Overview


The Brain eQTL Almanac (Braineac) is a web-based resource to access the UK Brain Expression Consortium (UKBEC) dataset. The aim of Braineac is to release to the scientific community a valid instrument to investigate the genes and SNPs associated with neurological disorders.

 

 

What is possible with BRAINEAC?

- Visualise gene expression across the brain

- SNP acting as cis-eQTL on a selected gene and know where it's located
- Find if a one or more risk SNPs are operating as a eQTL and in which brain region

- Download the expression data by genes or  tissue to develop new methods



 

A. Visualise gene expression across the brain


         "By Gene" provides the gene expression across ten brain tissues (CRBL, FCTX, HIPP, MEDU, OCTX, PUTM, SNIG, TCTX, THAL and WHMT). To obtain the expression follow the next three steps.

  

1. Select tab "By Gene" and digit the gene symbol in the box.

selGene

Figure 1





          2. A table will appear underneath showing the transcript ID (tID). The tID is the transcript cluster ID from Affymetrix Human Exon 1.0 ST. Click into the row to select the transcript of interest.



selTranscript

Figure 2

 

          3. A new table is going to show you all the probesets belonging to the selected tID. Finally, in the same way as point 2, select the exon-specific probeset (exprID) to visualise the gene expression, ordered from highest expressed to the lowest expressed. Note: The exprID of the first row of this table has always a t in front, it means the expression is visualise by transcript-level.

               

 

selExpr

Figure 3







     

B. Detect if a SNP is acting on a selected gene

"By SNP" visualise the top ten most affected genes by SNP and relative p-values. It's also possible download the full list of genes affected.


     4. Once you visualise the gene expression (section A), insert the SNP ID (rs#...) in the "Stratify expression by SNP" (fig. 4a). A plot with the expression of each SNP by tissue will be visualise below the input box, it may take up to 20 seconds. If the SNP inserted is acting as cis-eQTL its respective p-value will be in red color (fig. 4b).



     visExpr

Figure 4a







visStr

Figure 4b



   

C. Find if one or more SNPs are operating as an eQTL

 

    5. Click in the tab "By SNP" and digit the SNP IDs in the textbox, you can digit one per row up to twenty SNP IDs. Once you have inputed all the SNP IDs press the submit button (fig. 5a). The results may take up to 60 to be reported. The results (fig. 5b) are composed by: Line describing how many SNP IDs were entered, a table with the ten most relevant exprID ordered by most significant p-value and a click button to download a comma separate file (.csv) with the entire results (for a full description of the results file, see "Full cis-eQTL results" section).



        selSNP

Figure 5a

 

 

SNPresults

Figure 5b

 

D. Download the expression data by single gene to develop new methods



   6. click in the tab "By Gene", then in the right side, click in the tab "Download Data (Single Gene)".  Now, digit the gene of interest and then select the transcript ID in the table below. 



downData

Figure 6

 



     7. Select the file format in the (R data or Excel). In case you select the Excel format in the step 7, you can also download the file in two different ways; expression data in a single file or expression data divided by tissue where each file correspond to a one specific tissue. Press "Download" button to obtain the file.



downData2

Figure 7



F. Download the expression data by tissue to develop new method



     8. To download the expression data by tissue, select the tab "Download Data" and then click the link to have the entire expression data for that specific tissue.


downData3

Figure 8

 

 

Full cis-eQTL results

 

Downloading the full cis-eQTL results, it is possible obtain a csv file containing all the results. The file is composed by:

-          GeneSymbol - Gene Name

-          marker - position of the SNP inserted

-          rsid - SNP ID 

-          exprID - exon-specific probeset affected by the SNP

-          The rest of the columns are the p-value for 10 different tissues plus the pvalue for aveAll. The aveAll is the expression profile across all the tissues.