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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 14:15] – [Useful tools for functional and pathway analysis] admin
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-===== Useful tools for functional and pathway analysis =====+===== Useful tools for functional and pathway analysis and target identification =====
  
 +  * [[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.
  
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   * 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.