Include gene expression level in genotype and metagenotype display names

[jseager7]

Currently, the gene expression level for alleles is displayed in the pop-up for genotypes and metagenotypes, but it is not included in the display name itself. This makes it difficult to see when a phenotype is being caused only by a change in gene expression level.

The expression level should be added to the genotype and metagenotype display names, enclosed in square brackets, and displayed after the allele type (which is in normal brackets). For example:

phzA1+ (wild_type) [Wild type product level] Pseudomonas aeruginosa (PA14)

When there is more than one allele in the genotype, then the expression level has to be included after every allele. For example:

phzA1+ (wild_type) [Wild type product level] phzA2+ (wild_type) [Wild type product level] Pseudomonas aeruginosa (PA14)

When the allele type is "deletion", there will be no expression level, so the genotype name will be displayed as normal:

rhlIdelta (deletion) Pseudomonas aeruginosa (PA14)

The expression level will also have to be displayed in metagenotypes, next to both the pathogen and the host alleles. For example:

AvrStb6+ (wild_type) [WT level] Zymoseptoria tritici (IPO323) stb6 (wild_type) [Knockdown] Triticum aestivum (cv. Chinese Spring)

---

In the JSON export, the expression level is linked to each allele in a genotype, and can be found on each genotype object, under the allele objects in the loci array:

"0d2bc8d23a8667f4-genotype-10": {
  "loci": [
    [
      {
        "expression": "Wild type product level",
        "id": "G4N0Z0:0d2bc8d23a8667f4-4"
      }
    ]
  ],
  "organism_strain": "Guy11",
  "organism_taxonid": 318829
},

When the allele type is 'deletion', there will be no expression level (because a deleted gene can't be expressed). Here's an example of a genotype with no expression on its allele:

"0d2bc8d23a8667f4-genotype-6": {
  "loci": [
    [
      {
        "id": "G4N184:0d2bc8d23a8667f4-1"
      }
    ]
  ],
  "organism_strain": "Guy11",
  "organism_taxonid": 318829
},

The allele referenced by the genotype has the allele_type property with the value "deletion".

"G4N184:0d2bc8d23a8667f4-1": {
  "allele_type": "deletion",
  "gene": "Magnaporthe oryzae G4N184",
  "name": "sep6delta",
  "primary_identifier": "G4N184:0d2bc8d23a8667f4-1",
  "synonyms": []
},

[sahujashobanta]

Does this rule hold true for Gene For Gene Phenotype also ?

[jseager7]

@sahujashobanta Yes, it also applies to the Gene For Gene Phenotype annotation type, and also to the Pathogen Phenotype and Host Phenotype annotation types.

However, it's not clear from the database description whether or not the expression level is loaded for the Pathogen Phenotype and Host Phenotype annotation types, so that change may need more discussion.

[sahujashobanta]

It's fixed .

[jseager7]

@sahujashobanta Apologies for the late reply. I've confirmed that the expression level is added for PHI Phenotypes, Gene-for-Gene Phenotypes, and Pathogen Phenotypes. However, it seems to be missing for Host Phenotypes.

For example, the following annotation should have the expression level 'Knockdown':

And all of the following annotations should have the expression level 'Not assayed'.

[jseager7]

Looks like the expression level is shown for Host Phenotype annotations now.