Discrepancy between JASPAR2024 website and pyjaspar results, possible species annotation issue for RUNX1

[SeongJun Kim]

Hello JASPAR team, 

First of all, thank you for your wonderful work and for maintaining such a valuable resource for the research community. 

While I was trying to fetch Homo sapiens profiles using pyjaspar for the JASPAR2024 release, I noticed some discrepancies between the data retrieved via the Python API and the results shown on the JASPAR website. 

Here is the code I used:

from pyjaspar import jaspardb

jdb = jaspardb(release = "JASPAR2024")

motifs_hs = jdb.fetch_motifs(

collection=['CORE', 'UNVALIDATED'],

species=[9606],

all_versions=False)

Using this code, I obtained 1023 profiles. However, when I searched on the website (Advanced Search with Collection = All collections, Species = Homo sapiens, Versions = Latest version), I found 1058 profiles.

In particular, I noticed that RUNX1 (MA0002.1) is present on the website but absent in the pyjaspar results.

While checking the profile versions, I observed that:

• MA0002.1 is annotated as RUNX1, Homo sapiens

• MA0002.2 and MA0002.3 are annotated as Runx1, Mus musculus.
  
  

It seems that in newer versions, the species annotation for this profile shifted from Homo sapiens to Mus musculus, even though the Uniprot ID (Q01196) still points to the human protein.

This species/version reassignment might explain why the human MA0002.1 profile is not retrieved when specifying species=[9606] in pyjaspar, despite it appearing in the website search results. 

Best regards,
Seongjun Kim

[Aziz Khan]

Hi Seongjun,

Thanks for bringing this up.

This is because the websearch first filters the profiles based on the species and then picks the latest version. But the pyJASPAR filters the profiles on latest versions (if selected) first and then the species. We will make sure to use the same order of query. Regardless, we recommend using the taxon instead, in this case you could use the Vertebrates.

Best regards,

Aziz

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