owencqueen/cgbench_data huggingface dataset:
Biochemical Function A
Evidence showing the gene product performs a biochemical function shared with other known genes in the disease of interest. NOTE: The biochemical function of both gene products must have been proven experimentally, and not just predicted. When awarding points in this evidence category, the other known gene(s) should have compelling evidence to support the gene-disease relationship. Consider increasing points based on the strength of the evidence and number of other proteins with the same function that are involved in the same disease.
Biochemical Function B
Evidence showing the gene product performs a biochemical function consistent with the phenotype. NOTE: The biochemical function of both gene products must have been proven experimentally, and not just predicted. When awarding points in this evidence category, the other known gene(s) should have compelling evidence to support the gene-disease relationship. Consider increasing points based on the strength of the evidence and number of other proteins with the same function that are involved in the same disease.
Protein Interaction
Evidence showing the gene product interacts with proteins previously implicated in the disease of interest. Typical examples of this data include, but are not limited to, physical interaction via Yeast-2-Hybrid (Y2H) or co-immunoprecipitation (coIP). NOTE: The interaction of the gene products must have been proven experimentally, and not just predicted. Proteins previously implicated in the disease of interest should have compelling evidence to support the gene-disease relationship. NOTE: Some studies provide evidence that a variant in the gene of interest disrupts the interaction of the gene product with another protein. In these cases, the positive control (showing interaction between the two wild-type proteins) can be counted as evidence of protein interaction. Points can also be awarded to case-level (variant) evidence or functional alteration for the variant that disrupts the interaction.
Expression A
Evidence showing the gene is expressed in tissues relevant to the disease of interest and/or is altered in expression in patients who have the disease. This category is specific to methods to detect RNA transcripts (RNAseq, microarrays, qPCR, qRT-PCR, Real-Time PCR). An example scenario to consider for altered expression in patients includes studies in which expression of the gene of interest (and possibly additional genes) is examined in tissue and/or cell samples obtained from individuals with the disease of interest in which the molecular etiology is unknown.
Expression B
Evidence showing the gene is expressed in tissues relevant to the disease of interest and/or is altered in expression in patients who have the disease. This category is specific to methods to detect protein expression (western blot, immunohistochemistry). An example scenario to consider for altered expression in patients includes studies in which expression of the gene of interest (and possibly additional genes) is examined in tissue and/or cell samples obtained from individuals with the disease of interest in which the molecular etiology is unknown.
Functional Alteration Patient cells
Evidence showing that cultured cells, in which the function of the gene has been disrupted, have a phenotype consistent with the human disease process. This category is specific to experiments conducted in patient cells. Examples include experiments involving expression of a genetic variant, gene knock-down, or overexpression.
Functional Alteration Non-patient cells
Evidence showing that cultured cells, in which the function of the gene has been disrupted, have a phenotype consistent with the human disease process. This category is specific to experiments conducted in non-patient cells. Examples include experiments involving expression of a genetic variant, gene knock-down, or overexpression.
Model System Non-human model organism
A non-human model organism with a disrupted copy of the gene shows a phenotype consistent with the human disease state. NOTE: Cell culture models should recapitulate features of the diseased tissue (e.g., engineered heart tissue or cultured brain slices).
Model Systems Cell culture model
A cell culture model with a disrupted copy of the gene shows a phenotype consistent with the human disease state. NOTE: Cell culture models should recapitulate features of the diseased tissue (e.g., engineered heart tissue or cultured brain slices).
Rescue Human
Evidence showing that the phenotype in humans (i.e., patients with the condition) can be rescued. For example, successful enzyme replacement therapy for a lysosomal storage disease. If the phenotype is caused by loss of function, summarize evidence showing that the phenotype can be rescued by exogenous wild-type gene, gene product, or targeted gene editing. If the phenotype is caused by a gain-of-function variant, summarize evidence showing that a treatment which specifically blocks the action of the variant (e.g., siRNA, antibody, targeted gene editing) rescues the phenotype. While the default points and point range are the same for human and non-human model organism, consider awarding more points if the rescue was in a human.
Rescue Patient Cells
Evidence showing that the phenotype in patient cells can be rescued. If the phenotype is caused by loss of function, summarize evidence showing that the phenotype can be rescued by exogenous wild-type gene, gene product, or targeted gene editing. If the phenotype is caused by a gain-of-function variant, summarize evidence showing that a treatment which specifically blocks the action of the variant (e.g., siRNA, antibody, targeted gene editing) rescues the phenotype.
Rescue Non-human model organism
Evidence showing that the phenotype in non-human model organisms can be rescued. If the phenotype is caused by loss of function, summarize evidence showing that the phenotype can be rescued by exogenous wild-type gene, gene product, or targeted gene editing. If the phenotype is caused by a gain-of-function variant, summarize evidence showing that a treatment which specifically blocks the action of the variant (e.g., siRNA, antibody, targeted gene editing) rescues the phenotype.
Rescue Cell culture model
Evidence showing that the phenotype in cell culture models can be rescued (i.e. a cell culture model engineered to express the variant of interest). If the phenotype is caused by loss of function, summarize evidence showing that the phenotype can be rescued by exogenous wild-type gene, gene product, or targeted gene editing. If the phenotype is caused by a gain-of-function variant, summarize evidence showing that a treatment which specifically blocks the action of the variant (e.g., siRNA, antibody, targeted gene editing) rescues the phenotype.