Importing a region list

A region list must contain the chromosome, start location, and stop locations as the first three columns. The chromosome number in the region list must be compatible with the genomic annotation for the species if you plan to use any feature (like motif detection) that requires reference sequence information. 

• Import the region list as described above for text files. Select Other for data type. Chromosome name or number should be imported as a text field; location start and stop may be either integer or text. 
• Right-click on the imported spreadsheet in the spreadsheet tree
• Select Properties
• Select List of genomic regions from the Configure Spreadsheet dialog to add region to the properties
•  

The spreadsheet properties will now include region. If you would like to do any operation that requires looking up hte reference genomic sequence information for the regions based on genomic location, you will need to specify the species for this region list. 

• Right-click on the imported spreadsheet in the spreadsheet tree
• Select Properties
• Select Genomic from the Add Property drop-down menu
• Select Add
• Select the source Species and Genome Build from the drop-down menus
• Select OK

With a few additional options, the region list can be made viewable in the genome browser. 

• Right-click on the imported spreadsheet in the spreadsheet tree
• Select Properties
• Select Advanced..
• Select Edit next to the species name
• Specify the Cytoband file and 2Bit sequence file
• Select OK

Motif detection

Starting with a region list, you may detect either known or de novo motifs using the ChIP-Seq
workflow if your spreadsheet has been associated with a species and a reference genome as
described in the import section.

• Select ChIP-Seq from the Workflows drop-down menu
• Select Motif detection from the Peak Analysis section of the workflow

Both options (Discover de novo motifs and Search for known motifs) can now be performed. Motifs (de novo) may be displayed in the Genome Browser and known detected motifs may be viewed in web-log format by right-clicking on a header row of the motif spreadsheet.

Determining the average values for a region list

If you have a region list or a bed file and you have a microarray experiment with data, you can summarize the data according to the genomic coordinates contained in the region list. For instance, the region list contains a list of CpG islands, the experiment contains methylation percentage values for probes (β values), and you would like to summarize the methylation values for individual probes for the CpG islands. Or you have a list of copy number amplifications, microarray gene expression data, and you are interested in determining if the average intensities of the probes in those regions is higher than expected.

• Import the region list (or BED file) and specify the region property as explained elsewhere in this document

• With the region list spreadsheet selected, right-click in any column header and select Insert Average

• A dialog box similar to that shown. With the Add Average tab selected, specify the location where you like the new columns to appear by using the Add to the and of Column pull-down menus. Specify the top-level spreadsheet containing the data you wish to be averaged (β values, gene-intensity values, etc.) in the Get average from spreadsheet pull-down menu. Choose the radio button to specify how the averaging should be done. The bottom two choices (Mean of all samples and Mean value for all samples separately) are obvious; the first option (Mean of samples significant in region) is used when the region list has a SampleID associated with each region. In this case, the column designated as the SampleID column from the top-level spreadsheet will be used to identify the sample to be summarized for each region.

Find region overlaps

You have a list of regions from another analysis program (perhaps you detected peaks using an R program) and you’d like to compare that region list with a region list that Genomics Suite calculated. Perhaps you have two lists created by Genomics Suite (one generated from peak detection with one set of parameters and the other created with different parameters) and you’d like to see what the two lists have in common. You may use the Tools > Find Region Overlaps command to compare two or more region lists as shown.

There are two separate modes of operation for this command: Report all regions and Only report regions present in all list. The first option, Report all regions, will report all regions in both lists. If there is any region overlap between the lists, the intersection of the regions will be reported along with the start and stop coordinates of the intersection, the percent overlap between the intersected region with each of the regions in the input lists. If a region is found in only one list, it will be reported as well.

In contrast, the second option, Only report regions present in all lists, will intersect both lists and only reports regions found in all the lists. 

Importing genomic locations to be used with annotating SNVs

The Tools > Annotate SNVs feature requires four columns of data per genomic location: the position of the SNP (chr.basePosition), the SampleName, a reference base, and the SNP call (single nucleotide or genotype) as shown in Figure 20. 

• Prepare input list as shown in Figure 20 and save as either a tab-separated or comma separated
  file

• Use File > Import > Text to import the table. During import, change the data type of column 1 (as in Figure 3) to text by right-clicking on the color bar of column one and changing the data type to text. You may leave the other columns as categorical response types

• The correct properties must be set for this spreadsheet. Right-click on the newly imported spreadsheet in the navigator and select Properties

• Choose Other in the Configure Spreadsheet dialog (Figure 6)
• Make sure Genomic is selected in the Add Property pull-down menu and select Add In the next dialog box, select Genomic location instead of marker IDs in the Choose the type of genomic data. The Marker ID in column should be set to the first column. [If Marker ID in column does not contain any items in the pull-down list, it is likely that the first column was not a text column (drawn in gray) during import. If this happens, then right-click in the column header in the spreadsheet and change Type: to text.]

• Specify the Species from a pull-down menu selection or by typing in the species name. Select Edit Genome to specify the Species Name, Genome Version, Cytoband file, and 2Bit sequence file. The last two fields are optional. Select OK

Now that the properties have been set appropriately, Tools > Annotate SNVs may be invoked on this
spreadsheet.