MARQ 0.0.1

data/merb/app/views/help/quick.html.haml

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+:javascript
+  current = 'help'
+#quick
+
+  = partial 'menu', :selected => 'quick'
+
+
+  #video
+    =partial 'partials/video'
+
+  :redcloth
+   
+    <br>
+    If you prefer, you can follow the Quick Start Guide 
+    <a href="#TB_inline?height=410&width=640&inlineId=video" title="Quick Start Guide! video" class="thickbox">Video</a>
+    <br>
+    
+    h1. Launching a Job
+
+    This section will walk you through launching a typical MARQ job.
+
+    h2. 1. Select the organism the genes belong to
+
+    !/images/guide/organism.png!
+
+    The default is to make a cross platform query. You may query an specific
+    platform only, but you must specify the genes in the original platform id
+    format.
+
+    h2. 2. Paste your genes of interest 
+    
+    ... in the up and down text areas. You may use one or both.
+
+    !/images/guide/genes.png!
+
+
+    h2. 3. Select a name for your job and click Submit
+    
+    The name will be used to access the job at any latter time. If you do not
+    select one, a random one will be used. 
+
+    !/images/guide/name.png!
+
+    h2. 4. Wait for the computations to finish. 
+    
+    Please be patient, it might take a few minutes. The server needs to compute
+    the results and generate the html report; and then the browser needs to
+    render the html. Due to the amount of data displayed, each of these steps
+    may take a while.
+
+    h1. Inspecting the Results
+
+    The results page shows a table with the results sorted by their relation to the
+    query. Be sure to check the top and bottom of the list; some signatures may
+    have the conditions swapped in the comparison. Signature with the keyword
+    [ratio] appended to the name did not have enough replicates to compute
+    t-values and have their signatures derived from the log-ratios. 
+    
+    The scores goes from -1 to 1 in the case of a single list query, and from
+    -2 to 2 for a two list query. Since the scores depend strongly on the size
+    of the query lists, the permutation based p-values, also shown, are a more
+    reliable measure of relevance. These p-values have been corrected for FDR.
+
+    *Click the <span class='toggle_example'>[+]</span> link to 
+    display additional information* in for any of the signatures, including the dataset
+    description and images showing how the genes in the up and down lists.
+
+    Once the information is expanded, all the words in the description and title
+    (except for stopwords) will be click-able. *Click words to highlight signatures sharing that word*
+    and mark them in the adjoining hit-area, left of the table.
+
+    You may *double click on any place on the hit-area* to scroll the table
+    down to the corresponding signature.
+
+    !/images/guide/table.png!
+
+
+    h2. Examine annotations
+
+    Words are just one type of annotations for signatures. The annotation menu
+    shows additional annotations like  GO terms.
+    Selecting any of them will display a table with the annotations that are
+    significantly over-represented at both extremes of the results list. Only
+    word annotations are loaded by default, all the rest will be loaded when
+    selected the first time, which might take a little while. This table can
+    also be clicked to mark relevant signatures in the hit-area. The p-values
+    are corrected for multiple testing.
+
+    !/images/guide/annotations.png!
+
+    h2. View gene hits for a signature
+
+    Click on the hit bar views for the signatures (the green horizontal bars) to see detailed
+    information about the positions of the query genes in the signature. 
+
+    !/images/guide/hits.png!
+
+    Use the mouse to select interesting clusters of genes using click and drag
+    over the hit-area. Download those genes using the button 'Get Selected
+    Genes' to be used in another application like
+    "SENT":http://sent.dacya.ucm.es or
+    "GeneCodis":http://genecodis.dacya.ucm.es . Also, you may download the
+    log-ratios and t-values (if available for that signature) associated with
+    the query genes. 
+
+    Each genes has a link to its description entry an external reference site,
+    and to its profile in the GEO dataset (not available for GEO series or
+    datasets from other sources).
+
+    h2. Compare signatures (Rank Product)
+
+    You may select two or more signatures to perform meta-analysis. Use the
+    check boxes in the 'Compare' column to select the signatures. The first
+    check box, after <span><notextile>&uarr</notextile></span> select the
+    signature as-is. The other one, after the
+    <span><notextile>&darr</notextile></span> inverts the order of the genes,
+    and can be used to compare against signatures that may have the conditions
+    swapped in the comparison (thus appearing in the bottom of the list when
+    they should be on the top). Then click the 'Compare signatures' button.
+    
+    !/images/guide/compare.png!
+
+    The result of the meta-analysis compromises an up-regulated and a
+    down-regulated list of genes, which where found significantly de-regulated
+    in all the signatures using the Rank Product methodology. It also shows
+    separated tables for the genes in the up and down query lists. 
+    
+    !/images/guide/compare_page.png!
+
+    The complete details of the analysis can be downloaded in tab separated
+    format or in Excels xls. These files include, among other things, the log Rank
+    Product scores, the p-values, and whether the genes where included in the
+    original query lists. P-values are not FDR corrected, instead, we include
+    the PFP (equivalent to FDR) in the downloadable results.
+
+    h2. Download the signature information
+
+    You may download the log-ratios and t-values for all the genes in a signature from
+    the main results page.
+
+    !/images/guide/download.png!
+
+    Note that genes in these files are referenced by the applications internal
+    identifier format, which is usually the organism specific database id
+    format, as opposed to when they are downloaded from the hits page, where,
+    since only the genes in the query are included, they can be translated to
+    the original format used by the user.
+    
+

data/merb/app/views/layout/application.html.haml

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+!!!
+%html
+  %head
+    %meta{ 'http-equiv' => 'Content-Type', :content => 'text/html;charset=utf-8' }
+    %title= @title
+
+    %link{ :rel => "shortcut icon", :href => "/images/favicon.ico"}
+    = css_include_tag('thickbox', 'marq',  :bundle => 'marq_all')
+    = js_include_tag('wz_jsgraphics', 'jquery', 'jquery.scrollTo', 'jquery-ui.core', 'jquery-ui.hitarea', 'marq', 'jquery.tabs', 'thickbox','marq_pages', :bundle => 'marq_all')
+
+  %body
+    #layout
+      = partial 'partials/ie'
+      #header
+        %ul
+          %li.analysis 
+            %a{:href => '/'} New analysis
+          %li.help 
+            %a{:href => '/help'} Help
+      #content
+        = catch_content :for_layout
+        #clear_floats
+      #footer
+      :javascript
+        $('#header > ul > li.' + current).addClass('selected')
+
+

data/merb/app/views/main/index.html.haml

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+
+:javascript
+  current = 'analysis'
+  organisms = #{@organisms.to_json}
+
+#main
+  #ad_video
+    Check out the 
+    %a{ :href => "#TB_inline?height=410&width=640&inlineId=index_video", :title => "Quick Start Guide! video", :class => "thickbox"} Quick Start Guide Video
+
+    #index_video
+      = partial 'partials/video'
+
+  %form{:action => "/", :method => 'post'}
+    #genes
+      .textarea.parambox#up
+        %h2.boxtitle Up Regulated Genes
+        %textarea#ids_up{:name => :ids_up}
+      .textarea.parambox#down
+        %h2.boxtitle Down Regulated Genes
+        %textarea#ids_down{:name => :ids_down}
+      #fill
+        %span Zymolyase example (yeast): 
+        %a.toggle{:href => "#", :onclick => "fill_ids()"} [Load example]
+        %a.toggle{:href => "Miguel_Zymolyase"} [Results]
+
+    #parameters
+
+      #organisms.parambox
+        %h2.boxtitle Organism
+
+        %p Please Select the organism the genes belong to
+        %select#organism{:name => :organism}
+          - @organisms.keys.sort{|a,b| a <=>b}.each do |org|
+            - p = @organisms[org]
+            %option{:value => org }= p[0]
+
+      #platforms.parambox
+        %h2.boxtitle Platform
+
+        %p 
+
+          Select the platform the genes belong to. The genes must be in the
+          platform native format. If the Cross platform option is selected the
+          genes may be in any of the suported formats, as they will be
+          translated
+
+
+        %select#platform{:name => :platform}
+          %option#cross{:value =>'cross'} Cross platform query
+
+      #name.parambox
+        %h2.boxtitle Job Name
+        %p
+          Select a name for your job. A random one will be assigned if left blank
+        %input{ :name => :name}
+
+     
+      #submit.parambox
+        %input{:type => 'submit'}
+
+    #logos
+      %hr
+      %center
+        %a{:href => "http://artecs.dacya.ucm.es/atc/homepage.php"}
+          %img{:src => "images/logo_ARTECS.jpg"}
+        %a{:href => "http://biocomp.cnb.uam.es/"}
+          %img{:src => "images/logo_BCU.jpg"}
+        %a{:href => "http://www.ucm.es/info/mfar/"}
+          %img{:src => "images/logo_MICRO.png"}
+
+:javascript
+  
+  function fill_ids(){
+ 
+    var up = "HSP12\nYLR042C\nRFX1\nYPL088W\nYHL010C\nYHR087W\nCRG1\nDAL7\nHAL1\nSRL3\nGPD1\nPRM5\nPRM10\nPST1\nFMP33\nYLR194C\nCTT1\nSLT2\nYLR040C\nYKE4\nDDR48\nYLR414C\nCWP1\nYMR315W\nPIR3\nYPS3\nYIL024C\nYGL157W\nSED1\nGAT1\nGRE3\nYGR146C\nOAZ1\nNQM1\nKTR2\nSPI1\nPCM1\nSTF2\nPPX1\nHMX1\nMDN1\nMSB3\nCAK1\nYCL049C\nSIP18\nPNS1\nFIR1\nSVS1\nGPG1\nDAN4\nYNL058C\nSYM1\nSBE22\nYET1\nRBK1\nCRH1\nALD4\nPGM2\nYDR262W\nKRE11\nMCH5\nGRE2\nNUP85\nECM4\nSOL4\nHOR2\nTMA10\nMSG5\nYJL171C\nYJR008W\nYML131W\nDFG5\nPNC1\nPRY2\nCIS3\nGDB1\nRCR1\nYOL019W\nORC6\nSWC7\nSPG5\nPET10\nATG8\nPEX27\nYKL161C\nICT1\nTFS1\nGOR1\nBGL2\nDOG2\nGFA1\nIAH1\nMSB4\nDCS2\nYJL160C\nTIR2\nSMF1\nBZZ1\nMSC1\nFYV8\nRGS2\nEXG1\nFAS2\nCIT1\nDUN1\nYHR097C\nYMR181C\nSOR1\nCHS7\nRCN2\nYEH1\nACA1\nYNL194C\nYML087C\nGTT1\nECM13\nYHR033W\nDOG1\nENT3\nTHI22\nMET28\nYKL151C\nATP22\nSOM1\nFRE2\nHXT1\nYSP3\nYPR1\nSOL1\nAGX1\nFMP48\nIML2\nMID2\nNCA3\nYDL114W\nYOL048C\nYNR065C\nSLU7\nPTP2\nYNL208W\nYKL121W\nVPS27\nHXK1\nMET16\nHSP32\nLSC2\nYMR090W\nSLD2\nYIL108W\nPRR1\nGIC2\nPRX1\nADD37\nCMK2\nYPL23HSP12\nYLR042C\nRFX1\nYPL088W\nYHL010C\nYHR087W\nCRG1\nDAL7\nHAL1\nSRL3\nGPD1\nPRM5\nPRM10\nPST1\nFMP33\nYLR194C\nCTT1\nSLT2\nYLR040C\nYKE4\nDDR48\nYLR414C\nCWP1\nYMR315W\nPIR3\nYPS3\nYIL024C\nYGL157W\nSED1\nGAT1\nGRE3\nYGR146C\nOAZ1\nNQM1\nKTR2\nSPI1\nPCM1\nSTF2\nPPX1\nHMX1\nMDN1\nMSB3\nCAK1\nYCL049C\nSIP18\nPNS1\nFIR1\nSVS1\nGPG1\nDAN4\nYNL058C\nSYM1\nSBE22\nYET1\nRBK1\nCRH1\nALD4\nPGM2\nYDR262W\nKRE11\nMCH5\nGRE2\nNUP85\nECM4\nSOL4\nHOR2\nTMA10\nMSG5\nYJL171C\nYJR008W\nYML131W\nDFG5\nPNC1\nPRY2\nCIS3\nGDB1\nRCR1\nYOL019W\nORC6\nSWC7\nSPG5\nPET10\nATG8\nPEX27\nYKL161C\nICT1\nTFS1\nGOR1\nBGL2\nDOG2\nGFA1\nIAH1\nMSB4\nDCS2\nYJL160C\nTIR2\nSMF1\nBZZ1\nMSC1\nFYV8\nRGS2\nEXG1\nFAS2\nCIT1\nDUN1\nYHR097C\nYMR181C\nSOR1\nCHS7\nRCN2\nYEH1\nACA1\nYNL194C\nYML087C\nGTT1\nECM13\nYHR033W\nDOG1\nENT3\nTHI22\nMET28\nYKL151C\nATP22\nSOM1\nFRE2\nHXT1\nYSP3\nYPR1\nSOL1\nAGX1\nFMP48\nIML2\nMID2\nNCA3\nYDL114W\nYOL048C\nYNR065C\nSLU7\nPTP2\nYNL208W\nYKL121W\nVPS27\nHXK1\nMET16\nHSP32\nLSC2\nYMR090W\nSLD2\nYIL108W\nPRR1\nGIC2\nPRX1\nADD37\nCMK2\nYPL230W"
+    var down = "NIP7\nRAS1\nBRX1\nYIL064W\nNSR1\nTPN1\nFET3\nILV5\nDBP2\nLIA1\nPHO5\nFCY2\nOPT1\nPHO11\nZRT2\nSSU1\nMRH1\nSHM2\nAAH1\nATO3\nPHO3\nYHB1\nPHO12\nLAP4"
+    $('#ids_up').attr('value',up);
+    $('#ids_down').attr('value',down);
+    $('#organism').attr('value',"sgd"); 
+  }
+  
+  function organism_select(){
+    organism = $('select#organism').val();
+    $('select#platform option').not('#cross').remove();
+    $(organisms[organism][1]).each(function(){
+      $('select#platform').append('<option value="' + this + '" >' + this + '</option>')
+    })
+  }
+
+  $(function(){
+    $('select#organism').change(organism_select);
+    organism_select();
+    clear_textareas();
+
+  })

data/merb/app/views/normalize/index.html.haml

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+:javascript
+  current = 'translate'
+#translate
+  %form{:method => 'post', :enctype => "multipart/form-data"}
+     
+    #input
+      .parambox.select#organism
+        %h2.boxtitle Organism
+        %p 
+          Select the organism the genes belong to
+        %select#org{:name => 'org'}
+          - @organisms.each do |org|
+            %option{:value => org, :selected => (org == 'human')}= org
+
+      .textarea.parambox#original
+        %h2.boxtitle Original Genes
+        %textarea#missing{:name => 'missing'}= @missing.join("\n")
+
+    #output
+      .parambox.select#format
+        %h2.boxtitle Target ID
+        %p 
+          Select the format to which you wish the ids to be translated
+        %select#ids{:name => 'id'}
+          - @ids['human'].each do |id|
+            %option{:value => id}= id
+
+      .textarea.parambox#translations
+        %h2.boxtitle Translated Genes
+        %textarea#found{:name => 'found'}= @found.join("\n")
+
+    .parambox#submit.clear
+      %input{:type => 'submit'}
+
+  :javascript
+    eval('ids = #{@ids.to_json}')
+
+    $(function(){
+      $('select#org').change(function(){
+        $('select#ids').find('option').remove();
+        $(ids[$(this).val()]).each(function(){
+          $('select#ids').append("<option value='" + this + "'>" + this + "</option>")
+        })
+      })
+      $('select#org').val('human')
+    })
+
+:javascript
+  $(function(){
+    clear_textareas()
+  })

data/merb/app/views/partials/_annotations.html.haml

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+#annotations
+  %h3#annotations_title 
+    Annotations Menu
+  %a#close_annotations_menu{:href => '#'} [X]
+  %div
+    %label{:for => 'annotations_select'} Show:
+    %select#annotations_select
+      %option{:value => ""} Select one:
+      %option{:value => "Words"} Words
+      /%option{:value => "Polysearch"} Polysearch
+      /%option{:value => "UMLS"} UMLS
+      %option{:value => "GO_direct"} GO terms directly related
+      %option{:value => "GO_inverse"} GO terms inversely related
+      %option{:value => "GOSlim_direct"} GO Slim directly related
+      %option{:value => "GOSlim_inverse"} GO Slim inversely related
+  %hr
+  %div#enrichment_table_div
+    %table#enrichment_table
+      %thead
+        %tr
+          %th Term
+          %th P-Value
+      %tbody
+
+:javascript
+  $('a#close_annotations_menu').click(function(){$('#annotations_menu').toggle('slow');return false;})
+  
+  $('#annotations_select').val("");
+  $('#annotations_select').change(function(){
+     update_annotations_table();
+     if ($('#enrichment_table_div').hidden){
+       $('#enrichment_table_div').show();
+     }
+    }
+  );
+  
+  

data/merb/app/views/partials/_enrichment.html.haml

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+- terms = info[:terms]
+.table
+  %table
+    %thead
+      %tr
+        %th.term Term
+        %th.pvalue Value
+    %tbody
+      - terms.each do |p|
+        - term = p[0]
+        - value = p[1]
+        %tr
+          %td.term
+            %a.mark{:href => '#'}= term
+          %td.pvalue= "%1.3g" % value
+:javascript
+  $('a.mark').click(function(){mark("Words", $(this).html());update_hits()} )

data/merb/app/views/partials/_experiment.html.haml

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+.exp_details
+  %h3.exp 
+    Description
+    %span.dataset= span_words(info[:dataset], false)
+
+  %p.description
+
+    = span_words(info[:description])
+
+
+  %h3.exp
+    Hits
+    %a.logratios{:href => "/logratios?experiment=#{escapeURI(@experiment)}&job=#{@job}&genes="} [Get logratios]
+    - if @experiment !~ /\[ratio\]/
+      %a.ts{:href => "/ts?experiment=#{escapeURI(@experiment)}&job=#{@job}&genes="} [Get t-values]
+
+
+  - if info[:up]
+    %p.hits
+      %a.hits{:href => "/experiment_hits?job=#{ @job }&experiment=#{ escapeURI(@experiment) }&side=Up", :target => "_blank" } 
+        U:
+        %img{:src => info[:up]}
+
+  - if info[:down]
+    %p.hits
+      %a.hits{:href => "/experiment_hits?job=#{ @job }&experiment=#{ escapeURI(@experiment) }&side=Down", :target => "_blank" } 
+        D:
+        %img{:src => info[:down]}
+
+  %p.annotations
+    %ul.annotation_types
+
+

data/merb/app/views/partials/_ie.html.haml

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+#ie_warning
+  If you are using 
+  %span.ie internet explorer
+  and this site seems 
+  %span very slow 
+  you might
+  need to try a different browser like
+  %a{:href => "http://www.mozilla.com"} Firefox
+  ,
+  %a{:href => "http://www.apple.com/safari/"} Safari
+  or
+  %a{:href => "http://www.google.com/chrome/"} Google Chrome
+
+  :javascript
+    if (jQuery.browser.msie){
+      $('#ie_warning').show();
+    }
+
+

data/merb/app/views/partials/_video.html.haml

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+:redcloth
+  <center>
+          <object width="640" height="400"> <param name="movie" value="http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/mp4h264player.swf"></param> <param name="quality" value="high"></param> <param name="bgcolor" value="#FFFFFF"></param> <param name="flashVars" value="thumb=http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/FirstFrame.jpg&containerwidth=640&containerheight=400&content=http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/MarQ%20Quick%20Start%20Guide!.mp4&advseek=true"></param> <param name="allowFullScreen" value="true"></param> <param name="scale" value="showall"></param> <param name="allowScriptAccess" value="always"></param> <param name="base" value="http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/"></param> <embed src="http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/mp4h264player.swf" quality="high" bgcolor="#FFFFFF" width="640" height="400" type="application/x-shockwave-flash" allowScriptAccess="always" flashVars="thumb=http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/FirstFrame.jpg&containerwidth=640&containerheight=400&content=http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/MarQ%20Quick%20Start%20Guide!.mp4&advseek=true" allowFullScreen="true" base="http://content.screencast.com/users/Bioinfo-UCM/folders/Camtasia/media/2c6d8f83-26f5-42a7-bacc-a56613d99f41/" scale="showall"></embed> </object>
+  </center>
+

data/merb/app/views/results/compare.html.haml

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+:javascript
+  current = '#{@job}';
+
+
+%h2#title
+  Results for: 
+  %a.job{:href => "/#{ @job }"}= @job
+  > Shared genes by selected signatures
+
+#compare
+  #genes_compare
+    .menu_links
+      %a.select_table.selected.button{:href => '#', :rel => 'table_up'} Top up regulated genes
+      %a.select_table.button{:href => '#', :rel => 'table_down'} Top down regulated genes
+      - if @genes_up.any?
+        %a.select_table.button{:href => '#', :rel => 'table_query_up'} Genes in the up query
+      - if @genes_down.any?
+        %a.select_table.button{:href => '#', :rel => 'table_query_down'} Genes in the down query
+      .clear_floats
+
+
+    %table#table_genes_headers
+      %thead
+        %tr
+          %th.name Name
+          %th.synonyms Synonyms
+          %th.pvalue P-Val
+    %div.table_scroller
+      - if @scores_up.any?
+        %table#table_up.data
+          %tbody
+            - @sorted_up.each do |p|
+              - gene = p[0]
+              - score = p[1][0]
+              - pvalue = p[1][1]
+              %tr{:id => gene}
+                %td.name 
+                  - url = gene_url(@org, gene)  
+                  - if url != nil
+                    %a.geneurl{:href => "#{url}"}= gene
+                  - else
+                    = gene
+                %td.synonyms= @synonyms[gene].uniq.join(", ")
+                %td.pvalue= print_pvalue pvalue, 0.00001
+
+      - if @scores_down.any?
+        %table#table_down.data
+          %tbody
+            - @sorted_down.each do |p|
+              - gene = p[0]
+              - score = p[1][0]
+              - pvalue = p[1][1]
+              %tr{:id => gene}
+                %td.name
+                  - url = gene_url(@org, gene)  
+                  - if url != nil
+                    %a.geneurl{:href => "#{url}"}= gene
+                  - else
+                    = gene
+                %td.synonyms= @synonyms[gene].uniq.join(", ")
+                %td.pvalue= print_pvalue pvalue, 0.00001
+
+      - if @genes_up.any?
+        %table#table_query_up.data
+          %tbody
+            - @scores_up.select{|gene, info| @genes_up.include?  gene}.sort{|a,b| a[1][0] <=> b[1][0]}.each do |p|
+              - gene = p[0]
+              - used = @translations[gene]
+              - score = p[1][0]
+              - pvalue = p[1][1]
+              %tr{:id => gene}
+                %td.name
+                  - url = gene_url(@org,gene)
+                  - if gene != used
+                    -if url.nil?
+                      = "#{ used } (#{ gene })"
+                    - else
+                      %a.geneurl{:href => "#{url}"}= "#{ used } (#{ gene })"
+                  - else
+                    - if url.nil?
+                      = gene
+                    - else
+                      %a.geneurl{:href => "#{url}"}= gene
+                %td.synonyms= @synonyms[gene].uniq.join(", ")
+                %td.pvalue= print_pvalue pvalue, 0.00001
+
+      - if @genes_down.any?
+        %table#table_query_down.data
+          %tbody
+            - @scores_down.select{|gene, info| @genes_down.include?  gene}.sort{|a,b| a[1][0] <=> b[1][0]}.each do |p|
+              - gene = p[0]
+              - used = @translations[gene]
+              - score = p[1][0]
+              - pvalue = p[1][1]
+              %tr{:id => gene}
+                %td.name
+                  - url = gene_url(@org,gene)
+                  - if gene != used
+                    -if url.nil?
+                      = "#{ used } (#{ gene })"
+                    - else
+                      %a.geneurl{:href => "#{url}"}= "#{ used } (#{ gene })"
+                  - else
+                    - if url.nil?
+                      = gene
+                    - else
+                      %a.geneurl{:href => "#{url}"}= gene
+                %td.synonyms= @synonyms[gene].uniq.join(", ")
+                %td.pvalue= print_pvalue pvalue, 0.00001
+
+    .menu_links
+      %a.tab.button{:href => @url + '&format=tsv'} Download in Tab Separated Values  
+      %a.excel.button{:href => @url + '&format=excel'} Download in Excel
+      .clear_floats
+  
+:javascript
+  function select_table(table){
+    $('table.data').each(function(){
+      if ($(this).attr('id') != table ){
+        $(this).hide();
+      }else{ 
+        $(this).show();
+      }
+    })
+  }
+
+  $(function(){
+    select_table('table_up');
+    $('.select_table').click(function(){
+      select_table($(this).attr('rel'))
+      return false
+    })
+  })
+
+:javascript
+  
+  function fit_size(){
+    var scroller = $('.table_scroller');
+    fit_window(scroller, 45)
+  }
+
+  
+  $(function(){
+    $('#genes_compare').width($('#table_genes_headers').width() + 20);
+    fit_size();
+    
+   $(".select_table").click(function () { 
+    $(".select_table").removeClass("selected");
+    $(this).addClass("selected"); 
+   });
+ 
+    $(window).resize(function(){
+      fit_size();
+    });
+    
+   $("#genes_compare").tabs();
+  
+  }) 
+  
+
+