Tutorial

 

1.Data access

Gene official symbol or Entrezgene ID is required while retrieving information from AlzBase.Four tyeps of gene queries are available in AlzBase (Figure.1).
A) Single gene query
B) Batch query
C) Advanced search
D) Correlation search


Tutorial

Figure 1 Data access of AlzBase.

 

2.About search result

Search result is summaried in a smart table that with sort function and filter function, which is shown on 'result web page' (Figure.2). And the title of the table is abbreviation.

Tutorial

Figure 2 Search result example of AlzBase.

Title of the table:
  • Gene: official gene symbol.
  • Entrez: Entrez gene ID at NCBI.
  • AD sum: Total numberof differential expression from all transcriptome studies of Alzheimer’s disease (AD).
  • AD Up: Total number of up regulation from all transcriptome studies of AD.
  • AD Dn: Total number of down regulation from all transcriptome studies of AD.
  • AD Pe: Total number of dys-regulation with unknown direction from all transcriptome studies of AD.
  • PD Up: Total number of up regulation from all transcriptome studies of Parkinson’s disease (PD).
  • PD Dn: Total number of down regulation from all transcriptome studies of PD.
  • BD Up: Total number of up regulation from all transcriptome studies of other neurological disordersc (BD).
  • BD Dn: Total number of down regulation from all transcriptome studies of other BD.
  • Aging: whether the gene expression is significantly correlated with brain aging.
  • T2D: wether the gene is significantly dys-regulated in T2D.
 

3.An example

Here, we use part of the DEG list calculated from dataset GSE33000 (1) as an example.

  • To search a list of genes, we may choose the 'List search' function. Just paste the gene list into the textbox, submit it to the server and the result pagewill show up (Figure 3A).
  • In the result page, we could use the sort function of the table to order the results, i.e. sort the table with 'AD_sum' and so on(Figure 3B).
  • In the correlation result page, we displaythe result through the Cytoscapenetwork picture and users also can download the result by clicking the 'GoBack&Download' button.(Figure 3C).
  • Simply click on the official gene symbol and we will get a detailed gene report page, in which users can obtain a comprehensiveview of each gene, including expression pattern, annotations from Allen brain atlasand GWAS related information.(Figure 3D).


Tutorial

Figure 3 Data retrieval in AlzBase.


Reference:

1. Gene expression profiles of human prefrontal cortex brain tissues, GEOID: GSE33000 <Link>, Last update date: Jul 31, 2014.