Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision |
useful_tools_for_functional_and_pathway_analysis [2019/10/25 04:09] – admin | useful_tools_for_functional_and_pathway_analysis [2020/04/22 18:09] – [Useful tools for functional and pathway analysis] isha |
---|
===== ===== | ===== Useful tools for functional and pathway analysis ===== |
| |
* [[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. |
* There are some [[https://www.biostars.org/p/274514/|R tools]] for pathway analysis including [[https://yulab-smu.github.io/clusterProfiler-book/|ClusterProfiler]]. | * There are some [[https://www.biostars.org/p/274514/|R tools]] for pathway analysis including [[https://yulab-smu.github.io/clusterProfiler-book/|ClusterProfiler]]. |
* Mouse Genome Informatics ([[http://www.informatics.jax.org/|MGI]]) has a nice hierarchal Gene Ontology [[http://www.informatics.jax.org/vocab/gene_ontology|Browser]] similar to Reactome. | * Mouse Genome Informatics ([[http://www.informatics.jax.org/|MGI]]) has a nice hierarchal Gene Ontology [[http://www.informatics.jax.org/vocab/gene_ontology|Browser]] similar to Reactome. |
| * 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. |
| |
| |
==== Reference: ==== | ==== Reference: ==== |