GeneList | About

GeneList makes it easy to navigate research resources for each gene in a list

Please Review the Terms of Use before using GeneList.

You can search GeneList using the 'Input' search panel. You can search by HGNC gene symbols (eg. CCNE1), Gene Ontology terms (eg. GO:2000082), and genomic coordinates (eg. chr1:100000-5000000). Searching by Gene Ontology term returns all genes annotated with the term. Searching by genomic coordinates returns all the protein coding genes withing the given range based on the Hg38 genome assembly coordinates. You can get a list of 10 random genes by clicking the 'Random' button in the header of the 'Input' panel. Clicking the 'Update' button returns your search results. No information on your searches is saved by GeneList.

You can also add a search term to be included in the PubMed and Google search results (eg. by entering 'TP53' in the 'Input' panel and 'Cancer' in the 'Search Term' panel, the PubMed link will link you to the PubMed search results for 'TP53 Cancer').

An R package is available to export lists of genes from R to gene-list.com
https://github.com/GeneList/GeneList

You can query and link to GeneList through the url.
(eg. http://gene-list.com/search/TRP53,KRAS,KIT?genome=mouse&search_term=Cancer)

Once the search results are returned, you are provided with a list of the genes with links to resources. Each gene panel can be expanded, by clicking the button on the far right of the gene panel (

), to show additional links to all the resources shown above.

By clicking the triangle in the top right of the search results panel header (), you can download the list of genes including the HNGC gene symbol, Entrez Gene ID, Ensembl Gene ID, and Uniprot ID, and export the gene list to g:Profiler, Reactome, Gene Mania, and Complex Portal.

The Gene IDs were retrieved from Ensembl BioMart.

Backgrounds were downloaded from Toptal.

References

Apweiler, R. et al. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32, D115-119 (2004).

Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).

Carbon, S. et al. AmiGO: online access to ontology and annotation data. Bioinformatics 25, 288-289 (2009).

Cerami, E. G. et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39, D685-690 (2011).

Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401-404 (2012).

Franz, M. et al. GeneMANIA update 2018. Nucleic Acids Res. 46, W60-W64 (2018).

Griffith, M. et al. DGIdb: mining the druggable genome. Nat. Methods 10, 1209-1210 (2013).Papatheodorou, I. et al. Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46, D246-D251 (2018).

Grossman, R. L. et al. Toward a Shared Vision for Cancer Genomic Data. N. Engl. J. Med. 375, 1109-1112 (2016).

GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580-585 (2013).

Hamosh, A. et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514-517 (2005).

Hermjakob, H. et al. IntAct: an open source molecular interaction database. Nucleic Acids Res. 32, D452-D455 (2004).

Huttlin, E. L. et al. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 162, 425 (2015).

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583-589 (2021).

Krassowski, M. et al. ActiveDriverDB: Interpreting Genetic Variation in Human and Cancer Genomes Using Post-translational Modification Sites and Signaling Networks (2021 Update). Front. Cell Dev. Biol. 9, 626821 (2021).

Landrum, M. J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980-D985 (2014).

Luck, K. et al. A reference map of the human binary protein interactome. Nature 580, 402-408 (2020).

MacDonald, J. R. et al. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 42, D986-D992 (2014).

Meldal, B. H. M. et al. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res. 43, D479-484 (2015).

Mungall, C. J. et al. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 45, D712-D722 (2017).

Navarro Gonzalez, J. et al. The UCSC Genome Browser database: 2021 update. Nucleic Acids Res. 49, D1046-D1057 (2021).

Oughtred, R. et al. The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. Publ. Protein Soc. 30, 187-200 (2021).

Povey, S. et al. The HUGO Gene Nomenclature Committee (HGNC). Hum. Genet. 109, 678-680 (2001).

Rappaport, N. et al. MalaCards: an integrated compendium for diseases and their annotation. Database J. Biol. Databases Curation 2013, bat018 (2013).

Robinson, P. N. et al. The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease. Am. J. Hum. Genet. 83, 610-615 (2008).

Smirnov, P. et al. PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. Nucleic Acids Res. 46, D994-D1002 (2018).

Stelzer, G. et al. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr. Protoc. Bioinforma. 54, 1.30.1-1.30.33 (2016).

Thorn, C. F. et al. PharmGKB: The Pharmacogenomics Knowledge Base. Methods Mol. Biol. Clifton NJ 1015, 311-320 (2013).

Wang, Y. et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol. 19, 151 (2018).

Weinstein, J. N. et al. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nat. Genet. 45, 1113-1120 (2013).

Yates, A. D. et al. Ensembl 2020. Nucleic Acids Res. 48, D682-D688 (2020).