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Data from external sources

Whereever content or functionality from the following external sources is included into the MFGA it is indicated.

This website includes functionality from the following sources:

• Icons from Icons8 https://icons8.com.
• All plots are implemented with Highcharts https://www.highcharts.com under a non-commercial license. Thus, the content cannot be used commercially or by governmental institutions.

This website uses data from the following sources:

• GTEx portal (https://gtexportal.org/home/datasets file: GTEx_Analysis_2016-01-15_v7_RNASeQCv1.1.8_gene_median_tpm.gct.gz). The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.
• Human Phenotype Ontology (version 1.2). Find out more at http://www.human-phenotype-ontology.org.
• Cell Ontology (190106 release https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-simple.json). Find out more at http://www.obofoundry.org/ontology/cl.html
• BRENDA Tissue Ontology Ontology (BTO release ODK release https://github.com/BRENDA-Enzymes/BTO/blob/master/bto-base.json). Find out more at https://www.brenda-enzymes.org/ The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Gremse M., Chang A., Schomburg I., Grote A., Scheer M., Ebeling C., Schomburg D., Nucleic Acids Res., 39:D507-13 (2011).
• HGNC database (retrieved in November 2018), HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom www.genenames.org.
  Published in: Yates B, Braschi B, Gray K, Seal R, Tweedie S, Bruford E. Genenames.org: the HGNC and VGNC resources in 2017. Nucleic Acids Res. 2017 Jan 4; 45(D1):D619-625. PMID:27799471.
• RefSeq database (retrieved in November 2018)
  Published in: O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45 PMID:26553804.
• The MFGA provides manually curated information from scientific publications. This content is marked with a link to the corresponding publication, its licensing terms and a reference. There are generally three licensing terms:
  • Publication not published under an open access license. Only MFGA curated content is shown.
  • Publication published under an open access license. Permits to share, copy, adapt and redistribute the material if appropriate credit is given. MFGA curated content is shown as well as images and tables of the publication.
  • Publication published under a no derivatives open access license. Permits to share, copy and redistribute if appropriate credit is given and the material remains unaltered. MFGA curated content is shown as well as images of the publication.

This website provides external links to:

• ReproGenomics Viewer: RGV. Published in Darde TA et al., 2019, Bioinformatics, The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community and Darde TA et al., 2015, Nucleic Acids Res, The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.
• GeneCards by Weizmann Institute of Science: www.genecards.org
  Published for the first time in: Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D. GeneCards: integrating information about genes, proteins and diseases. Trends in Genetics 13: 163 (1997).
• NCBI resource dbSNP: https://www.ncbi.nlm.nih.gov/snp/
  Published in: Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122
• Ensembl: http://www.ensembl.org/index.html
  Published in: Daniel R. Zerbino, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Giro´n, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William McLaren, Benjamin Moore, Jonathan Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew Yates, Paul Flicek Ensembl 2018. PMID: 29155950.
• amigo.geneontology.org: http://amigo.geneontology.org
  Published in : Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. May 2000;25(1):25-9. The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. Jan 2019;47(D1):D330-D338.
• uniprot.org: https://www.uniprot.org/
  Published in : The UniProt Consortium, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D506–D515, https://doi.org/10.1093/nar/gky1049.
• Human Phenotype Ontology (version 1.2). Find out more at http://www.human-phenotype-ontology.org.
• Cell Ontology (190106 release https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-simple.json). Find out more at http://www.obofoundry.org/ontology/cl.html.
• BRENDA Tissue Ontology Ontology (BTO release ODK release https://github.com/BRENDA-Enzymes/BTO/blob/master/bto-base.json). Find out more at https://www.brenda-enzymes.org/ The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Gremse M., Chang A., Schomburg I., Grote A., Scheer M., Ebeling C., Schomburg D., Nucleic Acids Res., 39:D507-13 (2011).
• Icons8 https://icons8.com.
• Highcharts https://www.highcharts.com.