4.0 Animal Models Module

4.1   New Features in SFARI Gene 3.0

The contents of the Animal Models module have been updated to eliminate redundancies, better categorize data according to the different model types (genetic, induced, rescue, inbred, and the newly included CNV models), and ensure the latest information is available to researchers. The newest features of the Animal Models module include:

• Improved Data Navigation
  • On the main Animal Models page, users can filter the data by module type by using the five provided filtering buttons. Clicking one of the filtering buttons will show users data gleaned from that particular type of model.

• Multifactorial Animal Models
  • SFARI Gene curates data from a variety of different animal models, and in some cases the data can be found in multiple models. For example, a model can be both induced and genetic; inbred and genetic; rescue and and induced. The latest iteration of SFARI Gene features unified and integrated data that allow users to access multifactorial entries from either model.

---

4.2   Quick Search and Advanced Search

Data from the Animal Models module can be found by using the full site search in the top navigation or the Quick Search or Advanced Search tools. The Quick Search tool can be found above the tables on each module page. The tables are dynamic, updating the information displayed as the user types. The Advanced Search tool, located on the Tools page of SFARI Gene, searches the entirety of the database, and provides additional filtering options to further refine the information found in the search.

---

4.3   Genetic Models

Genetic animal models are studies on animals selected because of the existence of a mutation in a particular gene. In SFARI Gene, genetic animal models can be viewed by selecting the Genetic filtering button. Every genetic module curated into the database contains the following information:

• Name – This section shows the name of the model.
• Model Species – This section shows the species on which the study was conducted.
• Aliases – This section lists any alternative names for the model.
• Reports – This section shows the total number of reports identified.
• Associated Human Genes – This section lists any human genes found to be associated with the model.
• Models and Rescue Models – This section lists the total number of models curated and how many of them are rescue models.
• Rescue Model Status – This section denotes whether or not the model is a rescue model with a yes or no.
• Summary – This section details the unique characteristics of the model.
• External Links – This section provides links to major external databases such as Entrez Gene, UniProt, and GeneCards.

In the tabs below, users can find a list of all reports related to the model, as well as links for more information about:

• Genetic Models – This tab provides details about the construct and phenotypic profiles observed in these models.
• Rescue Models – This tab lists any associated rescues performed on these models.
• Associated CNV Models – This tab provides insights into any associated animal CNV models. When there are no associated animal CNV models, this tab does not appear.

Genetic Model Details
Under the Genetic Models tab on every entry in the module, users can find the following construct details about the individual models curated in the database:

• Construct Name – This section shows the full construct name.
• Model Type – This section shows whether the entry is a genetic, rescue, inbred, CNV, or induced model.
• Model Genotype – The listed model genotype indicates whether the model described in the report carries one copy of the mutation (heterozygous) or two copies (homozygous).
• Mutation – This section provides a brief description of the mutation denoted in the report.
• Allele Type – This refers to the kind of mutation, whether knock-out, knock-in, global, or conditional.
• Strain of Origin – This refers to the strain where the given allele combination was first developed after successful germline transmission.
• Genetic Background – This is the current genetic background of the mouse model. This might be a mixed background generated after breeding experiments, or a different inbred strain generated after back crosses.
• ES Cell Line – This is the original embryonic stem cell line that was electroporated with the vector containing the targeting construct.
• Mutant ES Cell Line – On occasion the embryonic stem (ES) cell line carrying a given targeting construct will be given an identifiable name or tag, which can then be ordered from embryonic stem cell repositories.
• Model Source – The model source is the lab or other location from which the animal subject was acquired.

Genetic Phenotypic Profile
Using the toggles under the Genetic Models tab, users can explore the models’ phenotypic profiles. (This information can also be revealed by clicking the “Phenotypic Profile” button at the bottom of each entry.) Expanding the entries will provide users with phenotypic information about the models, including:

• Category – This section denotes the type of general physical, behavioral, or neurological category being studied.
• Entity – This section denotes the specific traits being observed and measured.
• Value Change – The value change describes whether the observed behaviors increased or decreased over the course of the study.
• Experimental Paradigm – This section provides information about the subject and methods of the experiment.
• Age at Testing – This section details the age of the test subjects at the time of the study.
• Study Author and Year – This section provides the author and year of the cited study.

For more information on collected phenotypes, please see the Phenotypic Profiles section of the User Guide.

Rescue Models
Under the Rescue Models tab, users can find information on rescues performed on the model that have been curated into SFARI Gene. Listed information includes:

• Number of models
• Rescue type
• Rescue agent

Associated CNVs
This tab displays information about any human CNVs found to be associated with the model, including:

• CNV name
• Total number of reports
• CNV type (deletion, duplication, or both)
• The number of case populations and individuals

---

4.4   CNV Models

CNV models are studies on animals in which a specific CNV has been generated. In SFARI Gene, CNV animal models can be viewed by selecting the CNV filtering button. Every individual CNV model curated into the database contains the following information:

• Name – This section shows the name of the model.
• Model Species – This section shows the species on which the study was conducted.
• Associated Human CNV – If a CNV has also been observed in humans, it is listed in this section.
• Reports – This section shows the total number of reports identified.
• Models and Rescue Models – This section lists the total number of CNV models curated and how many of them are rescue models.
• Summary – This section details the unique characteristics of the model.
• External Links – This section provides links to major external databases such as Entrez Gene, UniProt, and GeneCards.

In the tabs below, users can find a list of all reports related to the model, as well as links for more information about:

• CNV Models – This tab provides information about the experimental details and phenotypic profiles observed in these models.
• Associated Human CNVs – This tab displays information about any human CNVs found to be associated with the model.

CNV Models
Under the CNV Models tab on every entry in the module, users can find the following details about the individual models curated in the database:

• Model Type – This tab details whether the CNV identified in the model was caused by deletion, duplication, or both.
• Model Genotype – This section shows whether the entry is a genetic, rescue, inbred, or induced model.
• Mutation – This tab provides a brief description of the cause and location of the mutation.
• Allele Type – This refers to the kind of mutation, whether knock-out, knock-in, global, or conditional.
• Strain of Origin – This refers to the strain of the model in which the original induction took place.
• Genetic Background – This is the current genetic background of the mouse model. This might be a mixed background generated after breeding experiments, or a different inbred strain generated after back crosses.
• ES Cell Line – This is the original embryonic stem cell line that was electroporated with the vector containing the targeting construct.
• Model Source – The model source is the lab or other location from which the animal subject was acquired.

CNV Phenotypic Profile
Using the toggles under the CNV Models tab, users can explore the models’ phenotypic profiles. (This information can also be revealed by clicking the “Phenotypic Profile” button at the bottom of each entry.) Expanding the entries will provide users with phenotypical information about the models, including:

• Category – This section denotes the type of general physical, behavioral, or neurological category being studied.
• Entity – This section denotes the specific traits being observed and measured.
• Experimental Paradigm – This section provides information about the subject and methods of the experiment.
• Age at Testing – This section details the age of the test subjects at the time of the study.
• Study Author and Year – This section provides the author and year of the cited study.

For more information on collected phenotypes, please see the Phenotypic Profiles section of the User Guide.

Associated Human CNVs
This tab displays information about any human CNVs found to be associated with the model, including:

• CNV name
• The total number of reports
• CNV type (deletion, duplication, or both)
• The number of case populations and individuals

---

4.5   Rescue Models

Rescue animal models are studies on animals that have received either pharmaceutical, genetic, or cell transplant treatments during the course of the study. These treatments have the effect of ameliorating one or more of the associated phenotypes. In SFARI Gene, rescue animal models can be viewed by selecting the Rescue filtering button. Every individual rescue model curated into the database contains the following information:

• Name – This section shows the name of the model.
• Model Species – This section shows the species on which the study was conducted.
• Gene Aliases – This section lists any common aliases of genes observed in the model.
• Parent Model – This section provides a link to the parent model profile, if available.
• Reports – This section shows the total number of reports identified.
• Associated Human Genes – This section lists any human genes found to be associated with the model.
• Rescue Models – This section lists the total number of rescue models.
• Rescue Agent – This section shows the rescue agent used in the model.
• Model Summary – This section provides a brief summary of the model’s generation.
• External Links – This section provides links to major external databases such as Entrez Gene, UniProt, and GeneCards.

In the tabs below, users can find a list of all reports related to the model, as well as links for more information about:

• Rescue Models – This tab provides details about the rescue paradigms and phenotypic profiles observed in these models.
• Parent Profile – This tab provides a complete phenotypic description of an animal model before the study began.
• Related Rescues – This tab lists any other rescues that have been performed on the model.

Rescue Models
Under the Rescue Models tab on every entry in the module, users can find the following details about the rescue paradigms used in the models curated in the database:

• Model Source – The model source is the lab or other location from which the animal subject was acquired.
• Mutation – This section provides a brief description of the mutation denoted in the report.
• Model Type – This section details the type of rescue performed i.e. pharmaceutical, genetic, etc.
• Strain of Origin – This refers to the strain of the model in which the original induction took place.

Phenotypic Profile
Using the toggles under the Rescue Models tab, users can explore the models’ phenotypic profiles. (This information can also be revealed by clicking the “Phenotypic Profile” button at the bottom of each entry.) Expanding the entries will provide users with phenotypical information about the models, including:

• Category – This section denotes the type of general physical, behavioral, or neurological category being studied.
• Entity – This section denotes the specific traits being observed and measured.
• Value Change – The value change describes whether the observed behaviors increased or decreased over the course of the study.
• Experimental Paradigm – This section provides information about the subject and methods of the experiment.
• Age at Testing – This section details the age of the test subjects at the time of the study.
• Study Author and Year – This section provides the author and year of the cited study.

Parent Profile
Under the Parent Profile tab, users can find a phenotypic description of an animal model before the study began, with information including:

• Model Source – The model source is the lab or other location from which the animal subject was acquired.
• Mutation – This section provides a brief description of the mutation denoted in the report.
• Model Type – This section shows whether the entry is a genetic, rescue, inbred, CNV, or induced model.
• Strain of Origin – This refers to the strain of the model in which the original induction took place.

Related Rescues
Under the Related Rescues tab, users can find information on other rescues performed on the model that have been curated into SFARI Gene. Listed information includes:

• Number of models
• Model type
• Rescue type
• Rescue agent

For more information on collected phenotypes, please see the Phenotypic Profiles section of the User Guide.

---

4.6   Induced Models

Induced models are studies on animals in which a particular trait or disorder has been purposefully induced with a biological or chemical agent. In SFARI Gene, induced animal models can be viewed by selecting the Induced filtering button. Every individual induced model curated into the database contains the following information:

• Name – This section shows the name of the model.
• Model Species – This section shows the species on which the study was conducted.
• Model Subtype – This section denotes whether the model utilized a chemical or biological inducing factor.
• Reports – This section shows the total number of reports identified.
• Inducer Symbol – This section shows the most commonly used symbol for the model, if available.
• Induced Models and Rescue Models – This section lists the total number of induced models curated and how many of them are rescue models.
• Rescue Model Status – This section denotes whether or not the model is a rescue model with a yes or no.
• Summary – This section details the unique characteristics of the model.
• Human Clinical Evidence – If relevant any clinical evidence relevant to the human body is discovered in the model, it is listed in this section.
• External Links – This section provides links to major external databases such as NCBI.

In the tabs below, users can find a list of all reports related to the model, as well as links for more information about:

• Inducing Factor – This tab expands upon the exposure, mode of action, and usage of the study’s inducing factor.
• Induced Models – This tab provides details about the construct and phenotypic profiles observed in these models.
• Rescue Models – This tab lists any associated rescues performed on these models.

Inducing Factor Details
Under the Inducing Factor tab on every entry in the module, users can find the following information about the inducing agent used in the experiment:

• Exposure – This section denotes how the subjects were exposed to the inducing factor.
• Mode of Action – This section provides additional details about how the inducing factor was activated.
• Usage – This section further describes the function of the inducing factor.

Induced Model Details
Under the Induced Models tab on every entry in the module, users can find the following construct details about the individual models curated in the database

• Model Source – The model source is the lab or other location from which the animal subject was acquired.
• Construct Definition – The construct definition provides a brief overview of the compound administered and the subject used in the model.
• Model Type – This section shows whether the entry is a genetic, rescue, inbred, CNV, or induced model.
• Strain of Origin – This refers to the strain of the model in which the original induction took place.

Induced Phenotypic Profile
Using the toggles under the Induced Models tab, users can explore the models’ phenotypic profiles. (This information can also be revealed by clicking the “Phenotypic Profile” button at the bottom of each entry.) Expanding the entries will provide users with phenotypical information about the models, including:

• Category – This section denotes the type of general physical, behavioral, or neurological category being studied.
• Entity – This section denotes the specific traits being observed and measured.
• Value Change – The value change describes whether the observed behaviors increased or decreased over the course of the study.
• Experimental Paradigm – This section provides information about the subject and methods of the experiment.
• Age at Testing – This section details the age of the test subjects at the time of the study.
• Study Author and Year – This section provides the author and year of the cited study.

For more information on collected phenotypes, please see the Phenotypic Profiles section of the User Guide.

Rescue Models
Under the Rescue Models tab, users can find information on rescues performed on the model that have been curated into SFARI Gene. Listed information includes:

• Number of models
• Rescue type
• Rescue agent

---

4.7   Inbred Models

Inbred models are studies on animals that exhibit a particular phenotype of interest without carrying a known genetic mutation. Inbred animal models can be viewed by selecting the Inbred filtering button. Every individual inbred module curated into the database contains the following information:

• Name – This section shows the name of the model.
• Model Species – This section shows the species on which the study was conducted.
• Strain Name – This section shows the name of the particular genetic strain studied in the model.
• Reports – This section shows the total number of reports identified.
• Inbred Models and Rescue Models – This section lists the total number of inbred models curated and how many of them are rescue models.
• Rescue Model Status – This section denotes whether or not the model is a rescue model with a yes or no.
• Summary – This section details the unique characteristics of the model.
• External Links – This section provides links to major external databases such as NCBI.

In the tabs below, users can find a list of all reports related to the model, as well as links for more information about:

• Inbred Models – This tab provides details about the experimental details and phenotypic profiles observed in these models.
• Rescue Models – This tab lists any associated rescues performed on these models.

Inbred Model Details
Under the Inbred Models tab on every entry in the module, users can find the following experimental details about the individual models curated in the database:

• Model Source – The model source is the lab or other location from which the animal subject was acquired.
• Mutation – This section provides a description of the mutation observed in the model.
• Model Type – This section shows whether the entry is a genetic, rescue, inbred, CNV, or induced model.
• Strain of Origin – This refers to the strain of the model in which the original induction took place.

Inbred Phenotypic Profile
Using the toggles under the Inbred Models tab, users can explore the models’ phenotypic profiles. (This information can also be revealed by clicking the “Phenotypic Profile” button at the bottom of each entry.) Expanding the entries will provide users with phenotypical information about the models, including:

• Category – This section denotes the type of general physical, behavioral, or neurological category being studied.
• Entity – This section denotes the specific traits being observed and measured.
• Value Change – The value change describes whether the observed behaviors increased or decreased over the course of the study.
• Experimental Paradigm – This section provides information about the subject and methods of the experiment.
• Age at Testing – This section details the age of the test subjects at the time of the study.
• Study Author and Year – This section provides the author and year of the cited study.

For more information on collected phenotypes, please see the Phenotypic Profiles section of the User Guide.

Rescue Models
Under the Rescue Models tab, users can find information on rescues performed on the model that have been curated into SFARI Gene. Listed information includes:

• Number of models
• Model type
• Rescue type
• Rescue agent

---

4.8   Phenotypic Profiles

SFARI Gene uses a vast assortment of phenotypic profiles to better describe and catalogue data gleaned from animal models. We rely on data tables and charts from the PhenoBase database to provide our users with the most accurate, up-to-date, and helpful information. This key component of the Animal Models module contains a list of more than 100 standardized phenotype terms and characteristics of the animal models for 16 categories relevant to the clinical presentation of autism. They describe the presentation of the core behaviors of autism – such as repetitive behavior or learning and memory – in each of the animal models, along with their physiological and molecular characteristics.

---