See Release for the latest v5.6.1 and v5.6.2 changes.

See Terminology in the User Guide, especially the Cluster Hit Algo1 versus Algo2 description.

> Instructions

The Instructions window (on right) lists the projects which were selected for querying. The Notes states what the Olap column represents; if one or more project pairs used Algo1, it will be gene overlap; if all project pairs used Algo2, it will be exon overlap. Open the Query Setup window by clicking on its tab in the left panel.

Set up the desired filters and then select Run Search to execute it. When the search is complete, the query result panel will be displayed.   Rules: 1. Most filters can be used in conjunction with other filters; options will be disabled if they cannot be used with a selected filter. 2. The Single queries returns rows without a hit, and only list genes for one project. 3. All Pair hits queries return a row per hit pair, i.e. aligned region between to two chromosomes from two projects.

4. All Hit# are uniquely numbered for a chromosome pair, e.g. there will be a Hit# 3 on all chromosome pairs that have hits.

5. All Gene# are sequentially numbered per chromosome, e.g. there will be a Gene# 3 on all chromosomes that have at least 3 non-overlapping genes. Overlapping genes have the same number, but different suffixes, e.g. 4.b. 6. Major and Minor genes: A hit can align to multiple genes on either or both chromosomes; it is assigned to the best (major) gene on each end. For example, in the image on the right, the pink gene is the major gene as the hit (pink line) fits it best, whereas the burgundy gene is the minor gene. When queries involve genes, only the hits to the major genes will be shown except for the following queries, which will also list the minor genes:       Every*, Hit#, Gene#, and Multi with Minor* checked.

Annotation Description Enter a substring: the entire annotation string (i.e. column All_Anno) will be searched for the substring. Hits will be shown that have at least one gene, of two possible, with the annotation.

Location

The From and To are disabled for Single genes, Block#, Collinear set#, Hit#, and Gene#.

The Single queries produces rows of genes; there is no hit or block information since the rows do not represent hits.

• Orphan genes (no hits)
  Genes that do not a have a hit and meet the additional filters. The orphan genes are relative to the projects shown on the Instruction page. For example, if species X, Y and Z have synteny computed between all pairs, but only X and Y are selected, the orphan genes for X would be those with no hits to Y. If X,Y&Z are selected, the orphan genes for X would be those with no hits to Y and Z.
   
• All genes (w/o hits), i.e. genes with and without hits
  This shows all genes that meet the additional filters, regardless if they have a hit or not. There is always the same set of genes for a project, regardless of synteny.

Unselect species: When the Single or Gene# is selected, the check boxes beside the species names will be activated. In order to view the genes from just one species, deactivate the others. Additionally, a single chromosome can be selected, but location cannot be entered.

Each hit connects two species (projects) and hence represents a pair of aligned regions for two of the selected species. Filters are as follows:

In Block (Synteny Hit)

Annotated (Gene Hit)

Collinear size

For the following 4 filters, do not include the 'Chr' number. Instead use the chromosome pull-downs to narrow the search to a specific chromosome, as exampled in Block#.

Block#
Enter a single block number (the Block column is formatted Chr.Chr.Block#).
This will display all hits with this block number from any chromosome pair.
Example using the chromosome pull-downs: if you select Chr 1 from the first project, Chr 2 from a second project, and enter block=3, you will see hits in block 1.2.3.

Collinear Set#
Enter a set number (the Collinear column is formatted Chr.Chr.Size.Set#).
This will display all hits with this set number from any chromosome pair. See Block example.

Hit#
Enter a hit number. Both major and minor gene hits will be shown.
This will display all hits with this number from any chromosome pair. See Block example.

Gene#
Enter a Gene# number (the Gene# column is formatted Chr.Gene#.suffix, where suffix may be blank).
A gene will only show if it has a hit. All hits with the Gene# on either end will be shown.
If a gene has a suffix:
 • If only a number is entered, all genes with the numeric prefix will be displayed (including minor hits).
 • If a number.suffix is entered, the exact gene will be displayed, including minor hits.
Select a chromosome:
 • The hit has to have one end to the chromosome, but the Gene# can be on either end.
 • By unselecting the other species (see Unselect species), the Gene# will only be on the specified end.
Group:
 • When a gene hits multiple places on the same opposite chromosome, the hits are put in a group
   (see Grp# column), which can be viewed with the 2D Group pull-down option (similar to Multi-hit).

These two options are computed on the fly. They produce query results with values for the Grp# and GrpSize columns; this in turn allows the View 2D Group option to be used.

4.1. Multi-hit Genes>= N

List all hits genes that have >= N hits.
The target gene refers to the gene with >= N hits to the opposite species.
If Both Annotated Genes is selected, the multi-genes will be confined to N genes hits.
The options are as follows:

The table can list the same hit multiple times, because gene X and gene Y may be connected by a hit, and both genes have >=N hits, so the hit in both groups need to be shown. An example is shown on the right, where Hit#881 is in both Atha Grp#3 and Brap Grp#15. The image below shows the two groups, where the group hits are highlighted in magenta; these were produced using the View 2D option Group (selecting any hit in the group results in the same 2D display).

Using the hits that pass the other filters, SyMAP constructs putative gene families (PgeneFs) spanning the selected species. This is done by grouping hits which overlap on at least one genome.
Additional options are provided when >2 species are selected. Note, if you have more than 6 species selected, this stage can take an hour or more.

Each PgeneF is given a number, which is shown in the Query Results table (column name PgeneF). The size of the PgeneF is also shown (column PgFSize).

Filters using the PgeneF values:

Include/Exclude
These filters permit searching for gene families shared by one group of species but not present in another.

If a species is checked to include, then the PgeneF will only be retained if it includes at least one hit which hits that species.

For >2 species only: If a species is checked to exclude, then the PgeneF will be discarded if any of its hits are to that species.

For the included species:

1. Results Table

• Pair Hits:
  • The table contains columns for all of the selected species, but each hit only connects two species, and the other species columns are empty.
  • Each Hit# is only listed once unless minor genes are included (see Rules).
  • A gene may be listed more than once if it has multiple major hits.

• Single genes:
  • If the query specified Single genes, then each row represents one gene and shows data only for one species.

You can sort the columns by clicking the column name in the table, and rearrange them by dragging the column name. You can add/remove columns using the Select Columns button at the bottom.

The buttons on the bottom will be Select Columns and Hide Stats. If Select Columns is selected, it changes to Hide Columns and the Hide Stats is replaced with the 3 buttons explained below.

In the column panel shown above, hover over a column name to see its brief description. Following are the full descriptions of the columns.

Arab-Cabb orphans

Arab-Brap orphans

Arab-Brap-Cabb orphans

The selected columns are saved between sessions (described below), but the order is not.

2.4 Auto-save columns

If you have multiple SyMAP databases, when you change between them the columns displayed are relative to the last SyMAP database queried (they may seem some what random to a different SyMAP database).

Most of the statistics are self-explanatory except the following:

Annotated and Genes: The first is the number of hits that overlap one or more genes, where a gene can have multiple hits. The second is the number of Genes with at least one hit.

Groups: This statistic is only shown if the Grp# column is populated.

Regions: This statistic is only shown if PgeneF was checked, and it is the number of distinct regions covered on that species.

The Unselect All unselects any selected rows.

Select one or more rows. The sequences of the selected hit(s) are written out and a multiple alignment is created using MUSCLE (Edgar 2004 NAR:32). The figure on the right shows the MUSCLE alignment of four genes: 2 from B.rapa and 1 from Cabbage and A.thal.

This displays the 2D view for the selected entry (see 3-chromosomes). The region displayed can be specified by the drop-down beside the View 2D button, as follows:

The image on the right shows a Collinear set of 5. After the initial display, the 2D view can be changed as described in the User Guide.   The table below shows results when the Grp# column has a value (using Gene#, Multi-gene or PgeneF search). The Group option can be used with these rows.

CSV: Export the rows using the selected set of columns to a CSV format suitable for import into Excel. HTML: Export the rows using the selected set of columns to a HTML format suitable for viewing on the web (e.g. Example). FASTA: (Pairs Only) For each row, the two hit sequences from the Hstart to Hend are written to file. NOTE: this is a very slow function and takes minutes if many rows are selected. The Include Row column option is available because this column is alway present, but it may be desirable to not include it in the output.

The report is on the genes in the query table (last updated v5.6.2). This is most relevant when used with >2 species.

Interface

The menu shown on the right will have different options depending on the query preformed, as follows: → Collinear size: the report will be by unions of collinear sets. → Multi-hit genes: the report will be by groups. → Otherwise, the report is by rows. In all cases, a reference must be selected and the report is in reference to it. The SyMAP gene names are used in the report, which provides the chromosome numbers and order of genes. Other names can be shown by entering the appropriate keywords. Gene Annotation Columns: One or more annotation keywords can be entered in a comma-delimited list (e.g. product, ID); the keywords must be found in the All_Anno keyword column. A column will be created containing the values of all entered keywords. Columns can be entered for any of the species (not just the reference).

All species

Collinear Report: Collinear sets are grouped to show the union of overlapping sets.

The HTML report on the right shows the first union of the A.thal collinear sets. This was generated with Collinear all checked. If Row all was checked, the 1st three rows would not be shown. The '*' beside A.thal indicates it is the reference. The '1 [3]' indicates it is the first union with 3 collinear sets. For the non-reference gene columns, by default, the collinear set size.number is shown. For example, row 4 lists A.thal gene 1.59, which is on Chr01 and aligns to the following: Gene# Species Chr Collinear set 5153.a B.rapa Chr09 set 6 of size 6 28 B.rapa Chr10 set 104 of size 8 1 Cabbage Chr05 set 1 of size 8 The other genes in each collinear set are obvious since they share the same #N.M, e.g. #8.1 is shown in 8 rows. If Row all is checked, all genes in a collinear set may NOT be shown.

Gene Report: The report lists all genes from the reference species, and what genes each aligns to. The image below shows the top of two different reports, one with A.thal selected as reference and the other with B.rapa as reference.

The annotations correspond to the genes listed for the species, where the annotations are delimited by ";".
A "---" indicates that there is a gene with no corresponding annotation. This was produced from a query on 'zinc finger protein'; recall that the description only needs to be found in one gene's All_anno values, i.e. it is not necessarily in the reference gene of the report.

Group Report: This will only work with the Multi-gene query. It show rows where the reference aligns to at least N genes, where N is the number input for multi-genes.

The Row all option works with it, but it does not require N genes for every reference row. This is illustrated in the image on the below.

The Grp# are shown beneath the reference gene. In the example below, Grp# 6 is the B.rapa group and Grp# 74 is the Cabbage group.

Select two rows with the following requirements: (1) Both genes must exist in each row. (2) There must be a shared gene. The two chromosomes with the unique genes may be from the same species or different species. Select View 2D with either the Region and Collinear options. The image on the right used the Collinear options.   2D Highlight Conserved Genes shows how to highlight shared or unique genes in the 2D display of 3 chromosomes.

All query results are listed under the > Results tab on the left. Clicking this tab shows the table of queries illustrated above. Query results can be displayed by clicking a result on the left panel, or double-clicking it in the list of results table shown above.

The only way to remove query results from the left tab is by selecting them in this table followed by Remove Selected, all remove all with Remove All.