AlzCode

This page provides access to statistical approaches to evaluate the association of the queried gene set with AD by interrogating heterogeneous networks (including PPI, coexpression, functional gene network, miRNA-target binding, transcriptional regulatory networks), AD-related neuropathological traits (including CERAD, Braak and CDR) and clinical phenotypes.
Following the three steps below, you can evaluate the association of the gene set with AD by interrogating the networks, the neuropathological data and the phenotype data with our developed statistical approaches.

STEP 1: Input a gene set of your interest (one per line)

Note: two example gene sets are provided here for your convenience. You are free to make changes to the gene sets. Note that if any gene in the list is a member of the list of AD-associated genes in Step 2, this gene will be removed from the list of AD-associated genes. Gene set 1: the gene set contains 50 genes, which are collected from response to amyloid-beta (GO:1904645, an AD associated biological process).Gene set 2: the gene set contains 28 genes, which are collected from an AD associated phosphorylation event (PMID: 31926610).

STEP 2: Input Known AD-associated Genes

Note: We provide three lists of AD-associated genes obtained from AlzGene, OMIM, and GWAS catalog (p-value<5E-8), respectively. You are free to make changes (add or delete) to this list. By default, the list form AlzGene is shown in the input box.

STEP 3: Select Molecular Interaction Networks (you can choose one or multiple networks simultaneously)

The networks are used to evaluate how significant the queried gene set interacts with the list of AD-associated genes compared to random baseline. The significance is measured with a p-value calculated by permuation test.