RGD QTLS readme file. Last updated - May 1st 2008 contact: rgd.developers@mcw.edu The previous QTLS file was removed due to mapping and formatting errors. It has been replaced with two new files QTLS_RAT and QTLS_HUMAN with the QTLS for their respective species. The mouse QTL data in the old file was out of date, current mouse QTL data can be obtained from the MGI (http://www.informatics.jax.org). The files are tab-delimited data, one row per QTL record. MAIN CHANGES: - Separate files for rat and human QTLS. - Separate columns for mapping data on the 3.1 and 3.4 rat genome assemblies. - Additional columns were added to specify the method of positioning the QTL on the genome assembly (see below for details). - Columns specific to only one species are only in that species' file. Leftmost columns are in common for both files. - Within a tab delimited field multiple values are now separated by a semicolon ";" instead of a comma ",". This is to improve rendering of the files when viewed in Excel. POSITIONING METHODS: A QTL is positioned on a genome assembly by using the flanking and peak markers as provided by the paper detailing the QTL. For each assembly there are four columns in the QTL file, e.g. for the rat 3.4 assembly: 3.4_MAP_POS_CHR - the chromosome, this may in rare cases, due to assembly differences, not match the chromosome given in the column CHROMOSOME_FROM_REF which is curated from the original paper. 3.4_MAP_POS_START - the start position, always for the + strand 3.4_MAP_POS_STOP - the stop position, always for the + strand 3.4_MAP_POS_METHOD - see below To be used a marker must map to exactly one location a given assembly and be on a consistent chromosome with the other used markers. Ideally both flanking markers are used. If that is not possible a flank and a peak marker are used and the QTL is estimated to be symmetrical about the peak. If that is not possible the peak alone is used with an estimated QTL size about the peak. Finally if only one flank is available that is used with an estimated size extending from that flank (there may be directionality errors for this case as correct orientation can not be ensured in the absence of another marker). All estimates are bounded by the chromosome sizes. There is therefore a hierarchy of confidence in QTL position: 1 - by flanking markers 2 - by one flank and peak markers 3 - by peak only 4 - by one flank marker only Which method is used is listed in the column 3.4_MAP_POS_METHOD. Users wishing the highest quality data may wish to filter only for case 1, or case 1 and 2. In the event that no position can be assigned to a QTL on a given assembly the positioning fields are left blank. QTL size estimates: Until such time as we have better methods to alternatively position uncertain markers the QTL size estimates used for "3 - by peak only" and "4 - by one flank marker only" are made from the global distribution of QTL sizes. For human our current estimated QTL size is: 26 Mbp For rat our current estimated QTL size is: 45 Mbp COLUMN INFORMATION: First 25 columns in common between rat and human. Column 26 is RATMAP_ID for rat, OMIM_ID for human. Columns 27-30 given current human assembly position information or rat 3.4 assembly position information. Column 31-34 (QTLS_RAT only) rat 3.1 assembly position information Columns 35-38 (QTLS_RAT only) rat strain and cross information 1 QTL_RGD_ID the RGD_ID of the QTL 2 SPECIES rat or human 3 QTL_SYMBOL self explanatory 4 QTL_NAME self explanatory 5 CHROMOSOME_FROM_REF the chromosome from the original paper 6 LOD maximum LOD score if given in paper 7 P_VALUE p-value for QTL if given in paper 8 VARIANCE variance if given in paper 9 FLANK_1_RGD_ID RGD_ID for flank marker 1, if in paper 10 FLANK_1_SYMBOL symbol for flank marker 1, if in paper 11 FLANK_2_RGD_ID RGD_ID for flank marker 2, if in paper 12 FLANK_2_SYMBOL symbol for flank marker 2, if in paper 13 PEAK_RGD_ID RGD_ID for peak marker, if in paper 14 PEAK_MARKER_SYMBOL symbol for peak marker, if in paper 15 TRAIT_NAME trait crated for QTL 16 SUBTRAIT_NAME subtrait crated for QTL 17 TRAIT_METHODOLOGY description of how trait is determined 18 PHENOTYPES phenotype ontology annotation 19 ASSOCIATED_DISEASES diseases ontology annotation 20 CURATED_REF_RGD_ID RGD_ID of paper(s) on QTL 21 CURATED_REF_PUBMED_ID PUBMED_ID of paper(s) on QTL 22 CANDIDATE_GENE_RGD_IDS RGD_IDS genes mentioned by paper author 23 CANDIDATE_GENE_SYMBOLS 24 INHERITANCE_TYPE dominant, recessive etc. 25 RELATED_QTLS symbols of related QTLS 26 RATMAP_ID for rat, if available 26 OMIM_ID for human, if available 27-30 for rat, 3.4 assembly position (see explanation above) 27-30 for human, 36.2 assembly position 31-34 for rat only, 3.1 assembly position 35 STRAIN_RGD_IDS for rat only, RGD_IDS of strains crossed 36 STRAIN_RGD_SYMBOLS for rat only, symbols of strains crossed 37 CROSS_TYPE self explanatory 38 CROSS_PAIR pairing of strains for cross