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useful_tools_for_functional_and_pathway_analysis [2019/01/11 23:46] – admin | useful_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 and target identification ===== |
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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. \\ | * [[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. |
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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. |
* [[http://www.broadinstitute.org/gsea/msigdb/index.jsp%20|MSIGDB ]]has around 10,000 sets (collections) of interesting genes, including curated sets from publications (e.g. genes affected by specific genetic and chemical perturbations), canonical pathways, GO, microRNA and transcription factor (TF) targets, as well as Hallmarks of particular processes, oncogenic signatures and more. We have some custom made scripts for mining these sets. The BROAD institute has also their own software with sleek GUIs (GSEA). | * [[http://www.broadinstitute.org/gsea/msigdb/index.jsp%20|MSIGDB ]]has around 10,000 sets (collections) of interesting genes, including curated sets from publications (e.g. genes affected by specific genetic and chemical perturbations), canonical pathways, GO, microRNA and transcription factor (TF) targets, as well as Hallmarks of particular processes, oncogenic signatures and more. We have some custom made scripts for mining these sets. The BROAD institute has also their own software with sleek GUIs (GSEA). |
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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://homer.ucsd.edu/homer/motif/|HOMER]], [[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. |
| * 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. |
| * [[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. |
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==== Reference: ==== | ==== Reference: ==== |