1. Introduction
2. Starter's Guide
3. View VCMap
   • 3.1. Display a static map
   • 3.2. Display dynamic maps using Mapview
4. Search VCMap
   • 4.1. Search marker
   • 4.2. Query by chromosome region
5. Query Reports
6. VCMap Glossary

    The whole VCMap Help document - Printable Version.

VCMap is a tool that determines syntenic relationships between Rat, Mouse and Human and allows searching and visualization of these chromosomal regions in a variety of ways.

New to VCMap?-- Try the starter's guide, which which contains definitions and background information.

FAQ for VCMap Help

• What type of analysis can be done with VCMap?
• What are the limitations of VCMap?
• What are the options available to use VCMap?
• How to display static maps?
• How to use Mapview (display dynamic maps)?
• How do I search for markers in VCMap?
• How do I query by chromosomal regions?
• What is Query Result Page?

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2.1 Definitions

Comparative Maping: Comparative mapping is a strategy for mapping sequence-related information from one species to another. It is based on the fact that the regions of sequence have been conserved among species during evolution (syntenic regions).

VCMap build: The core homology and mapping data that has been used to construct VCMap database. These include publicly available sequence data of genes, ESTs, their UniGene relationships, RH map marker information etc. from human, mouse and rat.

Static maps: Static maps are fixed image maps that are pregenerated from the VCMap database. They provide an overview of the entire chromosome but are not interactive. The static maps can be reached using the Static Maps link available on the top left hand side of most VCMap pages.

Dynamic maps: Dynamic maps are displayed using an interactive Java display. These can be fully customized by the user from Mapview page.

Framework markers: In genetic and radiation hybrid maps, these are markers used as reference markers for interspecies comparisons.

Backbone species: The species against which the other two species are aligned (For example, selecting rat as the backbone species, Chr1 as the chromosome and human/mouse as the non-backbone species would show the entire rat Chr1 with syntenic regions from the other species aligned to the rat.)

Bin predicition: A 'bin' prediction is made by predicting the location of the homologous UniGenes of the backbone species, based upon the mapped borders (breakpoints) of the homologous region of the reference (non-backbone) species.

Stream prediction: A 'stream' prediction, either upstream or downstream of the gene, is based upon the position of the homologous UniGene in the non-backbone species.

2.2 What can you do with VCMap?

Using VCMap, the user can generate:

1. Visual representation of synteny between human, mouse and rats.
2. Compare different maps available for the same species and compare them individually with types of maps for other two species.
3. Obtain homologous marker information across these three species.
4. Obtain a visual display of mapped markers (SSLPs, UniGenes and genes) in terms of both RHMaps and genetic maps of the three species; also, tabulated list of makers and related data can be obtained for any marker listed in the maps.
5. Obtain detailed reports of individual markers on any chromosome from organism, including location, sequence, ESTs, genes, aliases, LOD scores of SSLP markers, corresponding homologous markers in the other two species compared to and corresponding links to external databases like GenBank, RGD etc.
6. RHMap locations of the markers and genetic map location whenever available.

2.3 What are the limitations of VCMap?

1. VCMap is constructed based on homologous UniGenes and other markers with known mapping information. So the map information is restricted to markers, which are sequenced and stored in various databases like RGD, GenBank, and UniGene etc. The physical map (from the genomic sequence) has not yet been integrated into the tool; however, work is in progress to do this.
2. VCMap does not currently use the genomic sequence for generating virtual syntenic maps. Consequently the user cannot directly obtain information about the genomic sequence between the markers. Ensembl, NCBI and other databases provide sequence information of specific genomic regions.

By choosing the type of map, organism and chromosome, the user can view static comparative maps or dynamic maps. The User can define the search parameters to find the required data from the VCMap .

1. View the static map display
2. View the dynamic map display using MapView
3. Search the VCMap build to obtain specific comparative data

All these options result in clickable markers hyperlinked to comprehensive Query Results.

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3.1 Display a pregenerated, static map

Static maps are pre-generated, non-interactive maps, which provide an overview of the syntenic relationships. Extensive datasets of virtual comparisons for each chromosome from rat, mouse and human exist as integral parts of VCMap build. In response to a search request (comprising of one backbone species and one of its chromosomes), the user can obtain 1 .a VCMap display of syntenic chromosomal segments from other two non-backbone species in almost a fixed (static) format and 2. mapped markers overlaid on these chromosomal segments. Being a static map, only a proportion of mapped markers can be displayed for any chromosomal interval.

To go to Static maps page, click on the link Static Maps on the left column of the VCMap Start page.

The “backbone” species is chosen from human, mouse or rat for which syntenic regions from other two species are queried. Upon clicking on one of its chromosomes, the VCMap generates a visual display of virtual comparative map with syntenic chromosomal segments and mapped markers.

Question: How do I interpret the static comparative maps?

Color code of the display consists of backbone species, non-backbone species, RH framework markers on the backbone, other mapped markers, and chromosome number above each syntenic chromosomal segment.

The result page has brief instructions, an option for viewing an expanded list of markers and the comparative map itself. By looking at the comparative map generated, the user can find out the possible syntenic chromosomal regions in non-backbone species compared to a whole chromosome from the backbone species. There are three ways to obtain marker details. They are:

a. Generate individual marker reports: The markers are hyperlinked to individual marker reports. Click on any marker to get a Query Result for that marker.

b. Generate chromosomal region reports: The chromosomal segments of the backbone species with definite breakpoints are differentially colored. By clicking on each segment, Chromosomal Region Report with expanded list of markers can be generated.

c. Search a specific chromosomal region: A table of expanded list of markers and VCMap predictions with in a specific chromosomal region can be generated. For this, enter the two flanking cR units from the generated map in the search fields and click GO.

For example, the VCMap result for such a query between 0.0 cR to 60.0cR for rat chromosome 1 backbone will look like:

Click to see result.

The marker reports have a clickable option to obtain MapView reports. The backbone species can be shuffled on a static map display by clicking on the hyperlinked blue chromosome numbers in the non-backbone species column.

3.2 Display dynamic maps using MapView?

Dynamic maps are highly interactive maps generated using MapView from the VCMap database in response to a specific user query. MapView can display multiple maps in a single window. The user can determine the types of maps to be compared and the features of the generated comparison to be displayed. The generated map has zoom option for the user to display the backbone markers in a specific region of comparison. The images are clickable to obtain the comparative data in the form of Query Pages.

To go to Dynamic Maps Page, click on MapView (Dynamic) link from the left side of the VCMap start page link. This will take the user to the MapView query page. Options for generating dynamic maps include:

a. Map data: Three kinds of Map data are available and the user can arrange these in any combination. Any combination of maps can be displayed for comparison.
Virtual syntenic maps The user can choose from rat, mouse and human. The version of VCMap build is 5.0_HS.
RH map options are varied for each species. For rat three versions are available while human and mouse have one standard version each.
Genetic maps from different sources are available for rat, mouse and human. Choose the appropriate build and version of the maps of choice.

b. VCMap predictions: If the user wants bin and stream predictions or framework markers, appropriate boxes are to be checked BEFORE the choices are submitted.

1. Querying virtual, genetic and RH maps: The Query interface for MapView is user friendly. The user is expected to choose
   - Single map or a map combination
   - A back bone species and 1 or 2 non-backbone species for each map option chosen a chromosome of the backbone species for the comparative analysis for each map option
2. Choosing prediction options
   User has an option to see the following VCMap predictions in different combinations directly on the map:
   Framework markers, Bin predictions and Stream predictions. The options are listed as:
   
   The options have to be chosen BEFORE the search parameters are submitted.

On submitting the search parameters, MapView loads the Java applet and the data first and opens a new browser window, which should be left open. The java display window will then appear with the maps specified by the user. The display window has multiple menu options on the top. These options can be used to fine-tune the map display.

1. How can I locate a marker on the generated map?
   To locate a marker on the map, go to Edit and choose Find. Enter the marker name in the query field. The user can arrive at this Find query from the map itself by clicking on the Find at the top right corner above the map.
   
2. How can I directly obtain the details of an alignment or a marker?
   By double-clicking an isolated marker or one in an alignment, Query Result can be obtained.
   
3. How can I display the details of the markers and VCMap predictions on the dynamic map?
   All the markers listed on the maps are clickable to generate ‘Individual Marker report’ or ‘Map report’.
   
4. How can be the VCMap predictions chosen by me displayed on the map?
   Once the map is generated, click on the Markers button at the top left of the page and make your choice from the list.
   
5. When Bin and Stream predictions are requested, the user has to click on Repack every time the scale is changed. This is because, by increasing or decreasing the resolution of the map, display of bin and stream predictions are also modified. Repack matches the display of the predictions to the scale of the displayed map.
   
6. 6. How can I modify the displayed maps in MapView?
   Zoom in and Zoom out: By sliding on the scale above the map the user can increase or decrease the resolution of the map. This is useful when the markers hidden in the static maps have to be visualized. By zooming out to the maximum, the resolution of the displayed map is increased to include all the available markers from the VCMap build.
   
7. What are the options for the marker display in a MapView map?
   By choosing different options available under View in the menu, characteristics of the displayed markers can be varied:
   
   Markers: under View by choosing Markers, the user has an option to choose:
   

   D-number : to obtain associated EST # if any
   Submitted: to obtain associated gene symbol
   Primary: to obtain Unigene/ UniSTS associated with that marker

   Marker Colors: under View by choosing Marker Colors, the user can provide different colors to the different marker types. A sliding scale is provided to expand the options of the colors.
   
   Show Markers: under View, by choosing Show Markers, the user can determine the type of markers and the priority for display.

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Searching for a specific Marker

From the VCMap start page, clicking on VCMap Query will allow the user to search for specific information from the VCMap build. There are two options:

4.1 Query by Marker

‘Querying by marker (Option 1)’ allows the user to search the anchor file to generate reports for an individual marker.

Enter the marker or cR details and click the display button.

For example, For Rn.14443 , the result will look like:

Click to see result.

This will generate individual marker report. To obtain data not shown in the report the search query can be expanded to have map positions flanking the marker:
Since Rn.14443 is mapped, choosing a region between 0 and 60 will result in:

Click to see result.

This tabulated report displays hyperlinked marker list, bin and stream predictions in the given chromosomal region where the query marker is mapped.

4.2 Query by Chromosomal regions

‘Querying by chromosomal region (option 2)’ displays the Chromosomal Region Report plus Bin and Stream Prediction Reports based on a specified backbone species for the entire chromosome or a selected region. Either distances or marker names can be entered to define the displayed region. Entering a single marker name will display the region +/- 50cR from the marker.

For rat chromosome 1, between 0 and 60 cR, the Query Result would look like:

Click to see result.

 

Question: What do I see if I query for specific region from the map?

Querying for a chromosomal region generates a Chromosomal Region Report consisting of table with hyperlinked marker symbols and corresponding genes if any. In this report, mapped markers for human, mouse and rat are listed in 3 columns.

Click to see result.

Bin predictions and Stream predictions, unique to VCMap are also listed on the same page.

 

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5.1. What type of reports can be obtained as a result of myVCMap query?

The VCMap Query Result provides 3 types of marker reports and predictions.

Individual Marker (Gene, UniGene, and EST) Report:

Example: Query Result for Rn.14443 [ View this VCMap Report ]

This report displays the underlying VCMap build data for a particular marker including the ESTs and UniGenes that were involved in creating the relationship and the best blast result scores between sequences from the Backbone and Reference (non-backbone) UniGene clusters.

Column	Example	Explanation
UniGene	Rn.14443	The UniGene cluster assigned to the gene marker
Gene symbol		The gene symbol associated with a particular gene if available
Aligned UniGenes	Hs.107528, Mm.45755	The UniGenes that contain the highest scored EST from a BLAST comparison
Mapped ESTs	AA924112, etc	The number of mapped ESTs associated with UniGene. This is followed by the chromosomal location and the name of the EST
Unmapped EST	AI011442, etc	The Ids of ESTs and CDNAs in the original UniGene cluster that were unmapped
Alignments		This is determined by comparing all ESTs from the backbone species with all ESTs from each non-backbone species. Only the best score of the BLAST results for each non-backbone species is shown. In the table, the first record on the left is the aligned EST in the backbone species, followed by the names of ESTs from non-backbone species, percent homology, length (bp) of the comparison, and the BLAST scores. The right hand column contains the associated UniGenes in the non-backbone species.

 

Map Data Report:

Clicking on any of the SSLP markers on the VCMap or in any of the reports will display a Map Data report such as this one shown for D10Rat71. The report lists the locus name, position in CentiRays, LOD score of placement (or F for framework marker) and a list of aliases - alternative names for this marker in RGD and other databases. Genetic map data is also shown for Human markers.

Rat RH Map V2.1
Locus	Position (cR)	LOD	Alias
D10Rat71	328.2	P	R0083-C09

Map data for Rat, Mouse and Human were obtained from the following sources:

• Rat: Rat Genome Database, http://rgd.mcw.edu/
• Mouse: Whitehead Institute: http://www-genome.wi.mit.edu/mouse_rh/
• Human: GB4 RH maps (NCBI GeneMap99, raw data: EBI http://corba.ebi.ac.uk/RHdb/species/HUMAN/gm99.html)

Chromosomal Region Report:

Example: Genes and UniGenes (markers) between 0.0 cR (Centi-Ray) and 51.4 cR in Rat Chr.01. [ View this VCMap Report]

The chromosomal region report is a combination of UniGene and RH map data. Results from the RH map show the placement lod score (e.g. P>3.0 indicates a placement at greater than LOD 3.0). The letter ‘F’ denotes framework markers. Whenever available, the UniGenes will also follow by gene symbols. Clicking on any of the UniGene IDs will take you to the individual marker report.

VCMap Predictions:

When the gene or EST of interest has not been mapped, a prediction can be made if the position of the homologous gene or EST in the reference (non-backbone) species is known. The gene (UniGene) prediction is based upon the BLAST result and the known syntenic region of chromosome between the different species. The borders of chromosomal conservation are also known as the chromosomal breakpoints. They are referred to as anchors in VCMap.

Two kinds of predictions are available for VC Map, Bin and Stream predictions:

• 'Bin' - Prediction within two anchored markers. (defining the limits of the bin).
• 'Stream' - Prediction outside a bin, only one anchor. (prediction is up or down stream of the anchor).

Bin Predictions

A 'bin' prediction is made by predicting the location of the homologous UniGenes of the backbone species, based upon the mapped borders (breakpoints) of the homologous region of the reference (non-backbone) species. The position of the predicted UniGene is defined by the first flanking UniGene anchor (Anchor1 UniGene) and its position (Anchor1 Position), and the second flanking UniGene anchor (Anchor2 UniGene) and its position (Anchor2 Position). This is shown diagrammatically in the example below:

The top of a bin report for the Rat Chr01, 0-54cR region is shown below: [ View this VCMap Report]. An explanation of each column heading is provided in the table below.

Column	Example	Explanation
Predicted Unigene	Rn.3	The UniGene in the backbone species predicted by the location of the homologous UniGene
Chr	1	The chromosome in the backbone species
Anchor1 position		The position of the first flanking anchor (breakpoint) of the backbone species
Anchor1 UniGene		The first flanking UniGene anchor of the backbone species
Anchor2 Position		The position of the second flanking UniGene anchor (breakpoint) of the backbone species
Anchor2 UniGene	Rn.2	The second flanking anchor (breakpoint) of the backbone species.
From Species	Human	The species of the UniGene used to assign the location of the predicted UniGene
Chr	3	The chromosomal location of the homologous UniGene in the reference species
Homolog position		The position of the homologous UniGene of the non-backbone species
Homolog UniGene	Hs.103	The homologous UniGene of the non-backbone species
Syn Anchor1 position		The position of the first flanking anchor (breakpoint) of the non-backbone species
Syn Anchor1 UniGene	Hs.101	The first flanking UniGene anchor of the non-backbone species
Syn Anchor2 position		The position of the second flanking UniGene anchor (breakpoint) of the non-backbone species
Syn Anchor2 UniGene	Hs.102	The second flanking anchor (breakpoint) of the non- backbone species

 

Stream Predictions

A 'stream' prediction, either upstream or downstream of the gene, is based upon the position of the homologous UniGene in the reference (non-backbone) species. A diagram illustrating this is shown below. In this example the location of Rn.34 has been predicted to be between Rn.12 and Rn13 on Rat Chr 4 based on the sequence-based homology between Rn.34 and Hs.26. Rn.34 could lie anywhere between Rn.12 and Rn.13 as there are no other anchors between the two species to limit the syntenic region. This would be a downstream prediction as Hs.26 lies downstream of the nearest syntenic anchor, Hs.25.

Below is shown the Stream predictions for Rat Chr01, 0-54cR region [ View this VCMap Report]. An explanation of each column heading is provided in the table below.

Column	Example	Explanation
Predicted Unigene	Rn.34	The UniGene in the backbone species predicted by the location of the homologous UniGene
Chr	4	The chromosome in the backbone species
Anchor position		The position of the nearest anchor (breakpoint) in the syntenic region (the backbone species) for the gene of interest
From Species	Human	The species of the UniGene used to assign the location of the predicted UniGene
Chr	5	The chromosomal location of the homologous UniGene in the reference species
Homolog position		The position of the homologous UniGene of the non-backbone species
Homolog UniGene	Hs.26	The homologous UniGene of the non-backbone species
Syn Anchor position		The nearby syntenic anchor (breakpoint) location in the non-backbone species
Syn Anchor UniGene	Hs.101	The first flanking UniGene anchor of the non-backbone species
Syn Anchor2 position		The nearby syntenic anchor (breakpoint) UniGene in the non-backbone species
Up/down	down	Indicates the stream predicted UniGene is upstream or downstream of the syntenic marker in the non-backbone species

 

5.2 How do I save the query results?

From the static or dynamic maps can be saved in pdf format. Query Reports can be saved as a HTML page or imported to a Word or Excel file. For results in a different format, please contact the RGD staff.

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