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.

You are visiting: Search VCMap << VCMap Reports >> Glossary

[ back to top ]