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 EnsemblHomology

Source Notebook

Retrieve homology information by species and gene

Contributed by: Keiko Hirayama

ResourceFunction["EnsemblHomology"][species, gene]

gives homology information for a gene of a specified species.

Details and Options

EnsemblHomology is based on Ensembl, which provides comparative genomics information including gene orthologs.
Selected gene symbols or Ensembl gene IDs can be used.
The following options can be give:
"SequenceType""Protein"type of aligned sequence to be returned; allowed values include: "Protein", "cDNA"
"TargetSpecies"Allspecified species to fiilter result; selected TaxonomicSpecies entities or names of species are used

Examples

Basic Examples (2) 

Get homology information for a specified human gene:

In[1]:=
ResourceFunction[ "EnsemblHomology", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["human", "BRCA2"]
Out[1]=

Get homology information for a mouse gene specified by the Ensembl gene ID:

In[2]:=
ResourceFunction[ "EnsemblHomology", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["mus musculus", "ENSMUSG00000021250"]
Out[2]=

Scope (2) 

Get homology information for a specified human gene:

In[3]:=
fxr = ResourceFunction[ "EnsemblHomology", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"][ Entity["TaxonomicSpecies", "HomoSapiens::4pydj"], "FXR2"]
Out[3]=

Show diffs for aligned sequences:

In[4]:=
Diff @@ fxr[1 ;; 2, "AlignedSequence"]
In[5]:=
(* Evaluate this cell to get the example input *) CloudGet["https://www.wolframcloud.com/obj/2c700de5-f9f6-40bf-adaf-fc0e75c3a84f"]

Options (2) 

Get homology information with aligned cDNA sequences:

In[6]:=
ResourceFunction[ "EnsemblHomology", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["gorilla gorilla", "BAK1", {"SequenceType" -> "cDNA"}]
Out[6]=

Get homology information for a specified gene and a target species:

In[7]:=
ResourceFunction[ "EnsemblHomology", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"][ Entity["TaxonomicSpecies", "CanisLupusFamiliaris::4t62p"], "BAK1", {"TargetSpecies" -> Entity["TaxonomicSpecies", "MusMusculus::y84t7"]}]
Out[7]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.1 – 21 April 2025
  • 1.0.0 – 10 January 2025

Source Metadata

  • Citation:
    • Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, and Andrew D Yates
      Ensembl 2024 Nucleic Acids Res. 2024, 52(D1):D891–D899 PMID: 37953337

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