Intergenomics on QTLs

Input

• Workflow
  
  
  The user introduces the search constraints (search flow, search type, etc.) in the web-interface (SSI). A provisional data set is generated querying the local or the EnsEMBL database, depending on the choice of the user. If the user chose to use his/her own data, the provisional data set is empty. That provisional data set may be furthermore modified (reduced, extended, changed) and finally submitted. For a search based on synteny, the source species (* only one is required, but a multiple selection is also possible) and the target species are analyzed for syntenic genes shared by their QTLs/SLs. If the search is based on homology, the species are analogously analyzed for homologous genes shared by their QTLs/SLs. The final list is then displayed in detail or as a summary and refers to the target species. The result may then be sent for validation to a second interface (see chapter "Validation", below).

• Search flow
  
  

  Select source species: Rattus norvegicus Mus musculus

  Select target species: Homo sapiens Mus musculus

  
  
  • source: Start of the synteny/homology chain. Here you may select the organisms, whose QTLs will be checked jointly for common syntenic regions / homologous genes with the target species. (For a multiple selection, please keep the Ctrl-key pressed while selecting)
  
  
  • target: Chromosomal regions selected for one source species (two-way analysis), or eventually consensus regions between two source species (three-way analysis) are checked for further overlaps with syntenic regions or homologous genes in the target. For the case of synteny-based search, 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 he/she is most interested in.
  
  
• Search type
  
  Homology Synteny
  
  The search for consensus genes may be based on sequence comparisons of syntenic blocks or based on pair-wise gene homology. Both search types are complementary. A search based on synteny will be able to detect similarities beyond the coding regions, and will match genetic regions regardless of the gene functionality behind them. The search based on gene homology is not limited to syntenic blocks, and may affect gene homologues clearly outside of such blocks and - in contrast to synteny - is not affected by a threshold degree of similarity. Thus the performances with one and the other search method are very similar but always slightly different. Some genes are detected only by means of synteny and viceversa. The benefits of this slight discordance have been explained in a practical case by Serrano-Fernandez et al. (Genes and Immunity, in press). Both search types are based on EnsEMBL
  
  
• 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. This option is only valid for a search based on synteny.
  
  
• 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). This option is only valid for a search based on synteny.
  
  
• 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. This option is only valid for a search based on synteny.


• 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). This option is only valid for a search based on synteny.


• Metatrait selection
  
  

  Metatraits for Rattus_norvegicus    Consider whole genome    Custom Local database for EnsEMBL release 16 MS-EAERA-CIA EnsEMBL acute phase responseaia severityalcohol preferenceanxiety/emotionality related behavioratps induced immunological disorderblood glucoseblood pressureblood pressure fhbody weightbody weight gkcardiac mass indexcarrageean induced inflammationcataract iharachronic pancreatitis and diabetes mellituscia autoantibodycia severitycompensatory renal growthconditioned taste aversiondiabetes mellitus oletfeae severityestrogen dependent pituitary massexperimental encephalomyelitisgastric cancer resistancegastric cancer susceptibilityglucose intolerance stdhepatic copper contenthepatocarcinoma resistancehepatocarcinoma susceptibilityhypercalciuriahypoxia induced right ventricular hypertrophyinfertility severityinsulin dependent diabetes mellitusinsulin resistanceleft ventricular atrial natriuretic factorleft ventricular massliver neoplastic nodule remodelingmammary carcinoma susceptibilitymean arterial pressuremotor activitynon insulin dependent diabetesnon insulin dependent diabetes mellitusnon insulin dependent diabetes mellitus gkobesityoil induced arthritispancreas inflammationpia severityplasma insulin levelpristane induced arthritisproteinuriarenal damage susceptibilityrenal disease susceptibilityresistance to tongue carcinomassaccharin preferencescwia severitysensitivity to strokeserum aldosterone levelserum cholesterol levelserum phospholipid levelserum proteinserum triglyceride level blood pressure /cardiac mass blood pressure /heart weightsusceptibility to tongue carcinomast lymphoma susceptibilitythermal response to stressthymus enlargement 1thymus enlargement 2tongue squamous cell carcinomatotal cholesteroltriglyceride leveltype ii collagen induced arthritisvascular elastic tissue fragilityx ray hypersensitivity

  Metatraits for Mus_musculus    Consider whole genome    Custom Local database for EnsEMBL release 16 MS-EAERA-CIA EnsEMBL --- no data available ----

  Metatraits for Homo_sapiens    Consider whole genome    Custom Local database for EnsEMBL release 16 MS-EAERA-CIA EnsEMBL --- no data available ----

  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 insert his/her own data (option "custom"). 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). The option "Whole Genome" is only available for the target species and refers to an alternative usage of this software. It would check for all syntenic or homologous genes with respect to the ones in QTLs/SLs of the source species. This prospective approach is thought to be a help when searching for new SLs/QTLs in the target species.
  
  
• Submission text fields
  
  

  Positions for Rattus norvegicus: 10 25800000 65000000 EAE3 10 91900000 100110000 EAE12 12 28000000 36700000 EAE13 18 0 76800000 EAEZ 18 34000000 48500000 EAEY 19 29900000 43800000 EAE8 20 5100000 8500000 EAE1 4 19900000 43200000 EAE2 4 41000000 43200000 EAE11 5 64800000 97400000 EAEX

  Positions for Mus musculus: 10 0 29100000 EAE17 10 11000000 26100000 EAE15 11 0 78200000 EAE7 11 2600000 22200000 EAE6a 11 40900000 52600000 EAE6b 11 59200000 76500000 EAE23 11 85700000 115300000 EAE22 12 10000000 62100000 EAE16 13 56700000 64900000 EAE13 15 0 20900000 EAE2 16 0 31900000 EAE11 17 32550000 37120000 EAE1 17 33810000 33820000 EAE 17 39800000 42600000 EAE5 18 63700000 83000000 EAE25 19 33500000 52100000 EAE19 2 0 176000000 EAE8 2 49600000 124100000 EAE21 3 0 93700000 EAE3 3 16200000 46000000 EAE20 3 130500000 151300000 EAE10 7 17000000 28100000 EAE12 7 45300000 94300000 EAE4 7 98500000 106100000 EAE26 8 23100000 38700000 EAE24 8 23100000 68500000 EAE14 9 0 49600000 EAE9

  Positions for Homo sapiens: 1 2056000 4056000 D1S2781 D1S2781 1 3475000 5475000 D1S2660 D1S2660 1 12147000 14147000 D1S1597 D1S1597 1 20069000 22599500 D1S478 D1S478 1 20900000 22900000 GGAA30B06 GGAA30B06 1 38780000 40780000 MYCL1 MYCL1 1 45303500 47303500 D1S2797 D1S2797 1 47605000 49605000 D1S2724 D1S2724 1 58328500 60328500 D1S2770 D1S2770 1 61200000 63200000 D1S230 D1S230 1 66892000 66900000 ATA52G05 ATA52G05 1 72599000 74599000 D1S1665 D1S1665 1 75915000 77915000 D1S532 D1S532 1 90025600 92025600 D1S435 D1S435 1 94417700 96417700 D1S2664 D1S2664 1 104015000 106015000 D1S1631 D1S1631 1 109177500 111177500 D1S457 D1S457 1 153536000 155536000 D1S394 D1S394 1 153536000 157855800 D1S394 D1S394 1 155855800 157855800 D1S398 D1S398 1 183789400 185789400 D1S518 D1S518 1 191545000 196900000 D1S2794 D1S2794 1 192939000 194939000 D1S2816 D1S2816 1 199577000 202742000 D1S2760 D1S2760 1 200146700 202146700 D1S1725 D1S1725 1 205686000 207686000 D1S245 D1S245 1 222184000 224487500 D1S479 D1S479 1 239044000 241044000 D1S1590 D1S1590 10 3363000 5363000 D10S591 D10S591 10 6200000 9216000 D10S1751 D10S1751 10 17600000 19600000 D10S1423 D10S1423 10 28418500 30418500 D10S1214 D10S1214 10 29499800 33261000 D10S1426 D10S1426 10 31000000 33000000 D10S199 D10S199 10 42410000 44410000 D10S1669 D10S1669 10 53550000 55550000 D10S1790 D10S1790 10 68394000 70394000 D10S210 D10S210 10 70740000 72824000 D10S537 D10S537 10 86511000 88511000 D10S1769 D10S1769 10 88094700 90094700 D10S579 D10S579 10 91077500 93077500 D10S1753 D10S1753 10 1190109500 1192109500 D10S1693 D10S1693 11 0 2000000 D11S922 D11S922 11 928000 2928000 D11S4046 D11S4046 11 9542500 11542500 D11S4465 D11S4465 11 32329000 34823000 D11S4101 D11S4101 11 33604500 35604500 D11S1392 D11S1392 11 53965000 55965000 D11S1920 D11S1920 11 59554000 61554000 D11S1765 D11S1765 11 68388500 70388500 D11S4136 D11S4136 11 72402000 74402000 D11S4207 D11S4207 11 78691700 80691700 D11S2002 D11S2002 11 93571800 95571800 D11S1333 D11S1333 11 95387000 98763000 D11S1366 D11S1366 11 99594000 101594000 D11S898 D11S898 11 109761000 111761000 D11S1986 D11S1986 11 109761000 111761000 D11S1986 D11S1986 11 109761000 111761000 D11S1986 D11S1986 11 116235500 118235500 D11S1998 D11S1998 11 116534000 118534000 D11S4195 D11S4195 11 126000000 128000000 D11S1914 D11S1914 12 4615000 6615000 D12S1673 D12S1673 12 9253000 11253000 D12S77 D12S77 12 11341000 13976000 D12S391 D12S391 12 30100000 32100000 D12S1292 D12S1292 12 50483000 52483000 D12S398 D12S398 12 52156500 54156500 D12S1724 D12S1724 12 65787000 67787000 D12S313 D12S313 12 88325700 90325700 D12S1064 D12S1064 12 106524600 108524600 D12S84 D12S84 12 117600500 119600500 D12S395 D12S395 12 125314000 127314000 D12S2075 D12S2075 13 30807000 32807000 D13S1493 D13S1493 13 35361500 37361500 D13S1491 D13S1491 13 49276000 51276000 D13S1325 D13S1325 13 52503800 54503800 D13S1492 D13S1492 13 52503800 58082000 D13S1492 D13S1492 13 71455500 73455500 D13S156 D13S156 13 71950000 73950000 D13S792 D13S792 14 19191000 21678000 D14S585 D14S585 14 23646000 25687000 D14S1280 D14S1280 14 30744000 32744000 D14S741 D14S741 14 35318000 37318000 D14S306 D14S306 14 35318000 37318000 D14S306 D14S306 14 52096500 54096500 D14S281 D14S281 14 86368000 88368000 D14S1005 D14S1005 14 93424000 99359600 D14S605D D14S605D 14 95257000 98214500 D14S614 D14S614 15 21151600 23151600 D15S817 D15S817 15 30842500 32842500 D15S1040 D15S1040 15 32100000 34100000 D15S971 D15S971 15 43090000 45090000 D15S659 D15S659 15 43090000 45090000 D15S659 D15S659 15 50488500 52488500 D15S209 D15S209 15 54705500 56705500 D15S1022 D15S1022 15 61002000 63002000 D15S644 D15S644 15 61002000 63002000 D15S644 D15S644 15 66119300 68119300 D15S1025 D15S1025 15 80184000 84975500 D15S811 D15S811 15 84888000 86888000 D15S1046 D15S1046 15 88127500 90127500 D15S127 D15S127 15 90985700 92985700 D15S649 D15S649 16 3051000 5051000 D16S3027 D16S3027 16 7371500 9371500 D16S768 D16S768 16 23203000 25203000 D16S420 D16S420 16 25125000 27712000 D16S769 D16S769 16 70111000 72111000 D16S752 D16S752 16 70511400 72511400 D16S2624 D16S2624 16 76100000 78100000 D16S3097 D16S3097 17 5452000 7452000 D17S796 D17S796 17 9313000 11313000 D17S1879 D17S1879 17 9719000 112060000 D17S974 D17S974 17 27245500 29245500 D17S975 D17S975 17 33012000 35012000 D17S907 D17S907 17 37286900 51701000 D17S75 D17S75 17 49259500 51259500 D17S1820 D17S1820 17 52791000 54791000 GCT6E11 GCT6E11 17 59197000 62145700 D17S917 D17S917 17 63510000 65510000 D17S113 D17S113 17 70461000 72461000 D17S1848 D17S1848 17 72158000 74158000 D17S1535 D17S1535 17 110060000 112060000 D17S1303 D17S1303 18 2900000 4900000 D18S63 D18S63 18 3248000 5248000 D18S52 D18S52 18 35590000 40513500 D18S865 D18S865 18 50520000 52520000 D18S1127 D18S1127 18 58098000 60098000 D18S51 D18S51 18 58098000 60098000 D18S51 D18S51 18 63300000 65300000 D18S857 D18S857 18 64585000 68450000 D18S61 D18S61 18 69397500 71397500 D18S1161 D18S1161 19 2027000 4027000 D19S591 D19S591 19 2091000 4091000 D19S247 D19S247 19 7000000 9000000 D19S395 D19S395 19 7056000 9056000 D19S884 D19S884 19 8040500 10040500 D19S413 D19S413 19 9750000 10750000 ICAM1 ICAM1 19 16169000 18169000 D19S593 D19S593 19 32315000 34315000 D19S931 D19S931 19 43640700 45640700 D19S190 D19S190 19 47400000 49400000 D19S902 D19S902 19 47500600 49500600 D19S420 D19S420 19 48737800 50737800 D19S903 D19S903 19 49685000 51685000 D19S219 D19S219 19 54273000 56273000 D19S585 D19S585 19 54647500 58285500 D19S246 D19S246 19 57463000 59463000 D19S921 D19S921 2 4036500 6036500 D2S319 D2S319 2 10130900 12629000 D2S297 D2S297 2 13415000 15415000 D2S149 D2S149 2 18326900 20326900 D2S387 D2S387 2 33415700 35415700 D2S367 D2S367 2 37241700 39241700 D2S1346 D2S1346 2 45233000 47233000 D2S2378 D2S2378 2 48597000 50597000 D2S2739 D2S2739 2 53683000 55683000 D2S2153 D2S2153 2 67213500 69213500 D2S1779 D2S1779 2 81922000 83922000 D2S1396 D2S1396 2 81956000 85921500 D2S428 D2S428 2 83921500 85921500 D2S394 D2S394 2 123345000 125345000 D2S347 D2S347 2 141108000 143108000 D2S129 D2S129 2 155486000 157486000 D2S142 D2S142 2 204430000 206430000 D2S1384 D2S1384 2 204430000 206430000 D2S1384 D2S1384 2 214262500 216262500 D2S1327 D2S1327 2 220551000 222551000 D2S424 D2S424 2 223037000 225037000 D2S408 D2S408 2 236522000 238522000 D2S338 D2S338 2 236522000 238522000 D2S338 D2S338 20 2460500 4460500 D20S473 D20S473 20 5745000 7745000 D20S892 D20S892 20 5760000 7760000 D20S603 D20S603 20 45615000 47615000 D20S891 D20S891 21 19568700 21568700 D21S1437 D21S1437 21 29627000 31627000 D21S1270 D21S1270 21 30655000 32655000 D21S2049 D21S2049 21 35217000 37217000 D21S2051 D21S2051 22 34801000 50278400 D22S91 D22S91 22 40335400 42335400 D22S417 D22S417 3 9529000 13300000 D3S3611 D3S3611 3 9831000 11831000 D3S3045 D3S3045 3 27701600 29701600 D3S1283 D3S1283 3 31137000 33137000 D3S2432 D3S2432 3 36029000 38029000 D3S1611 D3S1611 3 53055000 55055000 D3S1588 D3S1588 3 57174000 59174000 D3S2402 D3S2402 3 63340000 65340000 D3S3571 D3S3571 3 70466300 72466300 D3S3568 D3S3568 3 72179000 74179000 D3S2406 D3S2406 3 86839500 88839500 D3S2386 D3S2386 3 102496200 104496200 D3S2459 D3S2459 3 108000000 110000000 D3S4018 D3S4018 3 113582500 115582500 D3S3683 D3S3683 3 142511800 144511800 D3S3694 D3S3694 3 155705600 160769000 D3S3509 D3S3509 3 173884000 178106000 D3S2425 D3S2425 4 1000000 3000000 D4S432 D4S432 4 28600000 30600000 D4S418 D4S418 4 35439000 37439000 D4S2629 D4S2629 4 60986400 62986400 D4S1645 D4S1645 4 61250500 63250500 D4S398 D4S398 4 65628500 67628500 D4S416 D4S416 4 89292000 92521000 D4S2460 D4S2460 4 89591000 91591000 D4S2371 D4S2371 4 98893500 100893500 D4S1647 D4S1647 4 107345000 109345000 D4S3256 D4S3256 4 129756500 131756500 D4S2394 D4S2394 4 169242500 171242500 D4S2414 D4S2414 4 179864500 181864500 D4S2417 D4S2417 4 182378000 184378000 D4S3005 D4S3005 4 184931800 186931800 D4S1535 D4S1535 4 188759200 190803700 D4S2921 D4S2921 5 4047000 6047000 D5S406 D5S406 5 6711000 11193000 D5S1953 D5S1953 5 24730000 26730000 D5S502 D5S502 5 39061000 41061000 D5S418 D5S418 5 39263800 41263800 D5S2494 D5S2494 5 57500000 59500000 D5S2500 D5S2500 5 72163000 74163000 D5S112 D5S112 5 79873000 81873000 D5S1464 D5S1464 5 80541500 82541500 D5S2029 D5S2029 5 82683500 84683500 D5S107 D5S107 5 88250700 90250700 D5S1725 D5S1725 5 89290000 92520500 D5S1463 D5S1463 5 94887000 96887000 D5S644 D5S644 5 107600000 109600000 D5S1453 D5S1453 5 108096000 110096000 D5S1466 D5S1466 5 116064000 121487000 D5S494 D5S494 5 118178000 120178000 D5S1505 D5S1505 5 133374000 135374000 D5S2056 D5S2056 5 134378000 136378000 D5S816 D5S816 5 164050000 166050000 D5S2040 D5S2040 5 166556700 168556700 D5S1458 D5S1458 5 167305000 169305000 D5S2045 D5S2045 6 545800 2545800 D6S344 D6S344 6 11316000 13316000 D6S1034 D6S1034 6 15070500 17070500 D6S1630 D6S1630 6 15416500 17416500 D6S1605 D6S1605 6 27800000 32647500 D6S1615 D6S1615 6 29375000 31375000 D6S2444 D6S2444 6 29375000 32647500 D6S265 D6S265 6 29375000 32647500 D6S2444 D6S2444 6 29375000 32647500 D6S2444 D6S2444 6 29375000 32647500 TNFa TNFa 6 29375000 47210000 D6S265 D6S265 6 29375000 47210000 D6S265 D6S265 6 29375000 47210000 D6S265 D6S265 6 29375000 47210000 D6S265 D6S265 6 30647500 32647500 TNFa TNFa 6 30647500 32647500 TNFa TNFa 6 30788000 32788000 D6S2447 D6S2447 6 31000000 33000000 HO16369 HO16369 6 31263000 33263000 D6S1014 D6S1014 6 42548000 44548000 D6S271 D6S271 6 66237500 70921000 D6S1275 D6S1275 6 67547500 69547500 D6S1282 D6S1282 6 77300000 79300000 D6S460 D6S460 6 80268000 83191000 D6S1707 D6S1707 6 84950000 86950000 D6S1652 D6S1652 6 92060500 96514500 D6S424 D6S424 6 97761000 99761000 D6S1284 D6S1284 6 101404000 103404000 D6S1709 D6S1709 6 163207000 165207000 D6S1277 D6S1277 7 1842300 3842300 D7S2521 D7S2521 7 3242500 5242500 D7S517 D7S517 7 3359700 5359700 D7S2445 D7S2445 7 48133700 50133700 D7S1818 D7S1818 7 48133700 50133700 D7S1818 D7S1818 7 69526600 71526600 D7S2516 D7S2516 7 87055700 89055700 D7S630 D7S630 7 87055700 89055700 D7S630 D7S630 7 87055700 89055700 D7S630 D7S630 7 80460500 115694000 D7S677 D7S677 7 135124500 137124500 D7S1837 D7S1837 7 136958000 138500000 D7S684 D7S684 8 5504000 11920000 D8S277 D8S277 8 24463000 26463000 D8S1771 D8S1771 8 58758000 60758000 D8S1113 D8S1113 8 58758000 60758000 D8S1113 D8S1113 8 64779500 66779500 D8S1473 D8S1473 8 69063000 71063000 D8S543 D8S543 8 92447000 94447000 D8S1988 D8S1988 8 100418000 102418000 D8S1762 D8S1762 8 102669500 104669500 D8S1834 D8S1834 8 136700000 138700000 D8S1837 D8S1837 8 140533700 142533700 D8S1717 D8S1717 9 7043500 9043500 D9S286 D9S286 9 8300000 11006500 D9S144 D9S144 9 26993000 28993000 D9S746 D9S746 9 28302500 30302500 D9S52 D9S52 9 28850000 30850000 D9S1853 D9S1853 9 30034700 32034700 D9S147E D9S147E 9 54700000 56700000 D9S927 D9S927 9 67824000 69824000 D9S1799 D9S1799 9 72543000 74543000 D9S284 D9S284 9 80562800 82562800 D9S152 D9S152 9 110268500 112268500 D9S779 D9S779 9 129713000 131713000 D9S1847 D9S1847 X 3204800 5204800 DXS6807 DXS6807 X 24100000 28000000 DXS1218 DXS1218 X 25803500 27803500 DXS1061 DXS1061 X 52475500 54475500 DXS1044 DXS1044 X 66064000 68064000 DXS339 DXS339 X 66064000 68064000 DXS981 DXS981 X 71990000 73990000 DXS8037 DXS8037 X 100090000 102090000 DXS1153 (BEX1) X 123880000 125880000 DXS8009 DXS8009 X 128739000 130739000 DXS1187 DXS1187

  
  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, the data in the textarea may be modified, deleted or extended where necessary and if the user chooses to customize the metatraits, the textareas will appear empty. Then he/she may paste own genetic linkage data in base pairs in the corresponding textarea depending on the species and always according to the following format (TAB delimited):

  Position in base pairs (Syntax: chromosome / first bp / last bp / name)

  
  ... or paste directly the marker IDs according to the following formats (TAB delimited), where both format types (for flanking markers and for peak markers) may be mixed up in the same query:
  
  

  Positions for Mus musculus: D1Mit151 - Peak1 D1Mit123 - Peak2 D12Mit32 D12Mit124 Flanks1 D15Mit16 D15Mit30 Flanks2

  
  In the example above, the two first QTLs (two first lines) are defined by peak markers (only one marker followed by a "-"), while the two last QTLs are defined by a flanking marker at each QTL border.
  

  Position in markers Span size around peak marker (in Kbp): 5001000150020002500300035004000     (Syntax: flanking marker / flanking marker / name) or (Syntax: peak marker / - / name)

  
  The selectable span size around the marker describes the window (in base pairs) to be considered around a peak marker. Moreover, in the rare cases where the span between two flanking markers is less than the selected minimum span size, the QTL described by flanking markers is automatically extended according to this span size.
  
  NOTE: If a marker ID is incorrectly typed or if it is not included in the EnsEMBL database, the script will ignore it. To confirm, which markers have been taken into account by the script, please check the current output after submission of the marker data. If necessary, we recommend to search for a neighbouring marker that could be included in the database and try the submission procedure again.

Output

Rattus_norvegicus QTLs				Homology in Mus_musculus				Homology in Homo_sapiens
Chr.	Kbp Start	Kbp Size	Name	Chr.	Kbp Start	Kbp Size	Consensus	Chr. Kbp Start Kbp Size Consensus
10	25800	39200	EAE3	11	44794	0.5	44794-44794 (EAE6b)	no match
10	25800	39200	EAE3	11	44806	0.5	44806-44806 (EAE6b)	no match
10	25800	39200	EAE3	11	44820	11	44820-44831 (EAE6b)	5 158824 10 no match
10	25800	39200	EAE3	11	44859	25	44859-44884 (EAE6b)	5 158780 9 no match 5 158803 4 no match 5 158829 0.5 no match
10	25800	39200	EAE3	11	44908	31	44908-44940 (EAE6b)	5 158681 27 158681-158700 (IL12B) 5 158730 0.5 no match
10	25800	39200	EAE3	11	44952	4	44952-44956 (EAE6b)	no match
10	25800	39200	EAE3	11	44986	144	44986-45131 (EAE6b)	5 158478 102 no match 5 158593 43 no match
10	25800	39200	EAE3	11	45141	94	45141-45236 (EAE6b)	5 158373 92 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 second source 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 both source species (in case of three-way analysis) or syntenic to the only 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.

Kbp in consensus (all species): 14169

Genes in consensus (all species): 283

Fragments (not joined) in consensus (sp1+sp2+ sp3_only_synt): 38537	Fragments (joined) in consensus (sp1+sp2+ sp3_only_synt): 1627
Fragments (not joined) in consensus (all species): not queried	Fragments (joined) in consensus (all species): 632
Kbp in consensus (sp1+sp2): 41612	Genes in consensus (sp1+sp2): not queried
Fragments (not joined) (sp1+sp2): 45917	Fragments (joined) (sp1+sp2): 3990
Fragments (not joined) in consensus (sp1+sp2): not queried	Fragments (joined) in consensus (sp1+sp2): 1238

The output statistics are furthermore summarized in a table. The user can read the nr. of base pairs and genes affected by the consensus and - in case of search based on synteny - details about the the number of DNA fragments matched and later merged with their corresponding base pair sizes.

Validation

• Data Normalization

Normalize QTL sizes (recommended)

QTLs and SLs may be located in chromosomal regions with unusual high or low gene density. This is particularly clear for QTLs / SLs affecting the MHC-Locus (very high gene density). When rearranging such a QTL / SL in each iteration its size is only respected in terms of base pairs. Normalization of the QTLs / SLs respects the original number of genes in the region to amielorate the effect of such disproportions in gene density on the permutation test.


• Iterations



Iterations for permutation test (consider a local installation for a sufficient nr. of iterations)

1234 5678910





With increasing number of iterations, the distribution of the results of the permutation test approximates to an ideal random distribution. Such distribution is then used to match the number of observed consensus genes. If clearly at marginal percentiles of the random distribution (e.g. over the 95th percentile = p<0.05), the result can be considered as not met by chance. The script allows a maximum of 10 iterations in its on-line version clearly below the 1000 recommended. However, because of limitations of computing ressources we cannot offer that possibility on the web. We encourage the interested users to consider a (free) local installation of our software to solve this (see availability).

WARNING: With increasing sizes of QTLs / SLs the chance to generate a random rearrangement of the QTLs / SLs without overlaps increases geometrically, thus greatly affecting the computing time. For the case of whole genome comparisons (see INPUT) the option for validation has been intentionally disregarded.


• Type of permutation



Permutations based on: homology





This box informs about the type of permutation that is being currently done. For validation of data generated by means of synteny, the type of permutation should by synteny, and analogously for data generated by means of homology. The web-interface allows only permutations based on homology, again because of lacking computing ressources. However the local installations would only need to activate a certain part of the script to use permutations based on synteny (it is already implemented). It is also important to keep in mind that the differences between both types of permutation are relatively little (about 10% difference in amount of genes detected) but the difference in computing time is dramatic (from few seconds to few minutes for homology, to several hours for synteny), so it may be interesting for the user to check always the type "homology" first and only dare the type "synteny" if the results for "homology" were promising enough.


• Show results

Show detailed results list

This option allows the user to get the detailed list of the results generated for each iteration. This may be particularly useful for exporting to other software programs in order to represent the random distribution curve and the cutoff of the observed value.



The figure illustrates the distribution of the number of consensus genes calculated for each iteration in the permutation test (blue vertical bars) in comparison to the observed ones (red bar). If the observed number of genes is found at the green region of the distribution, it can be said that the observed number of consensus genes is significantly higher than expected by pure chance. In other words, the QTLs / SLs analyzed must share indeed a common - at least partial - explanation for the observed phenotype. However, for a maximum of 10 iterations as offered by this web-interface, one should take the calculated p-value with caution (e.g. here p=0). A local installation of the application will allow you to increase the number of iterations. The p-value for 100 iterations will be a good trend indicator and it stabilises at the second decimal position before reaching the 1000th iteration.


• Segregation of consensuses



Rattus_norvegicus	Mus_musculus	Homo_sapiens
EAE12 (3)	EAE7# (7)	D17S907# (4)
EAE3 (7)	EAE23# (3)	D17S796 (1)
EAE12 (3)	EAE7# (7)	D17S1848# (1)
EAE9 (1)	EAE6a (1)	D2S1779 (1)
EAE3 (7)	EAE23# (3)	D17S975 (2)
EAE12 (3)	EAE7# (7)	D19S585# (1)
EAE3 (7)	EAE6b (2)	MSSL# (2)
EAE1 (1)	EAE1# (1)	D6S1615# (2)
EAE3 (7)	EAE23# (3)	D17S1879# (1)
EAE3 (7)	EAE7# (7)	D17S975 (2)
EAE3 (7)	EAE17 (1)	MSSL# (2)
EAE3 (7)	EAE6b (2)	D5S2056# (1)
EAE6 (1)	EAE7# (7)	D17S907# (4)
EAEZ# (2)	EAE7# (7)	D17S907# (4)
EAE4 (1)	EAE5 (1)	D6S1615# (2)
EAEZ# (2)	EAE25 (1)	D18S1127 (1)
EAE13 (1)	EAE7# (7)	D17S907# (4)



Each consensus region, taken as a whole, may be syntenic or homologous to one or more consensus regions of the other species. In the latter case we have a reasonable hint to think that a consensus that seggregates into two in another species could be bearing at least two genes relevant for the trait. The argumentation is then analogous for increasing number of combinations of consensuses. The table above shows all combinations found and includes a number in parenthesis after each merged QTL / SL that stands for the number of different combinations with consensuses of the other species homologous / syntenic to it, This number is an estimation of the minimum number of disease-relevant genes in that consensus.

Availability

The web interface is programmed in PHP4 and is divided in three subprograms:

	QTLMIX web interface (qtlmix.php) The main program: gets all search parameters and the QTL and SL data input, calculates the consensuses and generates the output.
	QTLMIX validation (check.php) merges overlapping QTLs / SLs and runs a permutation test on the same data, but randomized in position over the genome. Generates an overlook of the data frequency distribution and checks for seggregation of consensus regions.
	QTLMIX frequency distribution (freqdist.php) embedded in the former script, generates a png image with the distribution curve of the permutation test.

DATABASES

The local databases are available in different formats and always separately for each metatrais: multiple sclerosis (MS) and rheumatoid arthritis (RA) and their respective animal models in mouse and rat, the experimental autoimmune encephalomyelitis (EAE) and the collagen or pristane induced arthritis (CIA/PIA).

	Tables on EAE QTLs and susceptibility loci for MS (HTML, CSV or MYSQL-zipped format)
	Tables on CIA and PIA QTLs and susceptibility loci for RA (currently only as MYSQL-zipped format)
	ENSEMBL DATABASES on the human, mouse and rat genome and their syntenic relationships.

Authors