QTL Data Entry Forms
The Data Editor Forms for QTL Data are divided into six forms that correspond to the major types of data found in QTL mapping studies:
Combined, Forms 3, 4, and 5 describe a single QTL Experiment . A QTL Experiment is defined by QTL Mapping on a single Progeny Population. There may be multiple Progeny Populations used in a single manuscript. Thefore, Forms 3,4, and 5 may need to be filled out multiple times for each manuscript.
Brief descriptions of each form and a link to its prototype format are provided below. These are not active forms, they are simply ideas on how to organize QTL-related data.
From the MGD User point of view, one of the primary entry points
into the QTL data will be through the phenotype of the
complex trait. Additional entry points into QTL data will be similar to
those provided currently in MGD for genetic
mapping data . MGD users will have the option of generating or
retrieving a standard "QTL Report" .
Click HERE to see the prototype of Form 1.
This form includes the J# which links to the tables in MGD that contain the appropriate author and publication data.
1.1 jnum: J#, internal MGD publication tracking number
To confirm that the correct J# has been entered, a hypertext link to the MGD bibliography records could be provided here.
Click HERE to see the prototype of Form 2.
This form includes keyword information to identify the complex trait and information on the nature of the trait and how it was measured.
2.1 pheno_class: Phenotype Class , a controlled vocabulary for indicating the broad class to which a specific phenotype belongs. The categories represent the most common kinds of QTL studies and may be useful for narrowing searches for specific QTL papers
2.2 pheno_mode: Phenotype Mode , a controlled vocabulary for indicating how the phenotype of a complex trait is manifested.
2.2.1 induced_by: If the Phenotype Mode is "induced," a brief description of the method for inducing the trait can be entered.
2.3 pheno_name: Phenotype Name , a two to five word description of the complex trait phenotype
2.3.1 trait: Trait ,each Phenotype Name may be associated with multiple traits. For example, the complex phenotype under study may be "Multigenic Obesity" but this phenotype may be measured by observations on a number of specific traits such as body mass, blood cholesterol levels, etc. A phenotype does not necessarily have to have multiple traits associated with it
2.3.2 pheno_eval: Phenotype Evaluation , a semi-controlled vocabulary for how a trait is measured (qualitative, semi-quantitative, or quantitative)
2.4 alt_pheno: Alternative Phenotype Keyword , synonyms or other keywords associated with the complex trait. For example, a paper desribing "bronchial hyperresponsiveness" most likely would have the keyword "asthma" associated with it.
2.5 pheno_meth: Phenotype Method , this is where important information goes that doesn't fit into any of the categories above. If the
authors provide heritability information for the phenotype or any of the traits, this would be a good place to record that information for now.
Click HERE to see the prototype of Form 3.
This form needs to be filled out for each progeny pool used in a QTL Mapping experiment.
This form includes information about the progeny population used for a QTL experiment and how the progeny population was derived. Only one progeny population is allowed for each QTL Experiment, but each progeny population can be the result of multiple crosses.
Progeny Population
3.1 prog_gen: Progeny Generation ,indicates the generation of the progeny population (e.g., F2, N2, F6, etc.)
3.2 prog_nam: Progeny Name , if the progeny population is given a special or standard name, it can be entered here.
3.3 prog_num: Population Number , the number of animals evaluated for a particulary progeny pool or population.
Cross Data
3.4 fem_strain: Strain name for the female parent.
3.5 fem_type: Strain type for the female parent (eventually there will be a hyperlink directly to strain information based on the strain name).
3.6 fem_phen: Female Parent Phenotype , a short description of the phenotype of the female parent
3.7 male_strain: Strain name for the male parent .
3.8 male_type: Strain type for the male parent (eventually there will be a hyperlink directly to strain information based on strain name).
3.9 male_phen: Male Parent Phenotype , a short description of the phenotype of the male parent
3.10 cross_type: Cross Type , a controlled vocabulary that indicates the type of cross that generated the progeny pool for QTL mapping
Comments
3.11 comment: Comment , additional information regarding the cross.
An opportunity to enter data from multiple crosses for each progeny population will be provided as a single progeny could be the result of pooling progeny from more than one cross.
Click HERE to see the prototype of Form 4.
This form includes methodological information for genotyping, calculating linkages between markers and complex traits, and QTL mapping.
Marker Map Construction
4.1 genome_scan: Genome Scan , indicates if a genome scan was performed.
4.2 scan_meth: Genome Scan Method , a controlled vocabulary to indicate the method used for the genome scan.
4.3 chrom: Chromosome , if specific chromosomes were targetted for analysis and mapping, they are indicated here.
Genome Coverage
4.4 link_num: Number of Linkage Markers , the number of linkage markers used in an analysis.
4.5 mark_dist: Intermarker Distance , the average distance or range of distances between markers.
QTL Detection
4.6 link_meth: QTL Detection Method , a controlled vocabulary to indicate the method used to determine significant linkage between a trait and a specific marker.
4.7 sig_thresh: Significance Threshold , the threshold used to determine if an association between a marker and a trait was significant. This value usually will be P > 0.05 or P > 0.01.
QTL Estimation
4.8 qtl_meth: QTL Estimation Method , a controlled vocabulary to indicate the method used to determine the approximate location of a putative QTL relative to the markers used to detect the QTL.
Comments
4.9 qtl_comment: Comment , any comments on the methodology used for QTL detection and estimation that didn't fit into the predefined categories. Depending on the software package used for QTL analysis, the mode of action of a QTL can be "tested" by calculating lod scores assuming different kinds of models - uncontrained, dominant, recessive, additive. This kind of information is particularly important to record if it is discussed in the manuscript.
Software
4.10 qtl_comp: QTL Mapping Software , a controlled vocabulary to indicate the software used to determine linkage between genotype and phenotype.
Click HERE to see the prototype of Form 5.
This form needs to be filled out for each QTL marker in an experiment that is considered to be significantly associated with a complex phenotype trait. This form is the heart of the QTL data coding process and the QTL Report
This form includes information on the putative QTLs for each trait measured for a complex trait phenotype. The data represented includes (per QTL) the % of variation accounted for, the chromosomal location, the significance scores, and candidate genes in the QTL region. The information on candidate genes in the QTL region includes the information reported in the manuscript (legacy data) and links to the most recent mapping data for the QTL region (dynamic data).
Phenotype
5.1 trait: Trait, the complex phenotype trait associated with the QTL and marker.
QTL Detection
5.2 qtl_nam: QTL Symbol , the name of the hypothesized QT Locus.
5.3 qtl_mark: QTL Marker Symbol , the name of the marker with which a significant linkage with a QTL was determined.
5.4 phen_var: % Phenotypic Variance Accounted For , the maximum percentage of the total phenotypic variance int eh trait accounted for by the QTL.
5.5 QTL Detection Test, the QTL detection test method used.
5.5.1 QTL Detection Test Value, the value for the QTL detection for significant associations only.
5.5.2 p_val: P value , the P value for the significant test value in 5.5.1 if provided in the text.
5.6 QTL Effects, a series of checkboxes to indicate basic information on QTL effects.
QTL Location Estimation
5.7 chrom: Chromosome , the chromosome to which the QTL was mapped.
5.8 loc: QTL Location , the location of QTLs are imprecise and are described a number of different ways in the literature. Several alternatives for locational information are provided.
Candidate Genes
5.9 cangen_sym Candidate Gene Symbol , the approved gene symbol for the candidate genes mapped to the QTL region.
In the QTL Report, there will be an option to see the most recent list of genes to have been mapped to the putative QTL region. Eventually there might be a QTL Map Figure of some kind, too.
Click HERE to see the prototype of Form 6.
This form includes both a free text component for commenting on aspects of a QTL experiment that do not fit into the other forms AND a semi-controlled vocabulary of information that is commonly noted (but often not confirmed) in QTL studies.
6.1 phen_age: Phenotype:Age , a field to indicate if the expression of the phenotype is affected by age.
6.1.1 phen_sex: Phenotype:Sex , a field to indicate if expression of the phenotype is affected by sex.
6.1.2 phen_pat: Phenotype:Paternity , a field to indicate if there are paternal or maternal affects on expression of the trait.
6.2 trans_fx: Transgressive effects , a field to indicate if transgressive effects were noted.
6.3 mod_fx: Modifiers , a field to indicate if modifier loci were detected or hypothesized.
6.4 confirm: Confirmatory Analysis , a controlled vocabulary about confirmatory analyses performed to link a QTL to a specific gene. This included in the comment area because of the current dearth of confirmatory analyses in the literature.
6.5 comment: Comment , a free text comment field for additional information on the study.
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