Summary of Tips

1.DEG Frequency Distribution

There are 14145 genes recorded in AlzBase.The distribution of differential expressionfrequency is from 1 to 22. The gene count stands for the number of DEGs corresponding to the specific frequency. The accumulated count represents accumulated number of DEGs with frequency equal or greater than the specified number.


DEGs Frequency 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
Gene Counts 378 3117 2448 2368 1502 1125 849 669 509 341 268 176 123 97 66 40 23 19 14 5 1 5 2
Accumulated Amount 14145 13767 10650 8202 5834 4332 3207 2358 1689 1180 839 751 395 272 175 109 69 46 27 13 8 7 2

Table 1 DEG Frequency Distribution in AlzBase.

2.Top 109 gene in AlzBae vs. top genes from the genetic studies of AD

A total of 109 genes are selected from AlzBase with frequency of dys-regulation 15 times or higher. We also selected32 genes from the genetic studies of AD for comparison. A small portion of the comparison is shown below.


GeneSymbol EntrezID Log2_fold_change Non_Dementia(up_dn) In_blood(up_dn) Brain_Dis._up Brain_Dis._dwon Aging_related ......
ITPKB 3707 0.840954648 0_1 -- 15 0 Yes ...
TGFBR3 7049 0.81820538 -- 1_0 11 0 No ...
CXCR4 7852 0.982819742 -- 1_0 11 3 No ...
AEBP1 165 1.126772065 -- -- 10 1 No ...
NRN1 51299 -1.101020795 -- 1_0 1 5 No ...
NCALD 83988 -1.332401727 0_2 -- 0 10 Yes ...
RGS4 5999 -1.389027605 -- -- 1 21 Yes ...
GAD1 2571 -1.006724917 -- -- 2 17 No ...
ATP6V1G2 534 -1.081930369 0_2 -- 0 11 Yes ...
NSF 4905 -0.998945725 0_1 -- 1 11 Yes ...
APOE 348 0.109256026 0_4 -- 9 2 No ...
PLD3 23646 -0.605421329 0_2 -- 0 12 No ...
...... The complete comparison can be downloaded following the link [Click Here]

Table 2 Top 109 gene in AlzBae vs. top genes from the genetic studies of AD.

3.Neurological phenotype in mouse knockouts

Mouse knockout phenotypes have been curated at the MGI website (www.informatics.jax.org).There are 61 genes among the 141 top Genes with neuroligical phenotype. Top genes in AlzBase marked by ★, and top genes from the genetic studies of AD are marked by ▲.


Figure 1 Neurological phenotype in mouse knockouts.


4.Download

Here is the link of the summary files--[Click Here]-- you can acquire it.