5e00cd8a9a64cbb632e6b77adb3c634160e97742 lrnassar Thu Sep 16 15:25:20 2021 -0700 Fixing insecure form messages refs #28175 diff --git src/hg/htdocs/goldenPath/help/hgNearHelp.html src/hg/htdocs/goldenPath/help/hgNearHelp.html index 4df6955..c2378c5 100755 --- src/hg/htdocs/goldenPath/help/hgNearHelp.html +++ src/hg/htdocs/goldenPath/help/hgNearHelp.html @@ -1,629 +1,629 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Gene Sorter" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>UCSC Gene Sorter User's Guide</h1> <h2>Contents</h2> <h6><a href="#Intro">Introduction</a></h6> <h6><a href="#Start">Getting started</a></h6> <h6><a href="#Table">Understanding the Gene Sorter display</a></h6> <h6><a href="#Configure">Configuring the Gene Sorter display</a></h6> <h6><a href="#Filter">Filtering the gene display</a></h6> <h6><a href="#Download">Displaying sequence and text-based output</a></h6> <hr> -<form name="googleForm1" method="GET" action="http://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> +<form name="googleForm1" method="GET" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> <p>Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" VALUE="Submit"> </form></p> <p> <a href="../../contacts.html">Questions and feedback are welcome</a>.</p> <!-- Introduction --> <a name="Intro"></a> <h2>Introduction</h2> <p> Genes function and evolve together.To understand a gene, you often need to understand an entire gene family. Many such families are already known and described, such as the HOX family that mediates many aspects of limb and brain development and the Cytochrome P450 family that is central to the metabolism of many medications.</p> <p> One easy way to identify well-known relatives of a gene is by looking for genes with name similarity, because biologists tend to use similar names for similar genes. However, scientists only partly understand the function of perhaps one-third of the genes of the genome; therefore, other techniques for grouping genes into families are necessary.</p> <p> The UCSC Gene Sorter is an excellent resource for exploring gene families and the relationships among genes. This tool displays a table of genes within a selected genome that are related to one another. Several different relationships may be explored: protein-level homology, similarity of gene expression profiles, or genomic proximity. The Gene Sorter supports searches on a variety of terms and phrases, including the gene name, the UniProtKB protein name, a GenBank accession, or a word or phrase present in a gene's description. The gene family display is highly configurable, allowing the user to control the order and number of columns, the number of rows, and the genes displayed. The tool provides several output formats, including a simple tab-delimited format that may be imported into a spreadsheet or a relational database.</p> <p> An important use of the Gene Sorter is to gather together a collection of genes that share similar properties for statistical analysis. For instance, one might want to examine promoter regions of genes that share a similar expression pattern or look for protein sequence motifs in genes that share similar GO annotations.</p> <p> One of the most powerful features of the Gene Sorter is its filtering capabilities. The filter enables the user to quickly select an interesting subset of the 25,000 genes in the genome based on a variety of detailed and flexible selection criteria. For example, the filter may be used to select all human genes over-expressed in the cerebellum that have GO-annotated G-protein coupled receptor activity.</p> <p> The Gene Sorter was designed and implemented by Jim Kent, Fan Hsu, David Haussler, and the UCSC Genome Bioinformatics Group. This work is supported by a grant from the National Human Genome Research Institute and by the Howard Hughes Medical Institute.</p> <!-- Getting Started --> <a name="Start"></a> <h2>Getting started</h2> <p> To begin using the Gene Sorter, you will first have to select a genomic region and the type of gene relationship you wish to display. You may also want to change some of the Gene Sorter's configuration settings to tailor the display to your research needs. These configuration options are described in <a href="#Configure">Configuring the Gene Sorter display</a>.</p> <p> <strong>Starting the Gene Sorter</strong></p> <ol> <li> Open the Gene Sorter <a href="../../cgi-bin/hgNear" target="_blank">home page</a>.</li> <li> Specify the genome and assembly you wish to view by selecting the appropriate options from the <em>genome</em> and <em>assembly</em> pull-down menus.</li> <li> Type a term or phrase into the <em>search</em> text box to determine which genes will be displayed in the browser. Valid search terms (with human genome examples) include:</p> <ul> <li> a gene name (HOXA9)</li> <li> a UniProtKB protein name (HXA9)</li> <li> a word or phrase that occurs in the description of a gene (MAP kinase)</li> <li> a GenBank mRNA accession (U14680)</li> </ul> <li> Choose the gene relationship that you would like to examine by selecting an option from the <em>sort by</em> pull-down menu. Genes will be sorted in order of proximity to the chosen gene, based on one of the following criteria: <ul> <!--Commented out til implemented <li> Expression (GNF Atlas2) -- similarity in gene expression, based on GNF Atlas 2 data</li> <li> Expression (UCLA) -- similarity in gene expression, based on UCLA data</li> --> <li> Expression (GNF Atlas1) -- similarity in gene expression, based on GNF Atlas 1 data</li> <li> Protein Homology - BLASTP -- similarity in protein homology, based on the BLASTP E-value</li> <li> Protein Homology - Rankprop -- similarity in protein homology, based on the Rankprop algorithm</li> <li> Protein Homology - PSI-BLAST -- similarity in protein homology, based on the PSI-BLAST E-value</li> <li> Pfam Similarity -- similarity based on number of shared domains</li> <li> Gene Distance -- absolute distance (left or right) on the chromosome from the selected gene</li> <li> Chromosome -- list sorted by chromosomal location</li> <li> Name Similarity -- similarity to the name of selected gene, based on the first several characters of the name</li> <li> Alphabetical -- list sorted by gene name</li> <li> GO Similarity -- number of Gene Ontology (GO) terms shared with selected gene</li> </uL> <li> Choose the number of items to display from the <em>display</em> pull-down menu (the default is 50).</li> <li> Press the <em>Go!</em> button to display your search results.</li> </ol> <!-- Understanding the Gene Sorter display --> <a name="Table"></a> <h2>Understanding the Gene Sorter display</h2> <p> The main page of the Gene Sorter displays a table containing rows of genes and associated attributes. In most cases, the currently-selected gene is shown at the top of the list, highlighted in light green. The remaining genes are ordered relative to the selected gene based on the sort criteria specified in the <em>sort by</em> menu. For example, in a table sorted by gene distance, the genes are listed in order of greater to lesser chromosomal proximity to the selected gene.</p> <p> The initial Gene Sorter display shows only a default subset of the columns available. The set of columns may be expanded, reduced, and rearranged by using the Gene Sorter's <a href="#Configure">configuration utility</a>. To view information about the data shown in the column, click on the column's label.</p> <p> To select a different gene in the table, click on the name of the gene. The Gene Sorter will move the gene entry to the top of the list and highlight it. The remaining genes will be reordered relative to the new selection.</p> <p> <strong>Column descriptions</strong> (listed in alphabetical order)</p> <ul> <li> <strong># column:</strong> Displays the position of each gene in the table, which is useful when examining data in tables with many rows. Clicking on the gene number selects it and moves it to the top of the list.</li> <li> <strong>3' UTR Fold column:</strong> Shows the estimated energy in kcal/mol of folding the 3' UTR of a gene into the best predicted secondary structure. The energy calculations and secondary structure predictions were obtained from the RNAfold program, which is part of the Vienna RNA Package.</li> <li> <strong>5' UTR Fold column:</strong> Shows the estimated energy in kcal/mol of folding the 5' UTR of a gene into the best predicted secondary structure. The energy calculations and secondary structure predictions were obtained from the RNAfold program, which is part of the Vienna RNA Package.</li> <li> <strong>Abundance column (Yeast):</strong> Displays protein abundance information, as reported in Ghaemmaghami et al. <a href="http://www.nature.com/nature/journal/v425/n6959/abs/nature02046.html" target="_blank">Global analysis of protein expression in yeast</a>, <em>Nature</em> <strong>425</strong>(6959), 737-741 (2003). For more information, see the <a href="http://yeastgfp.yeastgenome.org/" target="_blank">Yeast GFP Fusion Localization Database</a>.</li> <li> <strong>Arbeitman et al. 2002 Life-Cycle Expression Data column (Fruitfly):</strong> Shows the median ratio of gene expression in various phases of the fly life cycle relative to the expression of the gene in mixed egg-to-adult cultures. The level of detail may be increased or decreased with the <a href="#Configure">configuration utility</a>. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>BLASTP Bits column:</strong> Shows the bit score measure of protein similarity between a gene and the selected gene. The greater the similarity between two proteins, the higher the bit score. For more information about how the bit score was calculated, click on the Bits column label.</li> <li> <strong>BLASTP E-Value column:</strong> Shows the Blastp E-value (expectation value) between each gene and the selected gene. The greater the similarity of two proteins, the lower the E-value is. Identical long proteins have an E-value of zero. Formally, an E-value is the number of other known genes that are expected to have at least this level of homology by chance. An E-value of less than 0.1 can be safely interpreted as the probability that a match this good would occur merely by chance. For more information about how the E-value was calculated, click on the E-Value column label. Clicking on a gene's E-value displays an alignment between the gene and the selected (highlighted) gene.</li> <li> <strong><em>C. elegans</em> column:</strong> Shows the best Blastp match to the WormBase protein set. Clicking on the ID number displays the corresponding WormBase database record.</li> <li> <strong>Coding SNPs column:</strong> Shows the Simple Nucleotide Polymorphisms (SNPs) located in the coding region of each gene. Clicking on a SNP ID displays the SNP record associated with the gene in NCBI's dbSNP.</li> <li> <strong>Description column:</strong> Shows a brief description of each gene taken from its mRNA record. Clicking on a description displays a page showing additional information and links for the gene.</li> <li> <strong>Drosophila column:</strong> Shows the FlyBase ID of the best Blastp match to the FlyBase protein set. Clicking on the FlyBase ID displays the corresponding FlyBase report.</li> <li> <strong>Ensembl column:</strong> Shows the Ensembl transcript ID associated with the gene. Ensembl is an automatic gene prediction pipeline and a major genome database and web site run by the Sanger Institute and the European Bioinformatics Institute (EMBL-EBI). It is especially effective at mapping genes that are known in one organism to another organism. Compared to other gene predictions, those of Ensembl tend to have high specificity but low sensitivity to genes not already associated with characterized mRNA or protein sequence. Clicking on an Ensembl ID displays the Ensembl GeneView page for the gene.</li> <li> <strong>Entrez Gene (Human):</strong> Formerly LocusLink. Shows the NCBI Entrez Gene ID associated with the gene. Clicking on the entry displays the Entrez Gene record. If the record shows a link to the Online Mendelian Inheritance in Man (OMIM) -- indicated by an orange square with an "O" inside it -- an OMIM record is available for the gene.</li> <li> <strong>Exon Count column:</strong> Displays the number of exons in the gene (coding and non-coding).</li> <li> <strong>Exp Delta column:</strong> Shows the similarity of the expression of each gene to the selected gene. Genes with identical expression profiles have a value of 0. This column shows data only for the 1000 genes (including splicing variants) that have the most similar expression profiles. For more information about how expression distance was calculated, click on the Exp Delta column label.</li> <a name="Expression"></a> <li> <strong>Expression columns:</strong> Show the ratio of expression of the gene in selected tissues or life cycle stages to the expression of the gene overall. A gene that is more highly expressed is colored red, and a less expressed gene is shown in green. The values are colored on a logarithmic scale. This coloring is standard, but is the opposite of what an inexperienced user might expect: in this case, red means go and green means stop! Black indicates that a gene is neither over nor under expressed in the tissue. Uncolored boxes (white on most browsers) represent missing data. Various attributes of the expression column displays may be configured using the <a href="#Configure">configuration utility</a>. Depending on the organism, the user may adjust the color scheme and brightness, toggle between expression ratio and absolute expression values, and increase or decrease the level of detail shown. In particular, color-blind users may wish to switch the coloring from red/green to yellow/blue. For more information about the selection criteria used for expression columns, click on the column's label.</li> <li> <strong>GenBank column:</strong> Shows the GenBank RefSeq or mRNA accession number associated with the gene. Clicking on the accession number displays the GenBank record associated with it.</li> <li> <strong>Gene Ontology column:</strong> Shows the Gene Ontology (GO) terms associated with the gene. GO terms are words from a controlled vocabulary assigned to a gene by human curators. Clicking on a GO term displays the associated Gene Ontology Consortium database record.</li> <li> <strong>Genome Position column:</strong> Shows the chromosomal location of each gene in the genome. Clicking on a chromosomal position displays the gene at that location in the UCSC Genome Browser.</li <li> <strong>GNF1M ID column (Mouse):</strong> Shows the Affymetrix ID from the GNF1M chip that best corresponds to each gene. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>GNF Atlas2 column (Human):</strong> Shows the ID of the probe in the GNF Atlas 2 that overlaps most with the selected gene. The GNF Altas 2 is based on two Affymetrix chips: the U133A and a custom-designed GNF1H chip.</li> <li> <strong>GNF Delta column:</strong> Shows the similarity of the expression of each gene to the selected gene. Genes with identical expression profiles have a value of 0. This column shows data only for the 1000 genes (including splicing variants) that have the most similar expression profiles.</li> <li> <strong>GNF U74a, GNF U74b, GNF U74c columns (Mouse):</strong> Shows data from the Mouse Gene Expression Atlas from the Genomics Institute of the Novartis Research Foundation (GNF) on the Affymetrix U74a, U74b, and U74c chips. By default, the columns display the median ratio of expression in a specific set of tissues relative to the expression of the gene overall. The level of detail may be increased or decreased with the <a href="#Configure">configuration utility</a>. Currently, the full spectrum of tissues is available only on the U74a chip. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>GNF U95 column (Human):</strong> Shows data from from the GNF Expression Atlas on the Affymetrix U95 chip. By default, the column displays the median ratio of expression in a specific set of tissues relative to the expression of the gene overall. The level of detail may be increased or decreased with the <a href="#Configure">configuration utility</a>. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more details about the experiments and methods used to create this data, click on the GNF U95 column's label.</li> <li> <strong>Human column (Mouse):</strong> Shows that best Blastp match to the known genes protein set from the UCSC Human Genome Browser database. Clicking the accession number displays the gene in the UCSC Human Genome Browser.</li> <li> <strong>Kim-Lab Life-Cycle Expression Data (All) column (<em>C. elegans</em>):</strong> Shows the ratio of gene in all phases of the worm life cycle relative to the expression of the gene in mixed wild-type adult cultures. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>Kim-Lab Life-Cycle Expression Data (Median) column (<em>C. elegans</em>):</strong> Shows the median ratio of gene expression in selected phases of the worm life cycle. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>Max GNF Atlas 2 column:</strong> Shows the maximum absolute expression level for any tissue in the GNF Gene Expression Atlas 2. Most of the values fall in the zero to 50,000 range, but a few outliers may range as high as 200,000. A value of less than 20 indicates the expression could not be detected in any tissue at levels significantly above the cross-hybridization controls.</li> <li> <strong>Max GNF U95 column (Human):</strong> Shows the maximum absolute expression level for any tissue. Most values range between zero and 30,000, but a few outliers may range as high as 52,000. A value of less than 20 indicates the expression could no be detected in any tissue at levels significantly above the cross-hybridization controls.</li> <li> <strong>Max Rinn Sex column (Mouse):</strong> Shows the maximum expression value in adult male and female mouse tissue as described in (Rinn et al., Developmental Cell, 2004). For more information about the methods used to generate these data, click on the Max Rinn Sex column header.</li> <li> <strong>Module column (Yeast):</strong> Shows the predicted regulatory module (a combination of transcription factor binding sites) that regulates the gene. The approach underlying this annotation is described in Segal, E. et al., <a href="http://robotics.stanford.edu/~erans/publications/segal_promoters.pdf" target="_blank">Genome-wide discovery of transcriptional modules from DNA sequence and gene expression</a>, <em>Bioinformatics</em> 19(Suppl 1), i273-i282 (2003). For more information about the methods used, click the Module column header. To view genes that share a regulatory module, select the <em>Regulatory Module</em> option from the <em>sort by</em> menu.</li> <li> <strong>MOE430 ID column (Mouse):</strong> Shows the Affymetrix ID from the MOE430 series of chips (A & B) that best corresponds to each gene. For more details about the experiments and methods used to create this data, click on the column's label.</li> <li> <strong>Mouse column (Human):</strong> Shows the accession number of the best Blastp match to the known genes protein set in the UCSC Mouse Genome Browser database. Clicking on the accession number displays the gene in the UCSC Mouse Genome Browser.</li> <li> <strong>Name column:</strong> Displays the name of the gene. When possible, the HUGO Gene Nomenclature Committee (HGNC) name is shown. If the gene does not yet have an HGNC name, the GenBank accession number of the associated RefSeq or mRNA record is shown instead. Clicking on the gene name selects it and moves it to the top of the list.</li> <li> <strong>% ID column:</strong> Shows the percentage identity at the protein level between the gene and the selected gene. For more information about how the % ID was calculated, click on the % ID column label.</li> <li> <strong>PDB column:</strong> Displays all Protein Data Bank (PDB) IDs associated with the gene. PDB is a database of proteins with known 3-D structures. In some cases these records will correspond to only a fragment of the gene. In other cases the PDB record may include other molecules with which the protein interacts. Clicking on a PDB entry displays the associated PDB Structure Explorer page.</br> <li> <strong>Pfam Domains column:</strong> Shows a list of Protein Family (Pfam) domains contained in the gene product. Clicking on a domain displays the associated Pfam record.</li> <li> <strong>PSI-BLAST E-Value column:</strong> Shows the PSI-BLAST E-value (expectation value) between the UniProtKB or TrEMBL protein associated with the gene and the protein associated with the selected (highlighted) gene. The greater the similarity of two proteins, the lower the E-value is. Identical long proteins have an E-value of zero. For more information about how the E-value was calculated, click on the E-Value column label. Clicking on a gene's E-value displays an alignment between the gene and the selected (highlighted) gene.</li> <li> <strong>Rankprop column:</strong> Displays protein similarity scores assigned by the Rankprop algorithm. The scores reported in this column range from zero to one, with one being the most significant. Currently, Rankprop does not report an E-value statistic. For more information on this algorithm, click on the Rankprop column label.</li> <li> <strong>RefSeq column:</strong> Displays the NCBI RefSeq accession associated with the gene, if available. RefSeq genes are a non-redundant set of high-quality mRNA sequences. Clicking on the accession number displays the NCBI Entrez Gene record for a RefSeq accession. If the record shows a link to the Online Mendelian Inheritance in Man (OMIM) -- represented by an orange box with an "O" on it -- an OMIM record is available for the gene. OMIM is often an excellent source of human-curated information about human genes.</li> <li> <strong>Regulatory Motif column (Yeast):</strong> Shows the predicted transcription factor binding sites that correlate with expression of the gene. regulatory module (a combination of transcription factor binding sites) that regulates the gene. The approach underlying this annotation is described in Segal, E. et al., <a href="http://robotics.stanford.edu/~erans/publications/segal_promoters.pdf" target="_blank">Genome-wide discovery of transcriptional modules from DNA sequence and gene expression</a>, <em>Bioinformatics</em> <strong>19</strong>(Suppl 1), i273-i282 (2003). For more information about the methods used, click the Module column header.</li> <li> <strong>SGD ORF:</strong> Shows the Saccharomyces Genome Database (SGD) ID associated with the gene.</li> <li> <strong>SP Acc column:</strong> Shows the UniProtKB protein accession of a gene. Clicking on an entry displays the corresponding UniProtKB NiceProt view of the protein.</li> <li> <strong>Superfamily column:</strong> Displays a list of Structural Classification of Protein (SCOP) superfamilies associated with a protein. The gene set was mapped to SCOP superfamilies using the Superfamily HMM library. Clicking on an entry displays the associated Superfamily record.</li> <li> <strong>U133 ID column (Human):</strong> Shows the Affymetrix ID from the HG-U133 chip that best corresponds to each gene. For more information about the selection criteria used for this column, click on the U133 ID column's label.</li> <li> <strong>U133Plus2 ID column (Human):</strong> Shows the Affymetrix ID from the HG-U133 Plus 2.0 chip that best corresponds to each gene. For more information about the selection criteria used for this column, click on the U133Plus2 ID column's label.</li> <li> <strong>U74 ID column (Mouse):</strong> Shows the Affymetrix ID from the U74 series of chips (a, b, c) that best corresponds to each gene. For more information about the selection criteria used for this column, click on the U74 ID column's label.</li> <li> <strong>U95 ID column (Human)</strong>: Shows the Affymetrix ID from the HG-U95 chip that best corresponds to each gene. For more information about the selection criteria used for this column, click on the U95 ID column's label.</li> <li> <strong>UCLA Long Expression column (Human):</strong> Shows UCLA expression data from normal tissues on the U133 chip. This column shows the ratio of expression of a gene in the entire tissue set relative to the expression of the gene overall. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more information about the methods used to generate this data, click on the UCLA Long Expression column's label.</li> <li> <strong>UCLA Short Expression column (Human):</strong> Shows UCLA expression data from normal tissues on the U133 chip. This column shows the ratio of expression of a gene in a particular subset of tissues relative to the expression of the gene overall. See the <a href="#Expression">Expression columns</a> description for more information about the display and configuration of this column. For more information about the methods used to generate this data, click on the UCLA Short Expression column's label.</li> <li> <strong>UniProtKB column:</strong> Displays the UniProtKB protein name of each gene, if it is available. Otherwise, it shows the primary accession number. Clicking on a protein name or accession displays the corresponding UniProtKB NiceProt view of the protein.</li> <li> <strong>WormBase column (<em>C. elegans</em>):</strong> Shows the ORF name associated with each gene. Clicking on an ORF name displays the associated WormBase record.</li> <li> <strong>Yeast column:</strong> Shows the best Blastp match to the Saccharomyces Genome Database (SGD) protein set. Clicking on the yeast ID displays the corresponding SGD record.</li> <li> <strong>Zebrafish column:</strong> Shows the Ensembl peptide ID of the best Blastp match to the Ensembl gene predictions on the zebrafish genome. Clicking on the Ensembl peptide ID displays it in Ensembl Zebrafish Protein View.</li> </ul> <!-- Configuring the Gene Sorter display --> <a name="Configure"></a> <h2>Configuring the Gene Sorter display</h2> <p> The Gene Sorter is highly configurable, allowing you to fine-tune the display to show just the genes and data columns in which you're interested in an order that best suits your research needs. Most of the configuration is controlled through settings on the Configuration page, accessed via the <em>configure</em> button at the top of the Gene Sorter page.</p> <p> <strong>Changing the number of rows displayed</strong><br> To increase or decrease the number of rows shown in the table, pick a new value from the <em>display</em> pull-down menu, then click the <em>Go!</em> button.</p> <p> <strong>Changing the number of columns displayed</strong><br> By default, the Gene Sorter shows only a small subset of the table columns available for the genome. You can view the full list of columns, or add or remove columns from your display, on the Configuration page.</p> <p> The configuration table shows all the columns available for the currently-selected genome, listed in left-to-right display order. To add or remove a column from the Gene Sorter display, click the <em>On</em> checkbox to toggle the setting (a check indicates that the column is displayed). To quickly change the <em>On</em> settings of all columns, click the <em>Hide All</em> or <em>Show All</em> button at the top of the page. Click the <em>Submit</em> button to display the changes in the Gene Sorter.</p> <p> <strong>Changing the column positions</strong><br> In addition to adding or removing columns, it is also possible to move the columns to the left or right within the Gene Sorter table. The order of the column names in the configuration table indicates the current relative position of the columns in the Gene Sorter display from left to right. To shift a column one position to the left, click the <em>up</em> arrow in the item's <em>Position</em> column. Similarly, click the <em>down</em> arrow to shift a column to the right. When you have finished making changes, click the <em>Submit</em> button.</p> <p> <strong>Changing the expression colors</strong><br> By default, the gene expression ratios are shown using a red/green color scheme, where red indicates a gene that is more highly expressed and green corresponds to less expression. Color-blind users may find it helpful to switch the coloring from red/green to yellow/blue. To do so, select the "yellow high/blue low" option from the <em>Expression ratio colors</em> pull-down menu on the Configuration page, then click the <em>Submit</em> button.</p> <p> <strong>Changing the brightness of expression colors</strong><br> To increase or decrease the brightness of the colors in an expression column, edit the <em>brightness</em> value for the corresponding entry in the configuration table. Values greater than 1.0 increase the brightness, while those less than 1.0 dim the color. Click the <em>Submit</em> button to display the new values.</p> <p> <strong>Changing the type of tissue data shown in expression columns</strong><br> By default, the expression columns show the median ratio of expression of a gene in a small selected set of tissues. Use the the <em>tissues</em> pull-down menu to configure the tissue display for the column. The "all replicas" option will show the value of each individual experimental replica of each tissue. The "median of replicas" option displays a single value for each tissue that represents the median of all replicas for that tissue.</p> <p> <strong>Toggling between ratio and absolute expression values </strong><br> By default, expression columns show the ratio of expression of a gene relative to expression of the gene overall. To view absolute expression values instead, select the "absolute" option from the <em>values</em> pull-down menu.</p> <p> <strong>Displaying splicing variants</strong><br> By default, the Gene Sorter shows only one splicing variant: the one that produces the largest protein. To show all splicing variants, click the <em>Show all splicing variants</em> checkbox. Note that in most cases, the column values (and sometimes the names) will be identical across variants.</p> <p> <strong>Restoring the default settings</strong><br> At any time during your Gene Sorter session, you can restore the Gene Sorter table to its default layout by clicking the <em>Default</em> button on the Configuration page, then clicking <em>Submit</em>.</p> <p> <strong>Saving a configuration for future use</strong><br> The Gene Sorter configuration utility allows you to store multiple configurations for use in future sessions. This feature is particularly useful if you require different layouts for different research uses. To save the current configuration of the Gene Sorter layout, click the <em>Save</em> button on the Configuration page. Type in a name for the configuration in the text box at the top of the page, then click <em>Save</em>.</p> <p> <strong>Loading a previously-saved configuration</strong><br> Once you have saved a configuration, you can load it back into your Gene Sorter in a future session. To load a configuration, click the <em>Load</em> button on the Configuration page. The Gene Sorter will display a list of the names of your saved configurations. Click on a name to highlight it, then click <em>Load</em> to reconfigure your Gene Sorter based on the saved settings.</p> <p> <strong>Viewing a list of saved configurations</strong><br> To display a list of configurations that you have saved, click the <em>Save</em> button on the Configuration page. If you have any saved configurations, the Gene Sorter will display an <em>Existing Setups</em> list that shows the configuration names. To permanently remove a configuration from the list, click on the name to highlight it, then click the <em>Delete Existing Setup</em> button.</p> <!-- Filtering the gene display --> <a name="Filter"></a> <h2>Filtering the gene display</h2> <p> The Gene Sorter's gene filtering capabilities provide a versatile way to fine-tune the display to show just the genes in which you are interested. Filters are applied to individual gene fields, and may be combined to increase the specificity of the search. To access the Filter page, click the <em>filter</em> button at the top of the Gene Sorter page.</p> <p> At any time during the filter setup process, you can click the <em>List Names</em> button on the Filter page to view a list of genes that will be returned when the current filter settings are applied to the genome. You may find this list helpful in fine-tuning the filter.</p> <p> <strong>Filtering based on matching one or more terms</strong><br> Filters based on names, IDs, or other words restrict the display to only those genes that match one or more terms typed into the <em>search</em> text box. Examples of values that can be filtered on this basis include the gene name, RefSeq accession number, gene description, coding SNPs, and GO terms.</p> <p> This search supports wildcard matching on "*" and "?". Multiple terms must be separated by a space or tab. For example, the search criteria "HOXA9 FOX*" on the gene name field returns the gene named HOXA9 and any gene whose name begins with the letters "FOX". When searching on fields that consist of values containing more than one word (GO terms, coding SNPs, Pfam domains, and gene descriptions), the multi-word elements must be enclosed in single quotes. For instance, a search on the description phrase "forkhead box protein" should be entered as "forkhead box protein". Use the "any" and "all" options to determine whether the search should return any gene that matches any term ("any") or only those genes that match all terms ("all").</p> <p> To facilitate searching on multiple terms, the Gene Sorter provides the option to paste in or upload a list of search terms. To paste in a list of terms, click the filter's <em>Paste List</em> button, then paste or type the terms into the text box. Terms must be separated by a space, a tab, or be entered on separate lines, and may not include wildcards. When you have completed the list, click the Submit button to return to the main Filter page. The file upload utility - accessed via the <em>Upload List</em> button - has a similar functionality.</p> <p> <strong>Filtering based on numerical ranges</strong><br> Several of the gene fields can be filtered by specifying a numerical range within which the value must fall. Examples of fields in this category include expression ratios, Blastp data, and genome position. To use this type of filter, enter the minimum and maximum values delimiting the range in which you are interested. In some cases, the range of valid values is indicated in the filter box.</p> <p> The genome position filter requires the name of a chromosome (in the format <em>chrN</em>) in addition to the chromosomal start and end positions. To list all genes on a chromosome, enter only the chromosome name.</p> <p> Expression filters include "any" and "all" options to determine whether the search should return a gene if any of the tissue expression values meet the minimum and maximum criteria ("any") or only if all tissue expression values meet the search criteria ("all").</p> <p> <strong>Saving filter settings</strong><br> The Gene Sorter provides a mechanism for saving filter settings for use in future sessions. To preserve the current filter configuration, click the <em>Save Filter</em> button on the Filter page. Type in a name for the filter, then click <em>Save</em> to save the filter and return to the Filter page.</p> <p> <strong>Loading a saved filter</strong><br> Once a filter configuration has been saved, you can retrieve it in later sessions by loading it back into your Gene Sorter. To load the saved filter settings, click the <em>Load Filter</em> button on the Filter page. Click on the name of the filter you wish to load, then click the <em>Load</em> button. Click the <em>Submit</em> button on the Filter page to apply the filter settings to the Gene Sorter.</p> <p> <strong>Viewing a list of saved filters</strong><br> To display a list of filter settings that you have saved, click the <em>Save</em> button on the Filter page. If you have any saved filters, the Gene Sorter will display an <em>Existing Setups</em> list that shows the filter names. To permanently remove a filter from the list, click on the name to highlight it, then click the <em>Delete Existing Setup</em> button.</p> <!-- Displaying sequence and text-based output --> <a name="Download"></a> <h2>Displaying sequence and text-based output</h2> <p> The Gene Sorter's graphical presentation of data facilitates the visual observation of relationships and patterns among the genes in the display. However, it is often useful to convert the data to a text-based format that can be easily saved to a file or loaded into another program, database, or spreadsheet for further analysis. The Gene Sorter provides a mechanism for saving the current display in a tab-delimited text file or showing a text-based view of the sequence underlying the current display.</p> <p> <strong>Creating text-based output</strong><br> To output the current Gene Sorter table as text, click the text button at the top of the page. The Gene Sorter will display each row of table data on a separate tab-delimited line.</p> <p> <strong>Viewing the underlying sequence</strong><br> To display the protein, mRNA, or genomic sequence underlying the current Gene Sorter table, click the sequence button at the top of the page. On the Get Sequence page, select the desired sequence configuration settings that you'd like, then click the <em>Get Sequence</em> button. The Gene Sorter will display a text-based list of FASTA format records for each gene displayed in the table. The FASTA records may be cut and pasted into Blat for further study.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->