GS-1) What is SFARI Gene?
SFARI Gene is a database built on information extracted from peer-reviewed scientific and clinical studies on the molecular genetics and biology of autism spectrum disorders (ASD).
GS-2) What are the new features of SFARI Gene 2.0?
SFARI Gene 2.0 provides new bioinformatics features and functionalities envisioned to accelerate discoveries by the autism research community. In addition to expanding the scientific content, the user interface has been revamped to enhance usability.
GS-3) What types of information does SFARI Gene 2.0 contain?
SFARI Gene integrates genetic, neurobiological, and clinical information about genes associated with ASD. SFARI Gene‘s content is entirely based on the peer-reviewed scientific literature and is manually annotated by expert biologists. Data presented in abstracts or at conferences are not included.
GS-4) What is the gene classification rationale in SFARI Gene 2.0?
Autism-related genes in SFARI Gene are classified into four categories:
(1) rAut: This category applies to genes implicated in rare monogenic forms of ASD, such as SHANK3. The types of allelic variants within this class include rare polymorphisms and single gene disruptions/mutations directly linked to ASD. Submicroscopic deletions/duplications (copy number variations) encompassing single genes specific for ASD are also included.
(2) sAut: This category includes genes implicated in syndromic forms of autism, in which a subpopulation of patients with a specific genetic syndrome, such as Angelman syndrome or fragile X syndrome, develops symptoms of autism.
(3) iAut: This category is for small risk-conferring candidate genes with common polymorphisms that are identified from genetic association studies in idiopathic ASD, or autism of unknown cause, which makes up the majority of autism cases.
(4) fAut: This category lists functional candidates relevant for ASD biology, not covered by any of the other genetic categories. Examples include the gene CADSP2, in which knockout mouse models exhibit autistic characteristics, but the gene itself has not been directly tied to known cases of autism.
A gene can belong to more than one category, depending on the mutation. For instance, a common variant may confer risk for developing idiopathic autism but an inactivating mutation in the same gene places it in the higher risk-conferring categories. In such cases, all the appropriate categories are used to annotate the genes.
Both rAut and sAut categories represent monogenic forms of ASD. However, we include a distinct class for each because sAut genes have been linked to syndromic forms of autism, such as fragile X syndrome, whereas rAut genes are only potential candidates for autism. sAut genes are present in individuals whose ASD was diagnosed secondary to the main clinical features of their genetic disorder. In contrast, rAut genes are identified in the course of genetic screening of individuals diagnosed with ASD.
GS-5) How is SFARI Gene 2.0 data organized?
A SFARI Gene entry is the presentation of a gene linked to ASD along with all of the gene’s molecular, neurobiological, and clinical attributes. The steps involved in the curation of a SFARI Gene entry are schematically shown in Figure GS-1.
GS-6) How do I access data within SFARI Gene 2.0?
Data can be accessed three ways using SFARI Gene 2.0:
GS-7) How do I search SFARI Gene 2.0 using Advanced Search?
The Advanced Search can be found under the Tools menu on the left-hand side of the screen. If you click Advanced Search, you will be taken to an interactive “Search SFARI Gene” box.
HG-1) What information does the Human Gene module contain?
The Human Gene module is an active collection of candidate genes identified through genetic association studies. It includes genes linked to syndromic autism as well as genes that harbor rare mutations linked to autism.
HG-2) What new features of the Human Gene module are present in SFARI Gene 2.0?
Several new features and functionalities were added to V2.0:
The Human Gene module was refined to now include a home page, which provides users with information about the module, module terminology, and module structure. A brief set of statistics is also provided at the bottom of the home page.
In a sidebar on the right side of The Human Gene home page, you will find links to the home pages of the other modules in addition to links to tools. This sidebar persists across all pages within SFARI Gene/AutDB to provide easy navigation for the user.
3. Expansion of Annotation
A column with links to the PubMed abstracts has been added to both the Rare and Common Sequence Variation tables so that mutation entries are linked with their corresponding PMIDs. In addition, a unique ID (called the Variant ID) is given to each variant listed.
HG-3) How do I enter the Human Gene database?
The Human Gene module can be entered a number of ways. One way is by clicking the ‘Human Gene’ Quick Link on the left-hand side of the SFARI Gene Home Page. A second way is by clicking the Human Gene icon (Figure HG-2) on the SFARI Gene Home Page:
HG-4) What do I see in the search result for the Human Gene module?
Let’s take the example of searching for ASD candidate genes on Chromosome 16. SFARI Gene will retrieve a comprehensive list of ASD candidate genes on that chromosome in a tabular format (Figure HG-3). The list will consist of candidates reported from genetic association studies, including rare single gene mutations, genes linked to syndromic autism, and functional candidates.
HG-5) How do I view the detailed annotation of a candidate gene?
Clicking a gene symbol in the search result table (see Figure HG-4) will take you to the detailed annotation page for that gene.
HG-6) What do I see in the detailed annotation of candidate genes?
Clicking a gene symbol in the search result table (see Figure HG-4) will take you to the detailed annotation page for that gene.
HG-7) What do I see in the Summary tab of candidate genes?
In the Summary tab, you’ll see four sections that provide an overview of the gene (see Figure HG-5):
HG-8) What do I see in the Sequence Variants tab of candidate genes?
In the Sequence Variants tab, you’ll see a detailed table of the rare (top header) and common (bottom header) variants for that particular gene. Not all genes will have rare and/or common variants.
HG-9) How is data within the Human Gene module linked to other modules of SFARI Gene 2.0?
The Human Gene module is linked to the other modules of SFARI Gene 2.0 by a tab-based format. Above either the search table display (Figure HG-4) or detail level display (Figure HG-6), you’ll see four tabs: Gene, Gene Scoring, Animal Model and PIN. Clicking on any of these tabs will take you to the corresponding information for that gene or those set of genes in each of those modules. For example, in Figure HG-4, clicking on the PIN tab will take you to a search table with all genes on chromosome 16 for which there is protein-protein interaction data.
HG-10) How do I edit/submit annotations to the Human Gene module?
NOTE: Registration with SFARI Gene is required to access the edit module.
HG-11) How do I view documentation about the curation of data within the Human Gene module?
You can find information on data curation for the Human Gene module by clicking the ‘Curation’ sub-navigation tab on the Human Gene home page (Figure HG-7).
HG-12) How do I view current statistics for data within the Human Gene module?
You can view current statistics for the Human Gene module by clicking the ‘Statistics’ sub-navigation tab on the Human Gene home page (Figure HG-8).
AM-1) What’s New in Animal Model Module V2.0?
Version 2.0 for the Animal Model module introduces new features and refinements that aim to provide added functionality to the users (see Figure AM-1):
AM-2) How do I view Animal Model module data?
You can access the Animal Model module data in three ways:
Figure AM-2a: Animal Model module home page featuring links to explore either the Genetic or Induced models.
2. You can also view animal model data from the Advanced Search menu by selecting ‘View All’ or searching for a particular entry (Figure AM-3).
Figure AM-2b: Advanced search menu for Animal Model data featuring ‘View All’ button and search entry boxes.
AM-3) How do I search data within the Animal Model module?
You can search data within the Animal Model in two ways:
You will then be able to choose the type of query within the selected model type using the “Search fields for Animal Model.” (Figure AM-7)
AM-4) What do I see in the search result for the Animal Model module using Advanced Search?
Searching for genetic animal models with the gene name "neuroligin" will retrieve a list of animal models in a table format under the Animal Model tab. Example of this display is shown in Figure AM-10.
Figure AM-4a: Display of search results using the example of mouse gene name Neuroligin. Search results appear in a summary table format showing: (A) Gene Symbol, (B) Gene Name, (C) Model Species, (D) Syntenic (two or more genes located on the same chromosome), (E) Primary Reference, (F) Number of Reports, and (G) Number of Models.
Searching for induced animal models with the inducer name "thalidomide" will retrieve a list of animal models under a table format. Example of this display is shown in Figure AM-11.
Figure AM-4b: Display of search results using the example of inducer Thalidomide. Search results appear in a summary table format showing: (A) Inducer Name, (B) Model Subtype (Chemical or Biological), (C) Number of Reports, (D) Number of Models, and (E) Primary Reference.
AM-5) What do I see in the detailed annotation of genetic animal models in SFARI Gene?
To view the detailed annotation of a genetic animal model, select the gene symbol from the search results table. Detailed annotation is displayed using a tab-based interface, with the information divided across three tabs – gene summary, construct details, and phenotypic profile. Each tab level includes header containing gene identification information and statistics, as shown in Figure AM-12.
Figure AM-5: Detail level display for Neuroligin 3. Each entry data is divided across three tabs with information header which includes the Gene Symbol, Model Species, Gene Name, aliases, and brief statistics – Total number of reports and total number of models.
AM-6) What do I see in the detailed annotation of induced animal models in SFARI Gene?
To view the detailed annotation of an induced animal model, select the inducer symbol from the search results table. Detailed annotation is displayed using a tab-based interface, with the information divided across three tabs – summary, construct details, and phenotypic profile. Each tab level includes a header containing inducer identification information and statistics, as shown in Figure AM-13.
Figure AM-6: Detail level display for Thalidomide. Each entry data is divided across three tabs with information header which includes the Inducer name, Inducer abbreviation, Model Subtype (Chemical/Biological), Model Species, link to external database, PubChem, and finally brief statistics about the number of reports and number of models.
AM-7) What do I see in the summary tab of genetic animal models in SFARI Gene?
The first tab of the detailed annotation of genetic models is the summary tab, which includes the following information: Model summary information, external links, and references, as shown in Figure AM-14.
AM-8) What do I see in the construct details tab of genetic animal models in SFARI Gene?
The second tab of the detailed annotation view of genetic models is the construct details tab, which includes a list of models of the gene along with construct information for all the models listed as shown in Figure AM-15. You can access the construct information by clicking on a model name to expand.
AM-9) What do I see in the phenotypic profile tab of genetic animal models in SFARI Gene?
The last tab of the detailed annotation view of genetic models in the phenotypic profile tab includes detailed phenotypic information for all the models of a particular gene. The phenotypic information is displayed using an entity-quantity (EQ) classification system, which describes the phenotype using standardized vocabulary.
Figure AM-9.1a: Detail level display for Nlgn3 (Phenotypic Profile Tab). Each entry is displayed in a detail level across three tabs. The last tab, Phenotypic Profile, lists all the models for a particular entry along with all the phenotypes listed in report, including ‘No Change’ entries. The phenotype change is described in the Quantity column using standardized vocabulary (Increased, Decreased, Abnormal), and the Entity column describes the phenotype being observed. Each entity is classified into one of sixteen categories described in PhenoBase. Each entry also includes a ‘View More’ button to display detailed description of change in phenotype and paradigm used to explore phenotype. Experimental Paradigm and Age of Testing information are also listed.
Figure AM-9.1b: Detail Information for entry within Phenotypic Profile. Shown here is an example description of a change in the Gene Regulation entry under the Molecular profile phenotype category. Information includes detailed description of actual change in phenotype along with more detailed experimental paradigm.
AM-10) What do I see in the inducer summary tab of induced animal models in SFARI Gene?
The first tab of the detailed annotation of induced models is the summary tab which includes the following information: Model summary, Human Clinical Evidence, Exposure, Mode of Action, Usage, and References, as shown in Figure AM-16.
AM-11) What do I see in the construct details tab of induced animal models in SFARI Gene
The second tab of the detailed annotation view of induced models is the construct details tab which includes a list of models of the gene along with construct information for each model.
AM-12) What do I see in the phenotypic profile tab of induced animal models in SFARI Gene?
The last tab of the detailed annotation view of genetic models is the phenotypic profile tab, which includes detailed phenotypic information for all the models of a particular gene. The phenotypic information is displayed using an entity-quantity (EQ) classification system which describes the phenotype using standardized vocabulary.
AM-13) What is PhenoBase?
PhenoBase is a key component of the Animal Model module. This dataset 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. PhenoBase describes 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.
Figure AM-13.1: PhenoBase Table View. Shown here is a sample view of the Social Behavior PhenoBase table which can be accessed by selecting the category name from the Phenotypic Profile tab. The table includes the following information: Phenotype Terms, Phenotype Definition, ASD Domain, and Experimental Paradigm.
PIN-1) What information does the PIN module contain?
The Protein Interaction (PIN) module of SFARI Gene 2.0 serves as a comprehensive, up-to-date reference for all known direct protein interactions of genes associated with autism spectrum disorders (ASD). It includes six major types of interactions: protein binding, RNA binding, promoter binding, protein modification, autoregulation, and direct regulation. Each protein interaction is manually curated from primary reference articles after consultation with public databases (BioGRID, HPRD, PubMed) and commercial resources (Pathway Studio 7.1).
PIN-2) What new features of the PIN module are present in SFARI Gene 2.0?
First released in June 2011, the PIN module has now been incorporated into the tab-based display of SFARI Gene 2.0. At the primary level, a summary of PIN search results is presented under a tab from which users can easily navigate to corresponding data in tabs for "Gene," "Gene Scoring," and "Animal Model" modules. At the secondary level, detailed PIN annotation for autism candidate genes is incorporated into a tab-based display for both graphical and tabular views of protein interactomes.
PIN-3) How do I enter the PIN database?
You can access PIN data by one of three ways:
PIN-4) What do I see in the search result for the PIN module?
When you browse or search for a gene using the PIN module, you will first encounter a summary row format showing the Gene Symbol, Gene Name, Number of Interactions, and links to the corresponding entries in the Human Gene and Animal Model modules of SFARI Gene (if available). To reach the secondary level of display (the “Detail” level), you should click on the desired gene symbol.
An example of a search result in the PIN module is illustrated in Figure PN-3. (Note: If you search by Interaction Type, the “No. of Interactions” column will only reflect the number of interactions corresponding to the interaction type of interest.)
Figure PN-3. PIN Search Result for NRXN1
PIN-5) How do I view detailed annotation for protein interactions?
To view detailed PIN annotation for an autism candidate gene, click on the gene symbol of interest in the PIN search results.
PIN-6) What do I see in the detailed annotation of protein interactions?
The PIN detailed annotation page illustrates two main sections:
1) Header: (Figure PN-4)
2) Tab-Based Display of PIN Interactome:
Figure PN-4. PIN Detailed Annotation Entry for NRXN1: Header.
PIN-7) What do I see in the Interactome tab of protein interactions?
The “Interactome” tab features the graphical view of the protein interactome (Figure PN-5). It presents an interactive slideshow which cycles through three views: full interaction, full interaction with autism candidate genes highlighted, and interactions between ASD-linked genes (Figure PN-6), all generated using Cytoscape. On the right side, we show that ASD-linked genes are represented in the interactomes by red circles. Below that is situated a legend for the tabular interactome containing the types of protein interactions included with the PIN dataset: Protein Binding, RNA Binding, Promoter Binding, Protein Modification, Direct Regulation, and Autoregulation.
Figure PN-5. PIN Detailed Annotation: “Interactome” tab shows graphical view of protein interactome
PIN-8) What do I see in the Interaction Table tab of protein interactions?
The “Interaction Table” tab features the tabular view of the protein interactome (Figure PN-7). It includes the interactor’s gene symbol, gene name, species, Entrez Gene ID, UniProt ID, interaction type (represented by legend in middle section of page), evidence, and reference. Columns for interaction type, evidence, and reference are hyperlinked such that users can click on the image/text to obtain definitions of those entries in the form of Metadata Tables (Figures PN-9-11).
PIN-9) How do I view documentation about the data curated within the PIN module?
Descriptions of PIN data content can be viewed in two ways:
These include the following tabs: About, Curation, Interaction, Evidence, Statistics
If you wish to obtain further information regarding an interactor’s species, evidence, or interaction type,” select the corresponding entry within the desired column of interest. You will then be presented with an abbreviated table of defining one of these three categories.
Figure PN-8. PIN Home Page of SFARI Gene 2.0.
PIN-10) How do I view current statistics for data within the PIN module?
Statistics for PIN data content are present in two sections of the PIN home page:
CNV-1) What information does the CNV module contain?
The CNV module of SFARI Gene is a comprehensive, up-to-date collection of all copy number variants associated with autism spectrum disorders (ASD). As with the other modules of SFARI Gene, the content of the CNV module originates entirely from published scientific literature. MindSpec researchers systematically search, collect, and extract information on CNVs from autistic case cohorts and, when available, unaffected control cohorts. CNVs in the module are organized based upon the locus (chromosomal region or band) in which they were observed in each annotated report.
Description. A brief synopsis of the cohort, including the source of the individuals within the cohort.
Cohort size. Case and control cohorts come in a wide range of sizes. Case cohorts of smaller sizes frequently provide more information on the phenotypic characteristics of affected individuals within the cohort, but are of less significance in statistically determining the pathogenic relevance of a CNV at a given locus across populations. On the other hand, larger case cohorts are more useful in statistically determining pathogenic CNV relevance, but typically they provide far less information on the phenotypic characteristics of affected individuals.
Diagnosis. Oftentimes, the diagnosis criteria (ADI-R, ADOS, etc.) is described, as is the number of individuals with specific primary diagnoses, such as autism, Asperger's syndrome, or PDD-NOS.
Age, Gender, and Geographical Ancestry. The age of a cohort is typically given as either a range of ages or a mean age. Males are diagnosed with ASD approximately 3x more than females. As such, large autistic case cohorts are typically designed to reflect this disparity, with roughly 70-85% of individuals within a case cohort being male. Control cohorts, on the other hand, are typically 50% male. The majority of cohorts are predominantly of Caucasian/European origin. As such, determining the pathogenic relevance of a CNV at a given locus across ethnic groups is difficult.
Methodology. Population data includes the methodology used to discover CNVs at the locus of interest and, in some cases, the methodology used to independently confirm or validate the CNV.
Many published reports in which copy number variants have been identified include information on the individuals (also referred to as cases or probands) within autistic populations. When provided, this information is curated and presented in the individual data section.
Case studies commonly feature detailed profiles on affected individuals from which we extract information to form the following categories:
Clinical and cognitive profile. These categories can potentially contain a broad range of information, depending on the source material. Among the types of information included in the clinical profile category are : clinical history; dysmorphic features; comorbidities commonly associated with ASD such as ADHD, epilepsy, or sleep disturbances; and growth parameters such as height, weight, and head circumference. When included in the published report, ADI-R and/or ADOS scores are listed. Otherwise, more qualitative measures of core ASD features (deficiencies in social interactions, communication deficits, and repetitive and restricted behaviors) are provided.
With regards to the cognitive profile, individuals with ASDs often exhibit a range of intellectual deficits. Information on IQ scores, or the extent of mental retardation, intellectual disability, or developmental delay is provided in this category. Cognitive profile may either be qualitative ("average", "below-average", etc.) or quantitative (with numerical score or percentile values), and in some cases the testing metholodogy is provided.
CNV Inheritance. A CNV can either arise de novo or be inherited on either the maternal chromosome or the paternal chromosome (although, in some cases, a CNV can be inherited from both parents). A de novo CNV spontaneously arises in an individual and is not transmitted from either parent, and there is considerable interest in the importance of de novo CNVs as a significant genetic cause for ASDs, especially in simplex families. However, both maternally-inherited and paternally-inherited CNVs are also believed to confer varying degrees of pathogenic risk. If the origin of a CNV has not been ascertained, then its inheritance is classified in the module as "Unknown".
Family Profile. In many cases, families with autistic individuals are frequently categorized as either simplex or mulitplex. In a simplex family, the proband identified in a CNV report is the only sibling in the proband's family with ASD. Simplex cases may also be referred to as sporadic cases in the scientific literature. In a multiplex family, in addition to the proband identified in a CNV report, there is at least one additional autistic sibling in the proband's family. When such information is provided, the Family Profile is listed as either Simplex or Multiplex. This information is essential in understanding how closely a given CNV co-segregates with disease.
CNV-Disease Segregation. Of particular importance in assessing the clinical importance of any given copy number variant is how closely the CNV associates or segregates with the disease. For example, if a copy number variant is only identified in one or more autistic siblings, but it is not present in any unaffected siblings, the CNV is said to be segregated with the disease. However, if a copy number variant is found both in an autistic individual and at least one of his or her unaffected siblings, or if a CNV is present in one autistic sibling but not in another affected sibling, then the CNV-disease association is characterized as not segregated. By their nature, de novo CNVs are considered to closely segregate with disease.
CNV-2) How do I enter the CNV database?
There are three ways to access the CNV database (Figure CNV-1):
CNV-3) What do I see in the search result for the CNV module?
The search result for the CNV module, such as that shown in Figure CNV-3 that shows the search results for chromosome 15, consists of a table with columns for Chromosome, CNV locus, CNV Type, # of studies, and Animal Model. If there is an animal model for a CNV locus in the database, a mouse icon will appear in the Animal Model column for that CNV locus.
CNV-4) How do I view the detailed annotation of a CNV locus?
To view the detailed annotation of a CNV locus, click on the name of the CNV locus. This will take you to the detailed annotation display for the selected CNV locus.
CNV-5) What do I see in the detailed annotation of a CNV locus?
The detailed annotation of a CNV locus is presented in a tab-based display format with tabs entitled “CNV Summary”, “Population Data”, “Individual Data”, and “Animal Model”; the contents of each of these tabs is described in greater detail.
CNV-6) What do I see in the CNV Summary tab?
The CNV summary tab contains the following content: Summary Information, which summarizes the relevance of CNVs at a particular locus to ASD; Additional Locus Information, which employs an expand/collapse functionality and provides links to the UCSC and NCBI Genome Browsers and the DECIPHER website (in those cases where there is a corresponding disease- or syndrome-associated microdeletion and/or microduplication in the DECIPHER database); and References, which are divided into major and minor reports via an expand/collapse functionality (Figure CNV-4).
CNV-7) What do I see in the Population Data tab?
As shown in Figures CNV-5 and CNV-6, the Population Data tab employs an expand/collapse functionality to separately display population case and control data and divides annotated population data between “Summary” and “Additional” tabs. The “Summary” tab of a CNV locus Population Data table (Figure CNV-5) shows the following information: Cohort ID; the first author & year of publication of the CNV report that featured the cohort in question; a brief description of the cohort; the size of the cohort; the diagnosis of the cohort; the age and gender of the cohort; the size of the largest CNV at the locus of interest found in a given report; and the number of deletions, duplications, and total CNVs at the locus of interest in a given report. The “Additional” tab (Figure CNV-6) shows the following information: Cohort ID; the geographical ancestry of the cohort; the discovery methodology, platform, algorithm and software used to identify CNVs; and the validation method used to confirm the CNVs, if applicable.
CNV-8) What do I see in the Individual Data tab?
As shown in Figures CNV-7 and CNV-8, the Individual Data tab employs an expand/collapse functionality to separately display individual case and control data and divides annotated individual data between “Summary” and “Additional” tabs. The “Summary” tab of a CNV locus Individual Data table (Figure CNV-7) shows the following information: Patient ID; the first author and year of publication of the CNV report that featured the individual in question; the age and gender of the individual; the primary diagnosis, clinical profile, and cognitive profile of the individual; the start and end coordinates, the size, and the type of CNV at the locus of interest in the individual; the genome build used to determine the coordinates of the CNV, and whether or not the CNV was validated by an independent secondary methodology following its discovery. Data in the Individual Data table is presented based on the size of the CNV within the locus of interest, from largest CNV to smallest CNV. The “Additional” tab (Figure CNV-8) shows the following information: Patient ID; a description of the validation methodology; the primary disorder inheritance; the mechanism of CNV inheritance; the family profile of the individual; the extent to which the CNV at the locus of interest segregates with disease in the individual; the gene content of the CNV; and altered gene expression.
CNV-9) What do I see in the Animal Model tab?
For those CNV loci for which there is a corresponding animal model, the animal model tab show a tab-based data display with tabs for “Model Summary”, “Construct Details”, and “Phenotypic Profile” (Figure CNV-9). The “Model Summary” tab includes mouse chromosome information, model summary, external links to the UCSC and NCBI Genome Browsers, an external link to the Mouse Genome Informatics website, and a table of references, with the first report in which the animal model was studied listed as the “Primary” report.
The “Construct Details” tab includes a list of models of the CNV locus along with construct information for those models (Figure CNV-10).
The “Phenotypic Profile” tab includes detailed phenotypic information for all the models of a particular CNV locus (Figure CNV-11). The phenotypic information is displayed using an entity-quantity (EQ) classification system, which describes the phenotype using standardized vocabulary.
CNV loci that do not have a corresponding animal model will show “No animal model currently available”.
CNV-10) How do I view documentation about the curation of data within the CNV module?
To view documentation about the curation of data within the CNV module, select the “Curation” sub-navigation tab on the CNV module Home Page.
CNV-11) How do I view current statistics for data within the CNV module?
To view current statistics for data within the CNV module, select the “Statistics” sub-navigation tab on the CNV module Home Page.
Figure CNV-13. Current statistics for the data within the CNV module can be viewed by selected the "Statistics" sub-navigation tab, highlighted here in red, on the CNV module Home Page.
WS -1) What is WorkSpace?
Workspace is a feature of SFARI Gene 2.0 that allows registered users to input the most up-to-date information into the SFARI Gene database.
WS-2) How do I access Workspace?
NOTE: Registration with SFARI Gene is required to access the Workspace feature of SFARI Gene. All Workspace actions will be associated with your user id.
WS-3) How do I upload a file into Workspace?
WS-4) How do I download a reference file from the SFARI Gene 2.0?
On the top left-hand side of the Control Panel for Workspace (Figure WS-1), there is a box titled “SFARI Gene Dataset Selection Download.” From the “Select a Category” drop-down menu, you may choose from the entire SFARI Gene dataset (All Gene) or select specific gene sets such as Rare, Syndromic, Association, Functional, or Others. You must then choose a name for this file, assign it to Workspace 1, 2, or 3 and click the “Save” button (Figure WS-6).
WS-5) How do I merge data between various files and Workspaces?
In the middle of the Control Panel, there is a box titled “Dataset Operations.” Select the Workspaces and file names for the gene sets you want to merge. In Figure 20, the file “Refset” in Workspace 1 and file “Mygeneset” in Workspace 2 are selected for merging.
WS-6) After all of the desired information input, how do I actually utilize Workspaces and information from the files?
You can view a particular Workspace by selecting one of the Workspace tabs in the bottom right-hand corner of the control panel. Links back to the control panel and to the other workspaces are located at the top left-hand and right-hand sides of the page, respectively.
Cit-1) How do I cite the content of SFARI Gene 2.0?
AutDB: a gene reference resource for autism research.