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useful_tools_for_functional_and_pathway_analysis [2019/01/12 01:46]
admin
useful_tools_for_functional_and_pathway_analysis [2020/04/22 21:09] (current)
isha [Useful tools for functional and pathway analysis]
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-=====   ​=====+===== 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.
  
   * [[http://​www.genemania.org/​|GeneMANIA]] performs functional analysis using protein and genetic interactions,​ pathways, co-expression,​ co-localization and protein domain similarity.   * [[http://​www.genemania.org/​|GeneMANIA]] performs functional analysis using protein and genetic interactions,​ pathways, co-expression,​ co-localization and protein domain similarity.
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   * In addition to TFT collection from MSigDB, other resources for identifying transcription factor targets include: [[http://​www.biobase-international.com/​gene-regulation|TRANSFAC]],​ [[https://​en.wikipedia.org/​wiki/​Open_Regulatory_Annotation_Database|ORegAnno]] and [[https://​github.com/​slowkow/​tftargets|tftargets]]. Alternatives computational tools, such as [[http://​meme-suite.org/​|MEME]],​ [[http://​pazar.info/​|PAZAR]],​ and [[http://​itfp.biosino.org/​itfp/​|ITFP]],​ should be used with care because their predictions are not as reliable as targets validated by real experiments.   * In addition to TFT collection from MSigDB, other resources for identifying transcription factor targets include: [[http://​www.biobase-international.com/​gene-regulation|TRANSFAC]],​ [[https://​en.wikipedia.org/​wiki/​Open_Regulatory_Annotation_Database|ORegAnno]] and [[https://​github.com/​slowkow/​tftargets|tftargets]]. Alternatives computational tools, such as [[http://​meme-suite.org/​|MEME]],​ [[http://​pazar.info/​|PAZAR]],​ and [[http://​itfp.biosino.org/​itfp/​|ITFP]],​ should be used with care because their predictions are not as reliable as targets validated by real experiments.
  
-  * [[https://​cran.r-project.org/​web/​packages/​gProfileR/​index.html|gProfileR]] does Pathway,​GO,​TF,​microRNA,​OMIM,​ and Phenotype over-representation analysis, with quite up to date annotations. ​\\+  * [[https://​cran.r-project.org/​web/​packages/​gProfileR/​index.html|gProfileR]] does Pathway,​GO,​TF,​microRNA,​OMIM,​ and Phenotype over-representation analysis, with quite up to date annotations.
  
   * [[http://​tcng.hgc.jp/​index.html?​t=network&​id=27|TCNG]],​ a cancer gene network of potential interest.   * [[http://​tcng.hgc.jp/​index.html?​t=network&​id=27|TCNG]],​ a cancer gene network of potential interest.
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   * Free alternatives to Ingenuity Pathway Analysis ([[https://​www.biostars.org/​p/​6203/​|IPA]]).   * Free alternatives to Ingenuity Pathway Analysis ([[https://​www.biostars.org/​p/​6203/​|IPA]]).
  
-  * See [[https://​www.biostars.org/​p/​6203/​|this]] Biostar trend for updates on recent tools such as [[http://​www.pathwaycommons.org/​pc/​|Pathwaycommons]],​ a kind of integrated approach including [[http://​www.reactome.org/​|Reactome]],​ and [[https://​pathview.uncc.edu/​|Pathview Web server]] . \\+  * See [[https://​www.biostars.org/​p/​6203/​|this]] Biostar trend for updates on recent tools such as [[http://​www.pathwaycommons.org/​pc/​|Pathwaycommons]],​ a kind of integrated approach including [[http://​www.reactome.org/​|Reactome]],​ and [[https://​pathview.uncc.edu/​|Pathview Web server]] .
   * The Human [[https://​www.proteinatlas.org/​|Protein Atlas]] is useful to get information on the expression of a particular protein at the cellular, normal tissue, and tumor levels.   * The Human [[https://​www.proteinatlas.org/​|Protein Atlas]] is useful to get information on the expression of a particular protein at the cellular, normal tissue, and tumor levels.
 +  * 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.
 +  * 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.
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