Intergenomics on QTLs

Topic
Quantitative trait loci (QTL) mapping efforts have been performed independently for several species for the same traits. If the animal models are driven by the same genetic mechanisms as those for the human diseases, we should expect to find common conserved sequences shared by the QTLs and susceptibility regions of all three organisms. Genes present as homologues in the QTLs of all three species, arise as best candidates to be relevant for the onset and/or further development of the disease.

Data sources
A comprehensive QTL database for rodent EAE was created with data collected from the public databases of the NCBI, the Jackson Laboratory (MGI: Mouse Genomics Informatics) and the Rat Genome Database (RGD) of the Medical College of Wisconsin. The data were complemented with human MS predisposition loci and genes assembled both from public databases of the NCBI and recent large scale genetic linkage studies on MS (mainly: J Neuroimmnol vol 143/1-2).

Statistical methods
Consensuses may occur by chance with a certain probability. In order to determine that probability, here we test the performance of the intergenomics QTL synteny tool on randomly located QTLs of the same size as the original ones (Monte Carlo simulation). With an increasing number of iterations, the calculated distribution fits the real random distribution. That distribution yields the probability of finding by chance a certain number of genes in consensuses. Whenever the observed number of genes in consensuses is above the 95th percentile limit, it can be concluded that the observed number is reached or surpassed only five from hundred cases (i.e. p<0.05).

WARNING: Depending on the number and the size of the loci added to the system, the consensus search may take several hours to complete. However, the browser allows mostly to follow the process as it goes on (does not apply to some versions of Konqueror).

Input

  • Selection of species

    Select source species:
    Select intermediate species:
    Select target species:

    • source: Start of the synteny chain. Here you may select the first organism, whose QTLs will be checked for common syntenic regions with the target species or, alternatively, the intermediate species if set.

    • intermediate (optional): For a three-way synteny check (the only currently available is rat-mouse-human) you may select an intermediate species to be compared with the source and check their consensuses with the target species.

    • target: Chromosomal regions selected for the source species (two-way analysis), or eventually consensus regions between the source and the intermediate species (three-way analysis) are checked for further overlaps with syntenic regions in the target. Results are more detailed for the target species than for the intermediate species. They include all syntenic regions affected (dark orange), as well as the ones among them located within disease susceptibility regions / QTLs (red). The user is therefore encouraged to select as target the species you he/she is most interested in.

    The identification of consensus regions is performed sequentially. The described selection boxes cater for that sequence. Please remember that only the order rat -> mouse -> human is currently supported by EnsEMBL (Compara Database v.16). Alternatively you may want to compare only two species at a time. In this case you should set the selection for the intermediate species at "---none---" and choose source and target species at will. Combinations allowed are:
    • rat -> mouse -> human
    • mouse -> human
  • rat -> human
  • rat -> mouse
  • Metatrait

    Select Metatrait:

    Metatrait stands for a group of traits (e.g. delay of disease development, intensity of the symptoms, etc.) accounting for the same superordinated phenotype (e.g. multiple sclerosis). The animal experimental autoimmune encephalomyelitis (EAE) is a model for the human multiple sclerosis (MS) and therefore both are merged here into the metatrait EAE/MS for comparative analysis. Although intense work is being done for other metatraits/diseases, the only one which is public at the moment is the aforementioned one. Nevertheless, the user is invited to select "--other--" to insert his/her own data. Selecting this option has the effect that the submission text fields (see below), which are reserved for the data on QTLs and susceptibility loci, appear empty and allow the user to paste data inside at will (for instance control data for calibration).

  • Gap tolerance

    Gap tolerance:

    Neighbouring syntenic DNA fragments will be merged together whenever the DNA gap between them is smaller than the tolerated value that is selected here. Although increasing the gap tolerance results in a reduction of the computation time, it also may end in the identification of genes which are fully located inside those gaps, and thus possibly not syntenic at all. We recommend therefore the use of a gap tolerance of 10000 bp (10 Kbp) for a quick overview, and 1000 bp (1 Kbp) for a detailed analysis.

  • Average percentage of sequence identity

    Avg. id. Species 1 -> 2:
    Avg. id. Species 1+2 -> 3:

    The thresholds that decide when an average percentage of identity between two DNA segments is enough to be considered as syntenic can be set manually here. The threshold value for species 1 (e.g. rat) and 2 (e.g. mouse) is default 90%. In contrast, the threshold for those towards the target species (e.g. human) may be set separately (by default 60% since the genomic drift between human and rodents is obviously greater than within rodents).

  • Borders

    Fix borders on centroid

  • There are two ways implemented for setting the limits of a QTL / susceptibility locus. The first one fixes those borders on the corresponding centroid value (default). That value corresponds to the most probable physical position of the given genetic marker as calculated from the genetic position by CARTOGRAPHER (Voigt et al. 2004 Non-linear conversion between genetic and physical chromosomal distances. Bioinformatics, in press). The conversion was made with an outlier tolerance of 20% and a scrolling window size of 20 points. For those markers not listed in base pair position or, instead, the physical position when available in EnsEMBL. The second way is to extend the borders to the external confidence interval as provided by CARTOGRAPHER.

  • Table Details

    Show detailed table

  • This checkbox allows to switch between the full table display (see OUTPUT) and the compact display showing only the final results (quicker).

  • Submission text fields

    Positions for Rattus norvegicus:
    Positions for Mus musculus:
    Positions for Homo sapiens:

    Once the query is submitted with the input parameters adjusted to the user's requisites, two or three textareas will appear below depending on the number of species involved in the analysis. By default the data on EAE and MS will be loaded into these fields. However, if the user chooses the metatrait "--other--" the textareas will appear empty. Then he/she may paste own genetic linkage data n the corresponding textarea depending on the species and always according to the following format (TAB delimited):
    CHROMOSOME   START(in bps)   END(in bps)   NAME

    One may furthermore edit the data provided by default and modify or delete some of the chromosomal regions displayed, or insert additional ones. After modifying the textarea the refresh button should be pushed to actualize the table.

Output

Rattus_norvegicus QTLs

Homology in Mus_musculus

Homology in Homo_sapiens

Chr.Kbp StartKbp SizeNameChr.Kbp StartKbp SizeConsensus
Chr.Kbp StartKbp SizeConsensus
102580039200EAE311447940.544794-44794 (EAE6b)no match
102580039200EAE311448060.544806-44806 (EAE6b)no match
102580039200EAE311448201144820-44831 (EAE6b)
515882410
no match
102580039200EAE311448592544859-44884 (EAE6b)
51587809
no match
51588034
no match
51588290.5
no match
102580039200EAE311449083144908-44940 (EAE6b)
515868127
158681-158700 (IL12B)
51587300.5
no match
102580039200EAE31144952444952-44956 (EAE6b)no match
102580039200EAE3114498614444986-45131 (EAE6b)
5158478102
no match
515859343
no match
102580039200EAE311451419445141-45236 (EAE6b)
515837392
no match


The output is formatted as a large HTML table. The left column series (yellow) displays the chromosomal regions analyzed for the source species. The middle part (light orange) - if present - shows the chromosomal regions inside of QTLs of the intermediate species that are syntenic to the ones of the left column series (yellow). The right column series displays the chromosomal regions syntenic to the foregoing consensus regions between source and intermediate species (in case of three-way analysis) or syntenic to the source species (in case of two-way analysis) outside (dark orange) or inside (red) of the QTLs or susceptibility loci of the target species. The loci displayed all link to the EnsEMBL contigview in order to assist in further analyses.

Availability

Current scripts and databases used by QTL VIEW include:
    QTLVIEW web interface: the main script described above in this help page (requires PHP4, and an actual web browser)

    QTLVIEW randomizer: a less user friendly - but considerably quicker - version of the foregoing script running on the same QTLs and susceptibility loci, but randomized in position over the genome (requires PHP4)

    QTLVIEW randomizer batch to automatize the foregoing script (C-SHELL script; requires Unix/Linux)

    QTLVIEW random distribution analyzer to calculate the quantiles (requires PERL)

    DATABASE on EAE QTLs and MS susceptibility loci (as CSV file; requires an SQL-based database system)

    ENSEMBL DATABASES on the human, mouse and rat genome and their syntenic relationship
Important considerations:

The scripts and database available here are Open Source. This means they are license-free in use and distribution. However, the authorship should be indicated whenever the scripts/database are publicly used. The links and paths to the database in the PHP scripts and between the PHP scripts refer strictly to our local network architecture and should therefore be readjusted after a local installation (!). Developers are encouraged to feed back corrections and improvements, and any user is of course welcome to collaborate in debugging the software.

Authors

QTL View was created by Pablo Serrano-Fernández, Steffen Möller, Saleh M. Ibrahim, Hans-Jürgen Thiesen (Immunology, University of Rostock), Uwe K. Zettl (Neurology, University of Rostock), René Gödde and Jörg T. Epplen (Human Genetics, University of Bochum).

For technical help, comments or questions please contact Pablo Serrano-Fernández or Steffen Möller.

Back to the application, back to the qtl.pzr.uni-rostock.de