{itemize}
    \item hippo.desexed
    \item hippo.male
    \item hippo.female
    \item lung.desexed
    \item lung.male
    \item lung.female
    \item liver.desexed
    \item liver.male
    \item liver.female
    \end{itemize}

\item[Phenotypes]: @MUS:/data/www/networks/\textbf{infiles/phenotypes.txt}\\
A total of \textbf{123} phenotypes (which I got from Martin) are used in the permutations

\item[Gene info from Biomart]: @MUS:/data/www/networks/\textbf{infiles/mart\_export.txt}
Contains all mouse gene ids, their positions and descriptions

\item[Probe annotation]: @MUS:/data/www/networks/\textbf{infiles/annot\_7\_sept\_2011.txt}\\
The same annotations as in the \textbf{annotdb} on MUS, where some of the gene identifiers have been updated to more recent ones (updated on 07.09.11 based on Ensembl)


\end{description}


\newpage

\section{Methods}
\subsection*{Permutations}
Initially 1000 permutations are completed and if the observed p-value is below 0.1, an additional 9000 permutations (total of 10,000 ) are carried out.

I use the following command script to do the permutations:

\begin{Schunk}
\begin{Sinput}
> sh /data/www/networks/networks.sh
\end{Sinput}
\end{Schunk}
 
\subsubsection*{Random phenotypes, fixed modules}
Every phenotype consists of a number of QTLs. I generated 123 'fake phenotypes', by randomly selecting a start position within the genome and from there I sequentially retrieved the same number of genes as within the 'real phenotype'. This way, the fake QTLs always contained the same number of genes as their real counterparts, but varied in length.\\

I repeated this 10.000 times (only 1000 times for high p-values) and for each module I counted the number of times I saw \textbf{more} genes within the fake phenotype compared to within the real phenotype.\\

So for example, if a module had 15 genes within a given phenotype, I counted how often this module had more than 15 genes within any of the randomly generated phenotypes.  I then divided this count by the number of iterations to obtain the p-value. \\

I did permutation analysis for each tissue within both A and B modules. Each permutation study resulted in a matrix of p-values (dim: 123*(number of modules)), providing a total of 12 such matrixes of different sizes (depending on the number of modules for the tissue).\\



\subsection{GO ANALYSIS}
\subsubsection{All the genes in all the modules}
\subsubsection{Genes within phenotypes}
\newpage

\section{Results}

\subsection*{Overview of modules}
%Example of uploading hippo modules \textbf{A} in R:
%<<echo=T,eval=F,keep.source=F>>=
%read.table("/data/www/networks/modules/A/hippo.txt", header=T, sep="\t")
%@
%For different tissues, change the filename (lung.txt, liver.txt etc.), and for B modules, %replace A in the path with B.
The twelve modules (see the Data Overview Section) belonging to the 3 tissues (hippo, lung and liver) are of different sizes and consist of varying number of probes. Probes that could not be mapped to single genes were not included in the subsequent analysis


\begin{table}[!htp] \footnotesize
\begin{center} 
\begin{tabular}{llccccc c}
\hline
\multicolumn{2}{c}{\multirow{2}{*}{\textbf{Datasets}}} & \textbf{No. of}& \multicolumn{3}{c}{\textbf{Size of modules}} & {\textbf{No. of}} & \textbf{No. of mapped}\\
\cline{4-6}&& \textbf{modules} & \textbf{mean} & \textbf{min} & \textbf{max} & \textbf{probes}  & \textbf{probes} \\
\hline
\multicolumn{1}{c}{\multirow{2}{*}{\emph{A}}} & \emph{hippo} & 23 & 544 & 39 & 2997 & 15736 & 13022(83\%)\\
&\multicolumn{1}{l}{\emph{liver}} & 5 & 182 & 45 & 538  & 912 & 713(78\%)\\
&\multicolumn{1}{l}{\emph{lung}} & 12 & 269 & 47 & 941 & 3226 &   2691(83\%)\\
\hline
\multicolumn{1}{c}{\multirow{8}{*}{\emph{B}}} & \emph{hippo.desexed}  & 10 & 812 & 79 & 2751 & 8121 & 6826 (84\%)\\
&\multicolumn{1}{l}{\emph{hippo.male}} & 12 & 692  & 82 & 3009 &  8301 & 6973(84\%)\\
&\multicolumn{1}{l}{\emph{hippo.female}} & 9 & 873 &  89 & 2666  &  7855 & 6592(84\%)\\
&\multicolumn{1}{l}{\emph{liver.desexed}} & 11 & 655 &145 & 2879 & 7201 & 6074(84\%)\\
 &\multicolumn{1}{l}{\emph{liver.male}} & 13 & 563  & 92 &  2598  &  7325 & 6190(85\%)\\
&\multicolumn{1}{l}{\emph{liver.female}} & 12 & 595 & 98 & 2583 & 7142 &  6026(84\%)\\
 &\multicolumn{1}{l}{\emph{lung.desexed}} & 15 & 548 & 26 & 2451 &  8216 & 6943(85\%)\\
 &\multicolumn{1}{l}{\emph{lung.male}} & 15 & 556 & 52 & 2127 & 8334  &  7041(84\%)\\
&\multicolumn{1}{l}{\emph{lung.female}} & 14 & 580 &  29 & 2646 & 8115  &  6860(85\%) \\
\hline
\end{tabular}
\caption[Modules summary]{Summary of the 12 modules. The table lists dataset names and the number of modules within each dataset. The mean, min and max sizes of modules within each dataset is also shown. The second last column shows the total numbers of probes within the dataset, where the last column shows how many of these probes were mapped to a gene.}
\label{tableModules}
\end{center} 
\end{table}
\subsection*{Permutations for fixed modules and random phenotypes}

The permutation test resulted in 12 p-value matrices with the following dimensions:

\begin{Schunk}
\begin{Sinput}
>  no_of_phenotypes * no_of_modules 
\end{Sinput}
\end{Schunk}
These P-value matrices are in:\\

MUS:/data/www/networks/\textbf{results/pval.matrices}\\

To retrieve the .RData files for these matrices, do:

\begin{Schunk}
\begin{Sinput}
> load("/data/www/networks/results/pval.matrices/A/hipA.RData")
> 
\end{Sinput}
\end{Schunk}

%save(lunA.pvals, file=''A/livA.RData'')

for \textbf{A} modules, and:
\begin{Schunk}
\begin{Sinput}
> load("/data/www/networks/results/pval.matrices/B/hipB.male.RData")
\end{Sinput}
\end{Schunk}


\subsubsection*{FALSE DISCOVERY RATE (FDR)}

Out of the three A modules, hippo is the only one with low FDRs. Both
liver and lung have FDR's larger than 1. (see /data/www/networks/results/fdr/A/)

% latex table generated in R 2.12.1 by xtable 1.5-6 package
% Thu Feb 16 16:57:02 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrrr}
  \hline
pval & total & observed & fdr \\ 
  \hline
0.10 & 2952 & 415 & 0.71 \\ 
  0.05 & 2952 & 253 & 0.58 \\ 
  0.01 & 2952 &  80 & 0.37 \\ 
  0.00 & 2952 &   8 & 0.37 \\ 
  0.00 & 2952 &   2 & 0.15 \\ 
   \hline
\end{tabular}
\caption{FDR for hippo A}
\end{center}
\end{table}
For a p-value of 0.01 and a total of 2952 values we would expect to
see 29.5 values below 0.01 by change, and we're seeing 80 (see table).


For a p-value of 0.001 we expect to see 2.95 values below 0.001 and we
see 8.


The modules and phenotypes for these 8 are: 

% latex table generated in R 2.12.1 by xtable 1.5-6 package
% Thu Feb 16 16:57:02 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrlll}
  \hline
 & pval & goterm & module & desc \\ 
  \hline
1 & 0.0000824062 & GO.0008134 & mod10 & transcription factor binding \\ 
  2 & 0.0005459538 & GO.0051409 & mod10 & response to nitrosative stress \\ 
  3 & 0.0003567428 & GO.0006461 & mod10 & protein complex assembly \\ 
  4 & 0.0008390679 & GO.0005243 & mod12 & gap-junction forming channel activity \\ 
  5 & 0.0001420631 & GO.0033270 & mod12 &  \\ 
  6 & 0.0008390679 & GO.0004768 & mod12 & stearoyl-CoA 9-desaturase activity \\ 
  7 & 0.0002570627 & GO.0006952 & mod12 & defense response \\ 
  8 & 0.0008390679 & GO.0019911 & mod12 & structural constituent of myelin sheath \\ 
  9 & 0.0000824429 & GO.0015630 & mod12 & microtubule cytoskeleton \\ 
  10 & 0.0000657223 & GO.0043209 & mod12 & myelin sheath \\ 
  11 & 0.0002091851 & GO.0001077 & mod13 &  \\ 
  12 & 0.0003882067 & GO.0012505 & mod14 & endomembrane system \\ 
  13 & 0.0000883345 & GO.0015111 & mod14 & iodide transporter activity \\ 
  14 & 0.0002180112 & GO.0004707 & mod14 & MAP kinase activity \\ 
  15 & 0.0002633707 & GO.0010744 & mod14 &  \\ 
  16 & 0.0000883345 & GO.0015705 & mod14 & iodide transport \\ 
  17 & 0.0004528492 & GO.0005739 & mod15 & mitochondrion \\ 
  18 & 0.0003651046 & GO.0005783 & mod15 & endoplasmic reticulum \\ 
  19 & 0.0007007192 & GO.0006355 & mod15 & regulation of transcription, DNA-dependent \\ 
  20 & 0.0005748463 & GO.0007409 & mod16 & axonogenesis \\ 
  21 & 0.0001500346 & GO.2000273 & mod16 &  \\ 
  22 & 0.0000264220 & GO.0043197 & mod16 & dendritic spine \\ 
  23 & 0.0001500346 & GO.0030546 & mod16 & receptor activator activity \\ 
  24 & 0.0000946322 & GO.0048168 & mod16 & regulation of neuronal synaptic plasticity \\ 
  25 & 0.0002986831 & GO.0050774 & mod16 & negative regulation of dendrite morphogenesis \\ 
  26 & 0.0000179386 & GO.0007249 & mod17 & I-kappaB kinase/NF-kappaB cascade \\ 
  27 & 0.0006456103 & GO.0000166 & mod17 & nucleotide binding \\ 
  28 & 0.0006274687 & GO.0001954 & mod18 & positive regulation of cell-matrix adhesion \\ 
  29 & 0.0008042646 & GO.0050715 & mod18 & positive regulation of cytokine secretion \\ 
  30 & 0.0007176893 & GO.0050660 & mod19 & FAD binding \\ 
  31 & 0.0009156887 & GO.0016747 & mod1 & transferase activity, transferring groups other than amino-acyl groups \\ 
  32 & 0.0000286516 & GO.0005515 & mod1 & protein binding \\ 
  33 & 0.0000000089 & GO.0005576 & mod1 & extracellular region \\ 
  34 & 0.0000008914 & GO.0005634 & mod1 & nucleus \\ 
  35 & 0.0000244665 & GO.0005739 & mod1 & mitochondrion \\ 
  36 & 0.0000095094 & GO.0005737 & mod1 & cytoplasm \\ 
  37 & 0.0000000198 & GO.0004872 & mod1 & receptor activity \\ 
  38 & 0.0000482682 & GO.0016021 & mod1 & integral to membrane \\ 
  39 & 0.0005385205 & GO.0000151 & mod1 & ubiquitin ligase complex \\ 
  40 & 0.0000000000 & GO.0004984 & mod1 & olfactory receptor activity \\ 
  41 & 0.0005952372 & GO.0005216 & mod20 & ion channel activity \\ 
  42 & 0.0006838080 & GO.0050840 & mod20 & extracellular matrix binding \\ 
  43 & 0.0009705715 & GO.0005811 & mod21 & lipid particle \\ 
  44 & 0.0006387601 & GO.0006970 & mod21 & response to osmotic stress \\ 
  45 & 0.0002517146 & GO.0045879 & mod22 & negative regulation of smoothened signaling pathway \\ 
  46 & 0.0000461331 & GO.0035137 & mod22 & hindlimb morphogenesis \\ 
  47 & 0.0000348022 & GO.0043025 & mod2 & cell soma \\ 
  48 & 0.0007262033 & GO.0008060 & mod2 & ARF GTPase activator activity \\ 
  49 & 0.0007892917 & GO.0030426 & mod2 & growth cone \\ 
  50 & 0.0000248485 & GO.0030672 & mod2 & synaptic vesicle membrane \\ 
  51 & 0.0006698639 & GO.0016887 & mod2 & ATPase activity \\ 
  52 & 0.0000000366 & GO.0005515 & mod2 & protein binding \\ 
  53 & 0.0007262033 & GO.0032312 & mod2 & regulation of ARF GTPase activity \\ 
  54 & 0.0001709674 & GO.0005576 & mod2 & extracellular region \\ 
  55 & 0.0004639059 & GO.0005524 & mod2 & ATP binding \\ 
  56 & 0.0009907783 & GO.0015031 & mod2 & protein transport \\ 
  57 & 0.0002685156 & GO.0030117 & mod2 & membrane coat \\ 
  58 & 0.0005491424 & GO.0005737 & mod2 & cytoplasm \\ 
  59 & 0.0004271649 & GO.0004872 & mod2 & receptor activity \\ 
  60 & 0.0002407380 & GO.0003713 & mod2 & transcription coactivator activity \\ 
  61 & 0.0003737496 & GO.0005794 & mod2 & Golgi apparatus \\ 
  62 & 0.0008798969 & GO.0019717 & mod2 & synaptosome \\ 
  63 & 0.0004134389 & GO.0003924 & mod2 & GTPase activity \\ 
  64 & 0.0001323645 & GO.0016020 & mod2 & membrane \\ 
  65 & 0.0000921105 & GO.0000166 & mod2 & nucleotide binding \\ 
  66 & 0.0005870915 & GO.0000139 & mod2 & Golgi membrane \\ 
  67 & 0.0001125951 & GO.0045202 & mod2 & synapse \\ 
  68 & 0.0005770143 & GO.0043234 & mod2 & protein complex \\ 
  69 & 0.0000000000 & GO.0004984 & mod2 & olfactory receptor activity \\ 
  70 & 0.0002510574 & GO.0042832 & mod3 & defense response to protozoan \\ 
  71 & 0.0002798727 & GO.0045885 & mod3 & positive regulation of survival gene product activity \\ 
  72 & 0.0003093219 & GO.0008380 & mod3 & RNA splicing \\ 
  73 & 0.0000015311 & GO.0007186 & mod3 & G-protein coupled receptor protein signaling pathway \\ 
  74 & 0.0005389773 & GO.0004252 & mod3 & serine-type endopeptidase activity \\ 
  75 & 0.0009320918 & GO.0016740 & mod3 & transferase activity \\ 
  76 & 0.0000031898 & GO.0005576 & mod3 & extracellular region \\ 
  77 & 0.0000063233 & GO.0005634 & mod3 & nucleus \\ 
  78 & 0.0000028173 & GO.0016503 & mod3 & pheromone receptor activity \\ 
  79 & 0.0000003357 & GO.0005743 & mod3 & mitochondrial inner membrane \\ 
  80 & 0.0000000000 & GO.0005739 & mod3 & mitochondrion \\ 
  81 & 0.0000000097 & GO.0005737 & mod3 & cytoplasm \\ 
  82 & 0.0001804190 & GO.0006810 & mod3 & transport \\ 
  83 & 0.0000000000 & GO.0004872 & mod3 & receptor activity \\ 
  84 & 0.0000607900 & GO.0003735 & mod3 & structural constituent of ribosome \\ 
  85 & 0.0000054073 & GO.0050896 & mod3 & response to stimulus \\ 
  86 & 0.0000865815 & GO.0005840 & mod3 & ribosome \\ 
  87 & 0.0002385407 & GO.0005829 & mod3 & cytosol \\ 
  88 & 0.0000000395 & GO.0016021 & mod3 & integral to membrane \\ 
  89 & 0.0000679317 & GO.0000166 & mod3 & nucleotide binding \\ 
  90 & 0.0002753050 & GO.0000139 & mod3 & Golgi membrane \\ 
  91 & 0.0004330441 & GO.0016192 & mod3 & vesicle-mediated transport \\ 
  92 & 0.0004091147 & GO.0030902 & mod3 & hindbrain development \\ 
  93 & 0.0006902688 & GO.0006397 & mod3 & mRNA processing \\ 
  94 & 0.0001731369 & GO.0043565 & mod3 & sequence-specific DNA binding \\ 
  95 & 0.0001178594 & GO.0007608 & mod3 & sensory perception of smell \\ 
  96 & 0.0000000000 & GO.0004984 & mod3 & olfactory receptor activity \\ 
  97 & 0.0000741335 & GO.0004930 & mod3 & G-protein coupled receptor activity \\ 
  98 & 0.0000074571 & GO.0006412 & mod3 & protein biosynthesis \\ 
  99 & 0.0008898149 & GO.0031902 & mod3 & late endosome membrane \\ 
  100 & 0.0000301804 & GO.0008137 & mod4 & NADH dehydrogenase (ubiquinone) activity \\ 
  101 & 0.0007069282 & GO.0004298 & mod4 & threonine endopeptidase activity \\ 
  102 & 0.0006697149 & GO.0022900 & mod4 &  \\ 
  103 & 0.0001620378 & GO.0005743 & mod4 & mitochondrial inner membrane \\ 
  104 & 0.0000019182 & GO.0005747 & mod4 & respiratory chain complex I (sensu Eukaryota) \\ 
  105 & 0.0000000046 & GO.0005739 & mod4 & mitochondrion \\ 
  106 & 0.0007405694 & GO.0003735 & mod4 & structural constituent of ribosome \\ 
  107 & 0.0008101608 & GO.0006749 & mod4 & glutathione metabolism \\ 
  108 & 0.0005797974 & GO.0014059 & mod4 & regulation of dopamine secretion \\ 
  109 & 0.0009224833 & GO.0005840 & mod4 & ribosome \\ 
  110 & 0.0005797974 & GO.0004775 & mod4 & succinate-CoA ligase (ADP-forming) activity \\ 
  111 & 0.0002435032 & GO.0000502 & mod4 & proteasome complex (sensu Eukaryota) \\ 
  112 & 0.0003857236 & GO.0031982 & mod4 & vesicle \\ 
  113 & 0.0001428547 & GO.0004984 & mod4 & olfactory receptor activity \\ 
  114 & 0.0000136547 & GO.0006412 & mod4 & protein biosynthesis \\ 
  115 & 0.0000159269 & GO.0070469 & mod4 &  \\ 
  116 & 0.0006109774 & GO.0048666 & mod5 & neuron development \\ 
  117 & 0.0005233652 & GO.0030424 & mod5 & axon \\ 
  118 & 0.0000004082 & GO.0008270 & mod5 & zinc ion binding \\ 
  119 & 0.0002081268 & GO.0030054 & mod5 & cell junction \\ 
  120 & 0.0000022816 & GO.0005515 & mod5 & protein binding \\ 
  121 & 0.0002542598 & GO.0005576 & mod5 & extracellular region \\ 
  122 & 0.0000383310 & GO.0005634 & mod5 & nucleus \\ 
  123 & 0.0000862148 & GO.0014069 & mod5 & postsynaptic density \\ 
  124 & 0.0005030213 & GO.0003779 & mod5 & actin binding \\ 
  125 & 0.0004732142 & GO.0001578 & mod5 & microtubule bundle formation \\ 
  126 & 0.0000000301 & GO.0003676 & mod5 & nucleic acid binding \\ 
  127 & 0.0000247841 & GO.0003677 & mod5 & DNA binding \\ 
  128 & 0.0003433981 & GO.0045211 & mod5 & postsynaptic membrane \\ 
  129 & 0.0000067064 & GO.0045202 & mod5 & synapse \\ 
  130 & 0.0000088248 & GO.0046872 & mod5 & metal ion binding \\ 
  131 & 0.0005594392 & GO.0007605 & mod5 & sensory perception of sound \\ 
  132 & 0.0002589811 & GO.0022614 & mod6 &  \\ 
  133 & 0.0000000000 & GO.0005576 & mod6 & extracellular region \\ 
  134 & 0.0000321171 & GO.0005578 & mod6 & extracellular matrix (sensu Metazoa) \\ 
  135 & 0.0006370289 & GO.0030175 & mod6 & filopodium \\ 
  136 & 0.0000826730 & GO.0005604 & mod6 & basement membrane \\ 
  137 & 0.0000000049 & GO.0005615 & mod6 & extracellular space \\ 
  138 & 0.0000048195 & GO.0005634 & mod6 & nucleus \\ 
  139 & 0.0000011860 & GO.0031012 & mod6 & extracellular matrix \\ 
  140 & 0.0009052030 & GO.0004859 & mod6 & phospholipase inhibitor activity \\ 
  141 & 0.0008664704 & GO.0032722 & mod6 &  \\ 
  142 & 0.0000694822 & GO.0016324 & mod6 & apical plasma membrane \\ 
  143 & 0.0008348947 & GO.0005764 & mod6 & lysosome \\ 
  144 & 0.0008664704 & GO.0031527 & mod6 & filopodium membrane \\ 
  145 & 0.0009052030 & GO.0051637 & mod6 & Gram-positive bacterial cell surface binding \\ 
  146 & 0.0009052030 & GO.0031404 & mod6 & chloride ion binding \\ 
  147 & 0.0000179905 & GO.0006355 & mod6 & regulation of transcription, DNA-dependent \\ 
  148 & 0.0002344667 & GO.0007568 & mod6 & aging \\ 
  149 & 0.0007312551 & GO.0003735 & mod7 & structural constituent of ribosome \\ 
  150 & 0.0009678576 & GO.0015935 & mod7 & small ribosomal subunit \\ 
  151 & 0.0003139236 & GO.0043198 & mod8 & dendritic shaft \\ 
  152 & 0.0001826790 & GO.0007026 & mod8 & negative regulation of microtubule depolymerization \\ 
  153 & 0.0000572590 & GO.0005515 & mod8 & protein binding \\ 
  154 & 0.0006646595 & GO.0005519 & mod8 & cytoskeletal regulatory protein binding \\ 
  155 & 0.0006190592 & GO.0030145 & mod8 & manganese ion binding \\ 
  156 & 0.0001793944 & GO.0005737 & mod8 & cytoplasm \\ 
  157 & 0.0006646595 & GO.0060124 & mod8 &  \\ 
  158 & 0.0001755808 & GO.0005829 & mod8 & cytosol \\ 
  159 & 0.0005940990 & GO.0045211 & mod8 & postsynaptic membrane \\ 
  160 & 0.0006012704 & GO.0006166 & mod9 & purine ribonucleoside salvage \\ 
  161 & 0.0006012704 & GO.0001675 & mod9 & acrosome formation \\ 
  162 & 0.0006012704 & GO.0018394 & mod9 & peptidyl-lysine acetylation \\ 
  163 & 0.0006012704 & GO.0001880 & mod9 & Mullerian duct regression \\ 
  164 & 0.0006802836 & GO.0016567 & modNA & protein ubiquitination \\ 
  165 & 0.0009456764 & GO.0046427 & modNA & positive regulation of JAK-STAT cascade \\ 
  166 & 0.0006491309 & GO.0043565 & modNA & sequence-specific DNA binding \\ 
   \hline
\end{tabular}
\caption{Hippo A modules and phenotypes with p-values< 0.001}
\end{center}
\end{table}% latex table generated in R 2.12.1 by xtable 1.5-6 package
% Thu Feb 16 16:57:03 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rrlll}
  \hline
 & pval & goterm & module & desc \\ 
  \hline
96 & 0.00 & GO.0004984 & mod3 & olfactory receptor activity \\ 
  83 & 0.00 & GO.0004872 & mod3 & receptor activity \\ 
  69 & 0.00 & GO.0004984 & mod2 & olfactory receptor activity \\ 
  40 & 0.00 & GO.0004984 & mod1 & olfactory receptor activity \\ 
  80 & 0.00 & GO.0005739 & mod3 & mitochondrion \\ 
  133 & 0.00 & GO.0005576 & mod6 & extracellular region \\ 
   \hline
\end{tabular}
\end{center}
\end{table}

To view the genes associated with these modules and phenotypes in R,
do (from MUS:/data/www/networks):



% latex table generated in R 2.12.1 by xtable 1.5-6 package
% Thu Feb 16 16:57:03 2012
\begin{table}[ht]
\begin{center}
\begin{tabular}{rlrll}
  \hline
 & phenotype & module & ens\_id & gene\_desc \\ 
  \hline
49 & Haem.HGB &  10 & ENSMUSG00000073478 & RIKEN cDNA D730003I15 gene [Source:MGI Symbol;Acc:MGI:1925971] \\ 
  50 & Haem.HGB &  10 & ENSMUSG00000026603 & SET and MYND domain containing 2 [Source:MGI Symbol;Acc:MGI:1915889] \\ 
  51 & Haem.HGB &  10 & ENSMUSG00000028600 & podocan [Source:MGI Symbol;Acc:MGI:2674939] \\ 
  52 & Haem.HGB &  10 & ENSMUSG00000028582 & coiled-coil and C2 domain containing 1B [Source:MGI Symbol;Acc:MGI:2443076] \\ 
  53 & Haem.HGB &  10 & ENSMUSG00000036533 & CDC42 effector protein (Rho GTPase binding) 3 [Source:MGI Symbol;Acc:MGI:2384718] \\ 
  54 & Haem.HGB &  10 & ENSMUSG00000036368 & family with sequence similarity 82, member A1 [Source:MGI Symbol;Acc:MGI:2147043] \\ 
   \hline
\end{tabular}
\caption{Genes within module 10 that are within the Haem.HGB QTLs }
\end{center}
\end{table}
For the B modules, the strongest signal is for hip_desexed with 22
p-values below 0.01 when 12,3 are expected. However, there are no
p-values below 0.001 for this dataset. All the other datasest for
modules B have high FDR values. 





\subsubsection*{GO analysis)}



\end{document}
