// JavaScript Document

something = 	'<h2>Help Bubble</h2><p>Explanation placeholder goes here</p><p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. Integer laoreet. Sed tincidunt, tortor vel laoreet dapibus, sem neque congue dolor, consectetur venenatis velit lacus ac tellus. Maecenas malesuada, quam in fringilla sodales, nibh nunc sodales enim, ut rutrum odio nulla ac nunc. Praesent suscipit aliquam sapien. Nunc congue nunc quis velit. Fusce leo. Morbi dictum odio vulputate ipsum. Integer tempor velit. Cras suscipit pellentesque velit. Nam blandit euismod libero. Praesent euismod mauris in purus. Cras interdum ligula at elit commodo blandit. Aliquam diam. Praesent ornare nisi mattis justo. Donec vitae massa eget enim cursus egestas. Praesent eleifend ligula ut nibh. Donec in lorem vel elit interdum sagittis. Sed est. Aenean commodo. </p>';

tbsgc = 		'<h2>Link to Tuberculosis Structural Genomics Consortium (TBSGC): </h2><p>Using this resource, you can find structural information as well as images for TB proteins.</p><p><img src="../assets/images/tbdb/help/content/tbsgc.gif" alt="TBSGC screenshot" border="1" /></p>';

pfam = 			'<h2>Link to this protein at the Sanger Pfam site</h2><p>The Pfam database is a large collection of protein families.</p><p><img src="../assets/images/tbdb/help/content/pfam.gif" alt="Pfam screenshot" border="1" /></p>';

geneFamily = 	'<h2>Link to Gene Family Details</h2><p>All related genes are displayed in a tree structure of more than 20 genomes, with multiple alignments below. Alignments are shown as protein, CDS, transcript, and nucleotides (including up- and downstream sequence).</p><p><img src="../assets/images/tbdb/help/content/geneFamilyTree.gif" alt="TBDB screenshot" border="1" /></p>';

tuberculist = 	'<h2>Tuberculist</h2><p>TubercuList provides a complete dataset of DNA and protein sequences derived from the paradigm strain M. tuberculosis H37Rv, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).<br /><img src="../assets/images/tbdb/help/content/tuberculist-new.gif" alt="Tuberculist screenshot" border="1" /></p>';
		
maxPlanck = 	'<h2>Link to Proteomics Experiments at Max Planck Institute Berlin</h2><p><img src="../assets/images/tbdb/help/content/2Dpage.gif" alt="2D page" border="1"></p>';
		
googleScholar =	'<h2>Link to relevant articles on Google Scholar</h2><p><img src="../assets/images/tbdb/help/content/google.gif" alt="Google" border="1"></p>';
		
featureMap = 	'<h2>Link to feature map</h2><p>A display of annotated features of the gene\'s genomic region, with links to individual feature data.<br><br><img src="../assets/images/tbdb/help/content/featuremap.gif" alt="Google" border="1"></p>';
		
argoApplet = 	'<h2>Argo Applet</h2><p>The Broad Institute\'s interactive genome viewer, embedded in the page as Java applet, lets you visualize the gene with customizable options.<br><br><img src="../assets/images/tbdb/help/content/argo-applet.gif" alt="Argo" border="1"></p>';
			
argoDesktop = 	'<h2>Argo Desktop</h2><p>Download the standalone version of the Broad Institute\'s interactive genome viewer, and view the gene and annotation data.<br></p>';
			
genomeSequence=	'<h2>Genome Sequence</h2><p>View and copy the nucleotide sequence of this gene.<br/><br/><img src="../assets/images/tbdb/help/content/browse-region.gif" alt="Browse Regions" border="1"></p>';
			
dotPlot = 		'<h2>Dotplot</h2><p>Compare matching regions of several strains of <i>M. tuberculosis</i> and related organisms. Start by selecting a reference genome and one or more other genomes to display.<br><img src="../assets/images/tbdb/help/content/dotplot.gif" alt="Dotplot" border="1"></p>';
		
operonBrowser =	'<h2>Operon Browser</h2><p>View predicted operons of this gene.<br><br><img src="../assets/images/tbdb/help/content/operonbrowser.gif" alt="Operon Browser" border="1"></p>';
		
localBlast = 	'<h2>Local BLAST Search</h2><p>Search for matching sequence regions in our database of TB strains and related organisms\' genomes. You can search protein or nucleotide sequences.<br><br><img src="../assets/images/tbdb/help/content/blast.gif" alt="Local BLAST Search" border="1"></p>';

ncbiBlast = 	'<h2>NCBI BLAST Search</h2><p>Search NCBI\'s database for matching sequence regions in TB strains and related organisms\' genomes. You can search protein or nucleotide sequences.</p>';

expressionConnection = 	'<h2>Gene Profiles</h2><p>Retrieve a list of publication datasets relevant to this gene, with links to gene expression patterns for the experiments conducted.<br><br><img src="../assets/images/tbdb/help/content/expressionConnection.gif" alt="Gene Profiles" border="1"></p>';

spotHistory = 	'<h2>Spot History</h2><p>View a bar graph of the expression intensity for this gene across all microarrays.<br><br><img src="../assets/images/tbdb/help/content/spotHistory.gif" alt="Spot History" border="1"></p>';

operonDetail = 	'<h2>Operon Feature Detail</h2><p>View feature information for the operon that regulates this gene.<br><br><img src="../assets/images/tbdb/help/content/operonDetail.gif" alt="Operon Feature Detail" border="1"></p>';

alleles =		'<h2>Alleles</h2><p>[text to come]</p>';

traSH =			'<h2>TraSH List</h2><p>Genes found to be essential in transposon site hybridization (TraSH) experiments</p>';

bioHealthBase = '<h2>Biodefense and Public Health Database</h2><p>Curated Epitope Search Results<br><br><img src="../assets/images/tbdb/help/content/bioHealthBase.gif" alt="BioHealthBase" border="1"></p>';

funcAnnotation = '<h2>Functional Annotations</h2><p><b>KEGG:</b> Kyoto Encyclopedia of Genes and Genomes<br><b>PWY:</b> BioCyc Pathways<br><b>EC:</b> Enzyme Committee Nomenclature<br><b>GO:</b> Gene Ontology</p>'; 

chromoMap = 	'<h2>Synteny Map</h2><p>This tool visualizes genome alignments of a reference genome with one or more other sequences, broken up into chromosomes.</p><p><img src="../assets/images/tbdb/help/content/chromoMap.gif" alt="Chromo Map" border="1"></p>';

genomeMap = 	'<h2>Genome Map</h2><p>This tool provides an interactive linear view of genome features of one or more sequences.</p><p><img src="../assets/images/tbdb/help/content/genomeMap.gif" alt="Genome Map" border="1"></p>';

geneExpressionScope = '<h2>GeneExpressionScope</h2><p>GeneExpressionScope enables users to view significance of the expression value of a single gene across all samples in the database. </p><p><img src="../assets/images/tbdb/help/content/geneExpressionScope.gif" alt="GeneExpressionScope" border="1"></p>';

functionalCOGCategories = '<h2>COG Categories</h2><p>COG stands for Clusters of Orthologous Groups of proteins and is a useful tool for characterizing the function of genes into broad categories.  COGs are constructed by identifying candidate sets of orthologs in at least three phylogenetically distance species.  The conservation of orthologs across diverse species ensures preservation of common functionality.</p><p><a href="http://www.ncbi.nlm.nih.gov/pubmed/12969510" target="_blank">See the abstract on PubMed</a></p>';     

positiveCorrelation = '<h2>Positively Correlated Genes</h2><p>Genes that exhibit a positive correlation with the gene of interest provide some evidence that they exist as part of the same operon, regulon, or are controlled by a common regulator.  We list genes in descending order with highest correlation coefficient first down to an arbitrary cuttoff of 0.3.  These are the genes that are highlighted in blue on the right tail of the histogram; the size of the bars on the histogram can provide you with an indication of the significance of the correlation against the background of how all genes compare.</p>';  

negativeCorrelation = '<h2>Negatively Correlated Genes</h2><p>Genes that exhibit a negtive correlation with the gene of interest show which genes are downregulated in response to the gene of interest being upregulated.  In effect the negatively regulated list moves against the gene of interest.  We list genes in ascending order with lowest correlation coefficient first down to an arbitrary cuttoff of -0.3.  These are the genes that are highlighted in blue on the left tail of the histogram; the size of the bars on the histogram can provide you with an indication of the significance of the correlation against the background of how all genes compare.</p>';

globalCorrelationHistogram = '<h2>Distribution of Gene Correlations</h2><p>The histogram below was constructed by comparing the correlation with the gene of interest to all other genes in the genome.  Since a singular correlation coefficient is difficult to interpret by itself the histogram illustrates how significant a high or low correlation may in fact be.  The tails of the distribution are highlighted in blue; the left tail corresponds to the genes listed under "Genes with negative correlation" while the right tails shows the genes under "Genes with positive correlation".</p>';  

positiveCOGEnrichment = '<h2>COG Categories Enriched with Positive Correlation</h2><p>COG categories that are statistically enriched in the right tail of the distribution appear in order from most to least significant.  Statistical significance was assessed by calculating p-values using the hypergeometric test and subsequent Bonferroni correction to address the problem of multiple comparisons.  COG groups with corrected p-values less than 0.05 are displayed.  The presence of a COG group in the enriched list shows at a global level what overarching functional processes are taking place when the gene of interest is activated.<p>';

negativeCOGEnrichment= '<h2>COG Categories Enriched with Negative Correlation</h2><p>COG categories that are statistically enriched in the left tail of the distribution appear in order from most to least significant.  Mouse over the letters to see the category name and correct p-value.  Statistical significance was assessed by calculating p-values using the hypergeometric test and subsequent Bonferonni correction to address the problem of multiple comparisons.  COG groups with corrected p-values less than 0.05 are displayed.  The presence of a COG group in the enriched list shows at a global level what overarching functional processes are down regulated when the gene of interest is activated.<p>';

geneCC =  		'<h2>Other Genes Correlation Catalog Pages</h2><p>Links to another page in the correlation catalog that is centered on that particular gene</p>';

descriptionCC =	'<h2>Description of the gene</h2><p>The gene annotation for a particular gene inluding synonyms and long names</p>';

linksCC =  		'<h2>Gene Details Page</h2><p>Exit the correlation catalg and go to the gene details page for a particular gene of interest</p>';

cogCC =  		'<h2>COG ID</h2><p>Go to the actual COG indentifier page at NCBI to see what other species in the bacterial kingdom also have orthologs.  This can be useful in determining how TB-specific the gene of interest is against the context of all sequenced genomes.</p>';

correlationCC =	'<h2>Pearson Correlation Coefficient</h2><p>This is the Pearson correlation coefficient that detects the presence of a linear relationship between two variables (genes).  It will vary between -1 (perfect negatively correlated) to 0 (perfectly uncorrelated) to +1 (perfectly positively correlated).  In practice, there are rarely any genes that will ever be perfectly positively or negatively correlated with most being closer to 0.  You can click on the scatterplot icon to bring up the correlation graph to inspect what treatments are driving the correlation.</p>';

target = 		'<h2>Tuberculosis Animal Research and Evaluation Taskforce</h2><p><img src="../assets/images/tbdb/help/content/target.gif" alt="TARGET" border="1"><br />TARGET evaluates M. tuberculosis and M. tuberculosis mutants in mice, guinea pigs, and hollow fibers to assess their virulence and capacity to induce, for example, acute, latent, or progressive tuberculosis.</p>';