/* examples.c - Put up text with quick usage and examples. */ #include "common.h" #include "linefile.h" #include "htmshell.h" #include "hgColors.h" #include "hgNear.h" void doExamples(struct sqlConnection *conn, struct column *colList) /* Put up controls and then some helpful text and examples. * Called when search box is empty. */ { displayData(conn, colList, NULL); hPrintf("

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About the Gene Sorter

" "

This program displays a sorted table of genes that are related to " "one another. The relationship can be one of several types, including " "protein-level homology, similarity of gene expression profiles, or " "genomic proximity.

" "

To display a gene and its relatives:" "

Select a genome and assembly from the corresponding pull-down menus. " "
Type a word or phrase into the search text box to specify " "which gene should be displayed in the Gene Sorter. " ); hPrintf("%s", genomeSetting("examples")); hPrintf("%s", "
Choose the gene relationship with which you would like to sort the list " "by selecting an option from the sort by pull-down menu." "
Press the Go! button to display your results. " "

" "

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Following a successful search, the Gene Sorter displays a table containing " "the specified gene -- highlighted in light green -- and its relatives, " "each on a separate line. To adjust the number of rows " "shown, select an option from the display pull-down menu.

" "

The default set of table columns -- " "which can be expanded, reduced, and rearranged via the configure " "button -- shows additional information about the genes. Some of the column " "data, such as those in the BLAST E-value and %ID columns, " "are calculated relative to the highlighted gene. To select a different gene " "in the list, click on its name. " "Clicking on a gene's Genome Position will open the UCSC Genome " "Browser to the location of that gene. Similarly, clicking on a gene's " "Description will open a page showing detailed information about " "the gene.

" "

One of the most powerful features of the Gene Sorter is its " "filtering capabilities, accessed via the filter button. Use the " "filter to fine-tune the list of displayed genes to a subset based on a " "selection of detailed and flexible 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.

" "

The Gene Sorter offers two options for displaying and downloading sequence " "associated with the genes in the table. Clicking on the sequence " "button will fetch associated protein, mRNA, promoter, or genomic sequence. " "To dump the table into a simple tab-delimited format suitable for " "import into a spreadsheet or relational database, click the text " "button. " "

The UCSC Gene Sorter was designed and implemented by Jim Kent, " "Fan Hsu, Donna Karolchik, 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.

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