Using this software0. For impatient users
1. Data inputs
2. Create a project
3. Annotate a project
Using user annotation track
4. Filter for quality scores
5. Main user interface
6. SVA genome browser
7. SVA tables
8. Selecting genes or regions
Bio-pathway or GO
Fisher's exact test
10. Exome or targeted capture sequencing
Interacting with displayed items in SVA genome browser - data from public databases
In the SVA genome browser display, sections in yellow background come from public databases.
1. Genes and transcripts
Below is a typical section of genes in the SVA genome browser. Both the blue drop down button on the left , and each of the individual transcript are clickable.
In general, a protein-coding gene is displayed as blue rectangles (exons) on a green background (introns). A non-protein-coding gene is displayed as orange rectangles (exons) on a white background (introns). The strand (orientation) of the gene is denoted with a red arrow. The canonical (most common) transcript of a gene has an orange border (for example the largest F8 transcript showed above.).
1.1 Clicking on the button will bring up a popup menu summarizing the genes and their transcripts in this section (figure above). This small popup menu firstly provides a very brief summary on the region and how many transcripts are plotted, then offers a function to list the detailed information for these transcripts.
Clicking on the "List all transcripts " will bring up a transcript table like this:
Each transcript is listed in one row of this table, therefore one gene (with several different transcripts) can be listed in several rows. From left to right, the columns displayed are:
Gene symbol, brief description of the gene, biological type of the gene, strand, start of the transcript, end of the transcript, number of exons of the transcript, gene ontolgy of the gene, hyperlink for the gene ontolgy term, Ensembl page for the gene, Ensembl page for the transcript, PubMed search for the gene.
1.2 Clicking on the individual transcript will bring up a popup menu briefly summarizing the transcript, and providing a list of external and internal resources. For example, clicking on the canonical F8 transcript will activate a pop up menu like this:
Probably more importantly, this allows you to introduce the coding INDELs or missense SNVs you identified to show what coding change they can result in:
In this example, we introduce (red arrow 1) a frameshifting coding INDEL (X_153810879_153810880_INS_T). This INDEL causes a number of amino acid changes (red arrow 2), and then a premature stop (red arrow 3). As expected, these changes cause severe biological outcome - type A hemophilia.
2. SNPs from public domains
SVA genome browser displays SNPs from a number of public domains: dbSNP, HapMap, Dr. Venter's sequence, the 1000 Human Genome Project, and the Illumina Infinium HD Human1M BeadChip. Again, both the blue drop down button on the left , and each of the individual SNP lines are clickable.
For example, clicking on the blue drop down button for "refSNP" section will bring up a pop up menu:
Further clicking on this menu will bring up a refSNP listing table:
And if you click on individual refSNP line will activate a pop up menu like this:
The interacting with other public SNP sections other than "refSNP" is similar.
3. INDELs from public domain
SVA genome browser displays INDELs from Dr. Venter's sequence:
As usual, you can list all Venter's indels in this region by clicking on the blue drop down button on the left:
Or, if you individually access Venter's INDEL record:
4. SVs from public domains
SV displays two sources of SVs from public domains: the DGV database and the SNP-tagged copy number variation reported by McCarroll et al..
The interacting with these data is similar. You can bring up the listing table:
Or, individually access them:
© 2011 Dongliang Ge, PhD.