Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
useful_tools_for_functional_and_pathway_analysis [2021/09/23 20:32] – [Useful tools for functional and pathway analysis] ishauseful_tools_for_functional_and_pathway_analysis [2024/03/28 15:32] (current) – [Useful tools for functional and pathway analysis and target identification] admin
Line 1: Line 1:
-===== Useful tools for functional and pathway analysis =====+===== Useful tools for functional and pathway analysis and target identification =====
  
 +If you have a list of genes, and you want to know their functions, the diseases and pathways they might be associated with, and some known or candidate drug targets for them, you can use the following tools and databases. Your gene list might have been obtained from differential expression or other omics analyses, gene network analysis, a genome-wide association study ([[https://en.wikipedia.org/wiki/Genome-wide_association_study|GWAS]]), and alike.
 +
 +  * [[https://agora.adknowledgeportal.org/|Agora]] hosts evidence for association of genes with Alzheimer's disease (AD) and includes over 600 potential drug [[https://agora.adknowledgeportal.org/genes/nominated-targets|targets]] for AD.
 +  * Functional genomics repository ([[https://tf.lisanwanglab.org/FILER/|FILER]]) and Alzheimer’s Disease Variants Portal ([[https://advp.niagads.org/|ADVP]]) are functional genomics database with harmonized, extensible, indexed, searchable human functional genomics data collected from 20 data sources and 80 cohorts, respectively.
   * [[http://www.humanmine.org/%20|Humanmine ]] : given a list of genes as input (Entrez/Ensembl/Symbol or a mix), it returns interaction networks, pathways, Gene Ontology categories, relevant literature, protein domains, chromosome distributions and much more on a single page. There are also nice summaries that pop-up by hovering the mouse over a gene name.   * [[http://www.humanmine.org/%20|Humanmine ]] : given a list of genes as input (Entrez/Ensembl/Symbol or a mix), it returns interaction networks, pathways, Gene Ontology categories, relevant literature, protein domains, chromosome distributions and much more on a single page. There are also nice summaries that pop-up by hovering the mouse over a gene name.
  
Line 51: Line 55:
   * Functional Enrichment Analysis [[https://yulab-smu.github.io/clusterProfiler-book/chapter1.html|overview]]. Isha's list of [[https://docs.google.com/presentation/d/1c4HAcImyyU1as5qEwzmH8QIAxD25N4Z5__sUZE3n6kk/edit#slide=id.g6f90f06c9f_0_0|functional enrichment]] analysis tools in R.   * Functional Enrichment Analysis [[https://yulab-smu.github.io/clusterProfiler-book/chapter1.html|overview]]. Isha's list of [[https://docs.google.com/presentation/d/1c4HAcImyyU1as5qEwzmH8QIAxD25N4Z5__sUZE3n6kk/edit#slide=id.g6f90f06c9f_0_0|functional enrichment]] analysis tools in R.
   * [[http://gepia.cancer-pku.cn/|GEPIA]] and [[http://gepia2.cancer-pku.cn/#index|GEPIA2]] are web based resources for interactive gene expression profiling and analysis. The data sources used are TCGA and GTEx.   * [[http://gepia.cancer-pku.cn/|GEPIA]] and [[http://gepia2.cancer-pku.cn/#index|GEPIA2]] are web based resources for interactive gene expression profiling and analysis. The data sources used are TCGA and GTEx.
 +  * [[https://academic.oup.com/nar/article/49/15/8471/6329115|VarSAn]]: associating pathways with a set of **genomic variants**  using network analysis. Results are similar to a simple overlap analysis using a hypergeometric test.