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| useful_tools_for_functional_and_pathway_analysis [2019/01/11 23:46] – admin | useful_tools_for_functional_and_pathway_analysis [2019/10/31 16:40] – admin |
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| ===== ===== | ===== Useful tools for functional and pathway analysis ===== |
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| * [[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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| * [[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. |
| * 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. |
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| * [[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. |
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| * [[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. |
| * 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]]). |
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| * 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. |
| | * Isha's list of [[https://docs.google.com/presentation/d/1c4HAcImyyU1as5qEwzmH8QIAxD25N4Z5__sUZE3n6kk/edit#slide=id.g6f90f06c9f_0_0|functional enrichment]] analysis tools in R. |
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| ==== Reference: ==== | ==== Reference: ==== |
