Mettl5 and other genes - phenotypes for males and females

[viomunoz]

Problem reporting significant phenotypes for only males or females for some parameters: Mettl5 https://www.mousephenotype.org/data/charts?accession=MGI:1922672&allele_accession_id=MGI:6273953&zygosity=homozygote&parameter_stable_id=IMPC_OFD_007_001&parameter_stable_id=IMPC_OFD_011_001&pipeline_stable_id=HMGU_001&procedure_stable_id=IMPC_OFD_001&parameter_stable_id=IMPC_OFD_007_001&parameter_stable_id=IMPC_OFD_011_001&phenotyping_center=HMGU

• Gene page indicates significant phenotype for both males and females
• Description of the experiment: males and females reported
• Graphs and summary stats only show males

[viomunoz]

[viomunoz]

Behaviour phenotypes appear as signficant in Significant Phenotypes table and No significant in chart pages

[viomunoz]

[viomunoz]

More examples in dev (it is DR18)

See a phenotype I chose at random:

https://dev.mousephenotype.org/data/phenotypes/MP:0001586

Il2ra: https://dev.mousephenotype.org/data/charts?accession=MGI:96549&allele_accession_id=MGI:5766766&zygosity=homozygote&parameter_stable_id=IMPC_HEM_002_001&pipeline_stable_id=ICS_001&procedure_stable_id=IMPC_HEM_002&parameter_stable_id=IMPC_HEM_002_001&phenotyping_center=ICS

Associated Phenotype : No significant association Male signficant, no p-values reported (Expect to see a signficant association being reported)

Msn: https://dev.mousephenotype.org/data/charts?accession=MGI:97167&allele_accession_id=MGI:5632533&zygosity=homozygote&parameter_stable_id=IMPC_HEM_002_001&pipeline_stable_id=JAX_001&procedure_stable_id=IMPC_HEM_002&parameter_stable_id=IMPC_HEM_002_001&phenotyping_center=JAX

Associated Phenotype : No significant association Females signficant, no p-value reported (Expect to see a signficant association being reported)

Ercc5: https://dev.mousephenotype.org/data/charts?accession=MGI:103582&allele_accession_id=MGI:5636892&zygosity=heterozygote&parameter_stable_id=IMPC_HEM_002_001&pipeline_stable_id=BCM_001&procedure_stable_id=IMPC_HEM_002&parameter_stable_id=IMPC_HEM_002_001&phenotyping_center=BCM

Associated Phenotype : decreased erythrocyte cell number Males and females signficant (Matches expectation - expect to see a signficant association being reported)

Atp13a3: https://dev.mousephenotype.org/data/charts?accession=MGI:2685387&allele_accession_id=MGI:6314147&zygosity=homozygote&parameter_stable_id=IMPC_HEM_002_001&pipeline_stable_id=JAX_001&procedure_stable_id=IMPC_HEM_002&parameter_stable_id=IMPC_HEM_002_001&phenotyping_center=JAX

Associated Phenotype : increased erythrocyte cell number Males and females significant (Matches expectation - expect to see a signficant association being reported)

[viomunoz]

Phenotype page

Chart page

[viomunoz]

Phenotype page should normally only have the symbol for the signficant sex, but this is less relevant

[viomunoz]

[ficolo]

https://github.com/mpi2/PhenotypeData/blob/4d5e7ec0f855cce1f900a2e517d5705f3ed03594/data-model/src/main/java/org/mousephenotype/cda/enumerations/SignificantType.java#L39

[rwilson-ebi]

Two separate problems

• Hamed has fixed the data labelling issue
• Web frontend issue to be addressed Plan to address with DR 19

Main issue Tag used to assign GP calls

• not just free text on the website