An User Guide to the QTLdb

A comprehensive tool set for QTL repository, comparisons, dynamic linking to comparative structural genome information for positional gene mining and more

  1. What are QTL?
  2. What is QTLdb? Are there any publications about it?
  3. What are the main distinctions between QTL and association mapping?
  4. What animal species are currently included in the QTLdb?
  5. What are "flanking markers" and what do they represent?
  6. What is Trait Ontology and how is it used in QTLdb?
  7. How are public QTL data curated into the QTLdb?
  8. Can I enter my QTL data into the QTLdb?
  9. What questions does the QTLdb attempt to address?
  10. What functionality does QTLdb offer?
  11. How to access the information in the QTLdb?
  12. What structural genomics information are aligned in the QTLdb and how to access them?
  13. Which trait(s) are found having more QTL?
  14. There are so many QTLs on a chromosome. Is there an easy way for me to narrow down the scope to the traits I am more interested? e.g. Can I view my selected sub-sets of traits?
  15. Are data within the QTLdb static?
  16. Are QTL_ID within the QTLdb stable?
  17. I wish to find a cytogenetic band region of interest for QTL, how can I do that?
  18. I wish to "zoom in" to examine a local region of my interested region, can I do it? how?
  19. Some chromosomes have awful lot of QTL that the chromosome view becomes a very wide picture (extends way out of computer screen to the right), making it hard to compare some alignments. Is there any way I can see a more manageable view?
  20. There are recently available genome sequences for cattle, chicken, and pigs. Has Animal QTLdb been made accessible to them?
  21. For genomic mining of a QTL region, we often need to align a QTL against its genome for underlining genes. Is it possible in the QTLdb?
  22. How accurate is the QTL location alignment to, say, transcript locations on the most recent genome assembly?
  23. Can I download the raw data from the QTLdb?
  24. I have downloaded some QTL data, and found many identical QTL (chromosome locations, traits, even publications. Is it possible that they are redundent curations?
  25. Are there any tools available that can help me to do some meta-analysis?
  26. What is an Animal QTLdb Release? What is involved in a release?
  27. What are Animal QTLdb data alliances?
  28. I have my data analysis on an older version of a genome assembly, is it possible to transfer QTL coordinates on the current assembly to the older assembly? How?
  29. Why sometimes I find QTL coordinates are not the same on your GBrowse / JBrowse and your web web site?
  30. Is there a better way to search QTLdb by multiple criteria for a literature without involving complicated multiple web form fields?
  31. Is there any license term on the QTLdb? (e.g. Open Data license or waiver)
  32. Terminology

  1. What are QTL?


    This graph is modified from the
    Rat GDB with kind permission

    Quantitative Trait Loci (QTL) are hypotheses that specific chromosomal regions contain genes that make a significant contribution to the expression of a complex trait. Hypothesed QTL are supported with, or generally identified by, analyzing or comparing the linkage (degree of co-variation) of polymorphic molecular markers and variation of phenotypic trait measurements. The methods to localize a QTL includes whole genome scan of linkage between genetic markers and phenotypes with specific family structure designed for such analysis, and assocition analysis of markers (e.g. SNPs) with certain traits (e.g. GWAS). Therefore as a matter of fact they are genomic mappings of traits. On this database site, they are interchangeably called "QTL", "QTL/(SNP)associations".

    The ultimate goal of complex trait dissection is to identify the actual genes involved in the trait and to understand the cellular roles and functions of these genes. Thus the purpose of the Animal QTLdb is to provide resources and tools for QTL regions of data mining, to facilitate the identification of such genes.

    The accuracy and precision of locating QTL depends, in part, on the density of the linkage map created. The higher the density of the map, the more precise the location of the putative QTL. When QTL can be mapped to a relatively small chromosomal region or regions other methods, such as positional cloning, can be used effectively to isolate specific genes. Unfortunately, the denser the map, the more likely that false positive QTL will be detected with linkage map based QTL methods. More precise mapping of traits are possible with newly available genome seuqnces and genome wide association analysis (GWAS).

    Most, but not all, complex traits are affectedned by more than one locus. QTL often interact in complex ways and their expression can also be influenced by non-genetic factors. Because QTL are hypotheses, they are subject to reinterpretation and revision. Because the location of QTL are provisional their nomenclature is likely to be fluid and temporary. (revised from Carol J. Bult)

  2. What is QTLdb? Are there any publications about it?

    QTLdb is an abbreviated name for "QTL Database", containing published QTL data organized into structured tables in a relational database, MySQL. The user and manager interface to the database takes advantage of world-wide web (WWW) and is programmed with perl/CGI.

    The active QTLdb development is a project carried out at the Iowa State University (see this note for its development history). The progress on the QTLdb development has been presented at the 13th North American Colloquium on Animal Cytogenetics & Gene Mapping (2003), Midwestern ADSA/ASAS Annual Meeting (2005), annual Plant and Animal Genome (PAG) conferences in 2005, 2006, 2007, 2008, 2009, and International Society for Animal Genetics (ISAG) in 2008. A number of papers by Hu et al. published on Mammalian Genome (2005, 2007), Nucleic Acids Research (2007, 2013 2016) and a full lecture paper published on the World Congress of Genetics Applied to Livestock Production (WCGALP, 2010) representing milestones in the course of the QTLdb development. See the publication notes for more details. The QTLdb has been listed by the NAR Database Collections, Neuroscience Lexicon, and others.

  3. What are the main distinctions between QTL and association mapping?

    The main differences between QTL and association mapping are: (1) the level of resolution (in terms of distance along the DNA or chromosome), and (2) the level of generality (in terms of the number of traits that can be studied with a given set of markers). (1) QTL analyses resolve the locations of genes (or gene clusters) influencing a trait down only to the level of chromosomal segments between one to 20 cM in size (roughly one million to 20 million base pairs). (Originally from http://www.panzea.org/info/faq.html)

  4. What animal species are currently included in the QTLdb?

    The Animal QTLdb is designed to house QTL results from multiple livestock species. The database was originally developed to house pig QTL (2005). Subsequently, QTL data from cattle and chicken were added (2006). From 2007 ro 2010, Jill Maddox's group started to curate sheep QTL into a copy of the Animal QTLdb installed at The University of Melbourne, Australia (It was migrated back to Iowa State University in 2010). Rainbow trout was added in 2011, horse was added in 2013, and Catfish was added in 2016, to the multiple species family served by the Animal QTLdb.

    QTL from other animal and aquaculture species will be added in the near future when possible. This is to serve our long term goal of assisting comparative QTL studies.

  5. What are "flanking markers" and what do they represent?

    There are different ways to determine a detected QTL is significant enough to be "real". Permutation test is one of those popular ones used by many people. According to Lander and Kruglyak (1995), a suggestive linkage is expected to occur one time at random in a genome scan and has an estimated minimum LOD score of 2.0; A significant linkage is expected to occur 0.05 times at random in a genome scan and has an estimated minimum LOD score of 3.4 (in real life the "cut-off" LOD scores may vary depend on actual permutation tests). Therefore, in an ideal situation, a QTL may be peaked by one marker and flanked by 2 pairs of markers (see Figure).

    In the QTLdb we try to use flanking markers A1, A2, B1, B2 when they are available.

  6. What is Trait Ontology and how is it used in QTLdb?

    Livestock production traits are sets of animal phenotypes described for their nature, quality, quantity and biological stage. Due to differences in methods of detection or measurement, scope of description and/or customs, a trait may be described in several different ways. In order to compare QTL discovered by different labs with different methods, we have to make a "standard" way of trait description in order to correctly compare them. To solve this problem, we introduced "Trait Ontology" to classify and organize the traits for management with database.

    Ontology is a classification methodology that defines a common vocabulary in a structured way for useful information sharing. Animal production traits may be classified in many different ways based on their functions, features, property, etc. One most useful construct of the trait ontology is that the animal traits may be classified by how they are measured as commercial products. In the QTLdb, we use three levels of controlled vocabulary to describe each production trait: Trait Class, Trait Type and Trait itself. For their definitions, see FAQ #129 "Terminology" below.

    The classification of traits helps to share common understanding of information structure among people or software agents.

  7. How are public QTL data curated into the QTLdb?

    Following are extracted from each publication: Experimental design, Population structure and design, Testing Model and Methods, Trait names on which significant QTL are detected, Trait Description and Measurements; QTL location (Chromosome, Position, 95% CI on the Location), Flanking markers (A1, A2, B1, B2 and the Peak; see Figure for FAQ #5), Test Statistics (LOD_score, LS_means, P_values, F_values, Variance), QTL effects (Dominance effect, Additive effect), Candidate genes, etc., when available. Publication title, authors, journal and abstracts are also included.

    Take pig data as an example, the QTLdb uses the USDA-MARC pig linkage map (MARC-Map) as a map reference to show relative locations of each QTL, as the MARC map is the single largest pig map to date, and its markers are used by most QTL studies for genome / chromosome scan. When a non-MARC-Map marker is used to describe a QTL, the actual marker location in the experimental map is interpolated to the MARC map and the interpolated map locations are stored in the QTLdb.

    The flanking or underlining markers on the QTL map are linked to the NCBI Gene DB.

  8. Can I enter my QTL data into the QTLdb?

    Yes. The Animal QTLdb is open to public for data entry and update. One must apply to be a curator in order to do so. Being a curator, you will be able to

    • keep your data private
    • update your data any time
    • view your data either aligned to its chromosome or along with other public data
    • release your data to public access once you decide so
    • withdraw your data for any problem found
    • all released public data will be populated to NCBI database automatically
    By submitting your data to the QTLdb, your data set will join the other QTL data set published in the past 10+ years, and subject to within and cross species comparisons. See paper by Hu et al. ("Animal QTLdb: Beyond a Repository - A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome, Volume 18, 1-4 (2007) for more details).

  9. What questions does the QTLdb attempt to address?

    The following questions were the initially projected to address:

    • What is the chromosomal location for a QTL? Can multiple QTL be viewed in a "synthetic" manner?
    • Is it possible that QTL from different studies be easily compared for their locations?
    • Can all markers underlining a QTL be shown and marker information easily retrievable?
    • What are the significance values for each QTL, with what method for detection?
    • Have any other phenotypic traits been mapped to the chromosome segment that my QTL appears to fall into or is part of it?
    • What percentage of phenotypic variation is associated with each QTL? Is the effect dominant or additive?
    • How is the possibility that markers flanking a QTL may be matched to sequences in a public dtabase for data mining or annontation?

    As we build up the QTLdb, we find that the utility of the QTLdb can extend beyond what we originally anticipated. Efforts are continually made to add more functionality to the utility of the QTLdb.

  10. What functionality does QTLdb offer?

    The animal QTLdb offer a number of functions for user to easily retrieve, compare and synthesize QTL information.

    By searching or browsing the QTLdb, one can

    1. Find all QTL on one chromosome
    2. Find all chromosomes that bear QTL for the same trait
    3. List all QTL from a particular publication
    4. Find all markers underlining a QTL
    5. Find DNA sequences associated with certain markers
    6. Use GeneDB to further search for candidate genes by comparative maps
    7. Find experiment details in brief for a given publication
    8. Find all parameters describing a QTL, as well as test statistics
    9. Find all associated genome features (SNP, BAC, Genes, Transcripts, etc. - available since 2006).
    10. Meta analysis of QTL for a single trait on a chromosome (available since 2010).
    11. ... more to come as we are continuously developing the QTLdb tools.

    The Figure on the right shows an example of multiple QTL identified by different studies map to pig chromosome 3. With further details, a user can synthesize a picture of his own on the most promising chromosomal region where best candidate gene for a trait may reside.

  11. How to access the information in the QTLdb?

    The QTLdb web interface is designed to be easily accessed by search and browse. Each searched or browsed resulting information is again dynamically linked for further search or browse. In this way users can quickly find information from the QTLdb with multi-directional information traverse. The following paths seem daunting to read but each is at only a couple mouse-clicks away:

    • Draw Single Trait QTL on Multiple Chromosomes
      Go to Search page, input a keyword Click "GO" Click on your trait Click on "Find all QTLs"
    • Draw Multiple QTL on Single Chromosome
      Go to the Browse page Click on your chromosome
    • List all QTL from a particular publication
      Go to Search page, input a keyword Click "GO" Click on "List QTLs"
    • Find a pig QTL in NCBI Gene Database
      Search or browse to a QTL map Click on a QTL symbol Clink on "GeneDB"
    • Find DNA sequences associated with certain markers
      Search or browse to a QTL map Click on a marker name Click on "UniSTS" link above the marker name Click on "GenBank Accession" link
    • Find experiment/ publication details that produced a QTL
      Search or browse to a QTL map Click on a QTL symbol Experiment detail in brief is in upper right box Publication detail is in the lower right box
    • Find all locations that QTL for a trait may have been mapped to
      Search or browse to a QTL map Click on a QTL symbol Click on "Trait Name" Click on "Find all QTL on this trait"
    • Find related traits from a known QTL trait
      Search or browse to a QTL map Click on a QTL symbol Click on a "Trait Name", or "Trait Type", or "Trait Class" Choose from returned trait ontology list other traits to search further
  12. What structural genomics information are aligned in the QTLdb and how to access them?

    Thanks to many collaborators who provided a number of useful structural genomics information for aligning to the QTL maps (Acknowledgement are on each respective web pages). These data includes radiation hybrid (RH) maps, BAC clone finger printed contig (FPC) maps, SNP maps, consensus linkage maps, genome maps, etc. For example, 6,500+ cattle SNPs and 1,300+ pig SNPs were aligned to respective QTL maps via RH to human comparative maps. 4,528 new porcine microsatellites from the Sino-Danish Pig Genome Sequencing Consortium were aligned to the pig QTL maps (see following table for a summary).

    Table 1. Data alignment status summary
    SpeciesGenome mapRH mapBAC FPCSNPsMicroarray ElementsHuman map
    AffyOligo
    Pigs
    Cattle
    ChickenplannedplannedPlannedplanned
    Horse-----
    Sheep----
    Rainbow trout-------

    (With reference to paper by Hu et al., "Animal QTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35 [Database issue]: D604-D609.). Note: With added function of GBrowse that we implemented in October 2008, QTL alignments to more genome feature are available. See FAQ #18 for more details.

    All aligned data can be accessed via either pop-up links or web forms on the "chromosome view" page of the QTLdb (see Figure below). Users can bring a QTL region (or interested map locations) across the aligned maps to serve the purpose of data mining, by using either the QTL bars or the web forms where map locations in cM must be provided.

    Please be aware that more data types are continually being added, and data updates are actively going on. Don't be surprised if you see things new.

  13. Which trait(s) are found having more QTLs?

    Backfat, Loin-eye area and Meat Color-L are the top three pig traits having highest number of QTL reported. Body weight in chicken has a dominant number of more QTL than other traits. Fat yield, milk yield and twinning are the three top cattle traits that QTL are measured for. For more, see respective species QTL database "summary" for details.

  14. There are so many QTLs on a chromosome. Is there an easy way for me to narrow down the scope to the traits I am more interested? e.g. Can I view my selected sub-sets of traits?

    Yes. There are two added features on the chromosome view of the QTLdb for you to easily view your interested traits: (1) all traits found on a chromosome are listed in a new pull-down menu below the chromosome graph, from which you can click to select the trait you wish to see; (2) all trait name first initials are also listed at the same spot, with which you can simply clisk the initials to see all traits started with that initial.

    On the top of the chromosome view screen, there is a "Search for QTL" search box. Within this search box, you can put in multiple trait symbols, delimited by a sapce, to get them all at once to a chromsome view. Note that wild card (*) are allowed for partial non-specific matches.

  15. Are data within QTLdb static?

    No. The Animal QTLdb as an online database tool being kept up-to-date with most current data curated from various resources in public domain. Since its first release in June 2004, release have been made as of . There are more than just new data additions in each release. For details, see #26 "What's involved in a release", and Animal QTLdb Releases History.

    If you see any new data that has not been included in the QTLdb, please drop us a note with the source of the publication - we will curate it into the database as soon as we can get around. Or better yet, you can register to become a QTL data curator for the QTLdb yourself. In this way you can enter your data, update your data, and also use the curator tools as a research platform (see below).

  16. Are QTL_ID within the QTLdb stable?

    Yes. A QTL_ID is assigned as a unique identifier when a QTL is entered into the database. Once the QTL is entered, the ID becomes permanent. i.e. Even if the QTL is deleted, modified, or becomes obsolete, the ID cannot be re-used.

    When the QTL data is synchronized to NCBI GeneDB, NCBI assigns each QTL a Gene ID, which is also permanent. The QTL_ID record goes along with the Gene ID, and displayed as: Primary source - AnimalQTLdb:#### (QTL_ID). For deleted QTL data, NCBI site will show "DISCONTINUED: This record was withdrawn by the AnimalQTLdb".

  17. I wish to find a cytogenetic band region of interest for QTL, how can I do that?

    The QTLdb is based on linkage maps. Before we may add the cyto-genetic band alignments to the linkage maps within the QTLdb, users have to make that alignment with other tools, such as the Arkdb (http://www.thearkdb.org/anubis), i.e. translate your cytogenetic band locations into linkage map locations, and then come to use the QTLdb to look for QTLs. In the Arkdb, you wish to build a within-species comparative map between the "Cytogenetic" map and the "USDA-MARC_v.2" map on the same chromosome. (see updates below)

    We have added cyto-genetic G-band chromosome drawings to the QTL maps for cattle, chicken, pigs and sheep as of November 16, 2010. The cyto-genetic chromosome maps and linkage maps are aligned side by side, so that you can visually find cytogenetic band locations where your interested QTL is likely to land. Please note that the alignment is scaled to fit the chromosome length, therefore the band to cM/bp locations are only approximate. Use your best visual judement plus more evidences if there are any, to assist you when it comes to fine localizations.

  18. I wish to "zoom in" to examine a local region of my interested region, can I do that? how?

    The QTL map does not have an intuitive "zooming" feature but offer users to choose the size of the map to view. The size options are listed by a pull-down menu selection on the top tool bar. On a "very large" scale, users can see all details of the map at highest marker densities.

    Also, combining the use of "Marker density" pull-down menu, you can see more markers in a larger picture, to achieve the "zooming" effects.

  19. Some chromosomes have awful lot of QTL that the chromosome view becomes a very wide picture (extends way out of computer screen to the right), making it hard to compare some alignments. Is there any way I can see a more manageable view?

    On the "chromosome view" of the QTL, there is a "Display QTL" search box in the top tool menu. If you type the QTL abbreviations of your interests and click on "Go", the database will return you a new chromosome view with the QTL of your choice only, making it more effective for you to make comparisons.

  20. There are recently available genome sequences for cattle, chicken, and pigs. Has Animal QTLdb been made accessible to them? Which genome build version are used?

    Yes. We have built in a function to convert (see FAQ #22) all QTL locations (cM) on the linkage maps to genome maps (Mbp), thus made it possible to align all QTL on respective genomes on their most recent genome builds.

  21. For genomic mining of a QTL region, we often need to align a QTL against its genome for underlining genes. Is it possible in the QTLdb?

    Yes it is possible.

    Previously, we aligned some genomics features such as SNPs, microarray elements, microsatellites and RH map markers against QTL in terms of their genomics locations, within the QTLdb. (Reference to FAQ #12)

    In October 2008, we have implemented GBrowse for QTL alignments against multiple genomic features. Now we are able to align the QTL locations against all genome features stored in Genbank, such as locations of transcripts, mRNA, CDS, Annotated Repeats, etc. We also customly add more elements for alignment. The most recent addition to the alignments is the 60K SNP chip elements for cattle and pig.

    The link to Gbrowse view can be found in the Animal QTLdb main pages for respective QTLdb species, and at the GBrowse directory page: http://www.animalgenome.org/gbrowse/.

    If you have your own set of genes and wish to see what QTL/association is/are aligned them, as long as you have their genome coordinates of your gene, you can do so:

    (1) Create a GFF file with your own data, in a tab delimited 9-column plain text file, as in:

    Chr.4  Source  FeatureName  106510877  125474284   .   .   .   my_ID=49;Name="FUS1"
    Chr.4  Source  FeatureName  107478402  107478893   .   .   .   my_ID=51;Name="FUS2"
    .....  ......  ...........  .........  .........   .   .   .   ....................
    (2) Click Add your own tracks towards the bottom of your GBrowse page to upload the GFF file you just made, to the GBrowse window where you may already browsed to a chromosome or a genome region of interests. In case the window is not refreshed, click Update Image to refresh.

  22. How accurate is the QTL location alignment to, say, transcript locations on the most recent genome assembly?

    The alignment of genome locations of QTL against that of transcripts or genes is accomplished by converting the linkage map QTL locations (cM) to its genome locations (bp) on the most recent assembly build (the updated genome build version used in the QTLdb can be found here). This is accomplished with references to available anchoring markers mapped on both (linkage and genome) maps.

    Often, a QTL boundary may not located exactly by an anchor marker. In such cases, the relative genome location of the QTL is estimated with an algorithm taking into account of the distance between the marker and the QTL boundary, the chromosome lengths of the linkage and genome maps, relative cM versis bp unit ratio for that particular chromosome, to calculate the offset of the QTL location relative to that of the anchor marker (interpolate). As such, the "bp" location of a QTL from its "cM" location is only a rough approximation. In addition, the sizes of QTL is often on the scale of centiMorgans ("cM"), which translate into genome maps in terms of a few hundred kelo- or mega-base pairs. Therefore large error sizes may be expected on such interpolation. On the other hand, the error ranges of original QTL reports are already on scale of "cM", we consider the current "bp" conversion pretty close to their "real" locations, and provide useful land marks for structural genome mining.

    While we caution users about the accuracy of exact "bp" locations found on the GBrowse or the downloaded data, we encourage users to re-estimate the QTL "bp" map locations, when possible, with their own methods/data. Nonetheless, it would be relatively safe to consider it a range instead of exact "bp" locations.

  23. Can I download the raw data from the QTLdb?

    Yes. Functions have been implemented so that there are multiple ways for you to download data from the QTLdb. (1) Links for downloading QTL coordinates (in cM or in bp) within a species can be found on respective species main pages of the QTLdb; (2) QTL coordinates and related data within a chromosome can be downloaded from the chromosomal view of a species; (3) Subsets of QTL data on a chromosome can be downloaded when term searches are applied to limited the view of QTL to that of your interests.

    Several file formats are available for the downloads: (1) Tab delimited plain text file containing QTL chromosomal locations in cM; (2) GFF files in which the QTL locations are in bp. The GFF download allows you to use the downloaded data file directly with other tools that take GFF file as input.

    The ways to download QTLdb data are updated on a data download page.

  24. I have downloaded some QTL data, and found many identical QTL (chromosome locations, traits, even publications. Is it possible that they are redundent curations?

    You may want to realize that the downloaded QTL data are only a snap shot of the data stored in the QTLdb. It depends on how you look at the data -- in some sense certain information may be "missing" if you scrutinize the data in a context that require extended information. For example, when you see two QTL that starts and ends on exact the same locations, your first impression might be that they are the same. It can be confusion in downloaded data sets since not all (comments and other loosely related) information are included, in a GFF download file. Verification of the data with the QTLdb online tools may be necessary. A useful way to verify if they are really "redundent" to compare them for all parameters, e.g. experiment methods, analysis methods, test statistics, flanking markers, etc.

    • Were they published in the same paper? -- Sometimes the same author(s) may analyze their data set with different methods, or re-analyzed their data with new data additions, and publish the results in a subsequent paper. It is likely the new results may resemble the previous ones.
    • Are their peak locations also the same? Are the peak/flanking markers also the same? (This would be an immediate indication that they are from different tests/analysis).
    • Are they for the same trait? Any trait variations on respective reports? -- Please note that there are many trait variations, e.g. ADG during gestation and ADG in feedlot; Fat content measured in loin and measured in ham; etc. In the QTLdb, "similar" QTL representations may all follow a "super trait" name for categorized comparisons (see FAQ #129 "Terminology" for more details).
    Cases exist where the same set of experiment data were analyzed with two different statistical methods, each was flaged with their significant p-values. In this case the information was only noted in "Comments" of a curation (found in QTL details).

    It is practically useful if you bring two suspecious QTL into respective QTL detail views for a side-by-side comparison. (Hint: formulate your URL to view details directly without having to go through browsing the web layers, i.e. put those two parts together:
    " http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID= " + " QTL_ID ", leaving no space, as in " http://www.animalgenome.org/cgi-bin/QTLdb/BT/qdetails?QTL_ID=4415 ".

    Feel free to contact us if you cannot resolve your confusions.

  25. Are there any tools available that can help me to do some meta-analysis?

    Yes, we have recently (October, 2010) developed a set of QTL meta-plot tools to help users performing simple meta-analysis on the fly. To use the tool, briefly, users will first need to select/browse to a species/chromosome of interest, then search for a trait or QTL to examine. When only the QTL for a single trait are displayed, a "Show MetaPlot" link appears (in the lower portion of a QTLdb chromosome view). When this link is clicked, the meta-plots will be displayed to the right of the QTL graphs on the QTLdb chromosome view. See this tutorial for more details.

  26. What is an Animal QTLdb Release? What is involved in a release?

    A "Release" of the Animal QTLdb is a process in which the new updates of the database on it's content (data), functions (database tools), and utilities (improved user accessibility to data and data analysis) are made available. Each release usually comes with a description of what's new on the release (see Releases History for examples). Upon each release, updated information are proliferated to the following sites in 5-10 days:

  27. What are Animal QTLdb data alliances?

    An Animal QTLdb Data Alliance is a genomics database partner with which we share data and make user experiences exploring these at each site seamlessly. Our current data alliances include: NCBI Entrez GeneDB, Ensembl, Reuters Data Center, and UCSC. Newly released QTL/association data are exported to them timely. Users can fully explore the power of their great tools for QTL and association data mining or exploration in the context of genome features.

    User contributed
  28. I have my data analysis on an older version of a genome assembly, is it possible to transfer QTL coordinates on the current assembly to the older assembly? How?

    Yes. While you may device your own ways to map genome coordinates of your interests from one genome assembly version to another, there are tools to help you to do so. These tools include but not limited to, UCSC liftOver, NCBI Remap, Ensembl API, CrossMap, among others. Sometimes, the flanking QTL genome coordinate pairs may not work out nicely with some tools. A trick used by Shangang Jia was to use only one side flanking location of a QTL to try out the LiftOver. You may like to repeat the same procedure in a separate run with flanking location of the other site, then assemble the results.

  29. Why sometimes I find QTL coordinates are not the same on your GBrowse / JBrowse and your web web site?

    We realize that while we commit our diligent works to keep the QTL data current and updated we should also keep users informaed of possible gaps from the steps how we update our data.

    The discrepancies you observe are most likely from our updates procedures in which the estimated genome coordinates are maintained (e.g. estimated bp from cM locations is subsequently corrected by actual SNP map coordinates when a SNP is present.)

    We do also realize there are time gaps between our data updates on the QTLdb, data download sites, GBrowse, and JBrowse sites, although we try to keep the gaps minimum as possible. A general advice is that the online Animal QTLdb web site reflects the most current data updates, i.e. data on other sites are propergated from here.

  30. Is there a better way to search QTLdb by multiple criteria for a literature without involving complicated multiple web form fields?

    Yes it is possible. The "publication search" within the QTLdb take a formaulated search string that includes several lines of information. For instance, in this example:

    title:Carcass; authors:Casas; year<2003

    Multiple criteria search string may be separated by semi-colon (";"), and each criteria is led with a key word separated from the search string with a colon (":"). Supported key words include 'author', 'title', 'journal', 'abstract', 'text', 'institute', 'affiliation' (actually only the first 4 letters should be sufficient). The only exception is "year", which can be in the form like: "year<1999", "year=1999", or "year>1999".

  31. Is there any license term on the QTLdb? (e.g. Open Data license or waiver)

    The data is made freely available for anyone to use as they want. For example, NCBI, UCSC, Ensembl and Thompson Reuters ingest the database and make it available via their sites. We have left it up to the user as to what they want to do with the data.

    We generally ask folks to cite on the publications that we have on the site.

  32. Terminology

    • Clinical Measurement Ontology (CMO) - is designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.
    • Flanking markers - Genetic markers that boundary either sides of a hypothesized QTL. A flanking marker can also represent the level of statistical significance when the QTL is detected. ( see FAQ #5 above for more details )
    • LocusLink - LocusLink organizes information around genes to generate a central hub for accessing gene-specific information for multiple species. It provides a single query interface to curated sequence and descriptive information about genetic loci and presents information on official nomenclature, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related web sites .(LocusLink DB has been phased out, replaced with "Gene"DB at the NCBI in 2005 and re-established data shared with Animal QTLdb in 2009)
    • Livestock Product Trait Ontology (LPT) - is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit.
    • Quantitative Trait Loci - Genetic loci contributing to quantitative traits variations. ( see FAQ #1 above for more info.)
    • Statistics test parameters
      • Posterior Probability Inclusion (PPI) - The proportion of samples in which at least one SNP from a given window was included in the model with a non-zero effect, is used for significance test in pleiotropy tests (Garrick DJ, Fernando RL, "Implementing a QTL detection study (GWAS) using genomic prediction methodology". Methods Mol Biol. 2013;1019:275-98).
      • iHS - Signature of Selection test: Log ratio between two integrated haplotype homozygosity scores
      • CLR - Signature of Selection test: Multilocus composite likelihood ratio test.
      • XPCLR - Signature of Selection test: Cross-population composite Likelihood ratio test (multilocus allele frequency differentiation between two populations).
      • EHH - Signature of Selection test: Extended haplotype homozygosity
      • XPEHH - Signature of Selection test: Cross-population extended haplotype homozygosity
      • Fst - Fixation index (FST) is a measure of population differentiation due to genetic structure. It is frequently estimated from genetic polymorphism data, such as single-nucleotide polymorphisms (SNP) or microsatellites. Developed as a special case of Wright's F-statistics, it is one of the most commonly used statistics in population genetics.
    • Suggestive linkage - ( see FAQ #5 above )
    • Significant linkage - ( see FAQ #5 above )
    • Trait Ontology - ( see FAQ #6 above )
    • Trait Class - Category of traits that describes one aspect of the pork product or process in which the product is made. e.g. Meat Quality.
    • Trait Name - A defined name for traits by the measurement locations, time, methods and measuring units. e.g. 24hr post mortem pH. Each trait is distinguished by its characteristics, methods of measurement, and product merit.
    • Trait Type / SuperTrait - It describes a specified property of the pork products or feature(s) that can influence the process in which pork product is made, a general physical or chemical property of, or the processes that lead to, or types of measurements that result in, an observation. In general, it refers to a trait by concept, regardless possible naming variations by measuring times, locations or methods ("trait modifiers"). e.g. Meat Color.
    • Vertebrate Trait Ontology (VT) - is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

First draft: January 5, 2005
Version 2: August, 12, 2006
Version 3: January, 11, 2007
Version 4: May, 17, 2007
Version 5: January, 6, 2009
Version 6: March, 23, 2010
Version 7: December, 29, 2010
Version 8: December, 11, 2011
Version 9: November, 20, 2012
Version 10: September 2, 2013
Version 11: December 12, 2016

Last update: April 26 2017 19:04:56.

By Zhiliang Hu
Associate Scientist
Dept of Animal Science
Iowa State University

Web Access Statistics © 2003-2017 NAGRP - Bioinformatics Coordination Program.
Contact: NAGRP Bioinformatics Team
Helpdesk