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Table 6 Species indicators of species assignation strategy which are adapted from Wang et al. [8]

From: Cross-species gene normalization by species inference

Species indicators Description Example
Identifier The gene is assigned a species when the gene is extracted by gene identifier extraction. A bar for Cat8 is not included, as only one gene (YOR019W, factor change 2.1) has a Cat8 site alone.
Prefix The first lowercase letter of the gene name is an abbreviation of its species. h ZIP 2 (human gene)
Previous indicator The tax_id is assigned to a gene entity if the species entity appears in front of the gene entity. Drosophila HCF
zebraflsh Ltk
Forward indicator The tax_id is assigned to a gene entity if the species entity is in front of the gene entity in the same sentence. The nearest species is used for assignment. Conversely, ISWI is a unique and essential gene in Drosophila, highlighting a possible divergent role for ISWI in flies and a distinct mechanism of interaction with the Sin3A/Rpd3 complex in higher eukaryotes.
Backward indicator The tax_id is assigned to a gene entity if the species entity precedes the gene entity in the same sentence. The nearest species is used for assignment. We identify the shady gene as encoding a cell signaling receptor, leukocyte tyrosine kinase (Ltk), that has recently been associated with human auto-immune disease.
Majority indicator The most frequently mentioned tax_id is assigned to the gene entity if it cannot be assigned by previous rules. The most frequent mention of PMCID: 2880583 is tax_id is 9606 (Human) as shown in Table 7.