eQTL Explorer Software USER GUIDE
Contents
1. 31 63470459 34 50873184 1 0909 0 01111403 1 0E 6 199033695 199 0 IDiRat 9 1199262243 199 0 CIS fat 1368526 _at 140 28131104 222 64897156 1 5872 4 0E 5 3 0E 6 8316120 8 8 0 IDiRat327 8210068 8 3 0 CIS fat 1375664_at 278 88485718 112 489151 2 4792 0 007322715 9 0E 6 182191418 182 0 IDiRat287 190264129 190 0 CIS kidney 1379594_at 30 75449371 29 6250515 1 0381 0 366047031 6 091E 5 ra ra r r m 0 m m r m 16444122 16 0 DiRati56 15833505 15 0 eQTL Explorer Software User Guide Viewing eQTL and pQTL annotations Place the mouse cursor over the eQTL or pQTL A tool tip text box will appear displaying information about that particular eQTL or pQTL Here is the information for eQTLs nrobeset 1374249 at chr 1 85341148 85343470 peakmarker Di Rat212 86588680 86588680 p value 9 0E 6 pstream Flanking marker DiRate4 76610805 76810977 Parental Fold Change 1 1985 p value 1 27115E 4 PNI Fold Change 1 2316 p value 9 0E 6 And similarly for pQTLs 100 ApOTLeluster 1 pe Blood pressure 6212486 176994310 lanking marker upstream DiMghs 150 lanking marker downstream C1Mgh3 od value 4 82 200 The links to external sources of information are accessed by2. After all parameters are selected press the Export button The software will ask you for an output file with the usual file request box The data will then be fetched from the database and written to the file Menu Bar Selecting the file menu it is possible to export a jpeg image of the genome panel at 96dpi or exit the program The display menu can be used to select the number of columns in the Genome Panel from 1 chromosome to 5 chromosomes wide in order to visualize large clusters of eQTLs more easily From the help menu it is possible to access a simplified help document and information about the program 6 The Genome Panel Once the data have been fetched you are presented with a display of eQTLs and pQTLs on the Genome Panel This panel displays all the chromosomes in 3 columns You can scroll through the chromosomes by using the scrollbar on the right hand side of the panel Each chromosome is one chromosome panel demarcated by black boundary line y E C y eae Eca l bad Ca be Pye eQTLs in each row are ordered by their p value The eQTL with the lowest p value is nearest to the chromosome At certain p values the number of eQTLs is so large at a particular locus that they reach the extreme left of the boundary of the chromosome panel eQTL Explorer Software User Guide Please click on a particular chromosome to zoom in and visualize all the eQTLs and their information The number of
3. even further using the Advanced Options tab eQTL explorer File Display Help PQTL OPTIONS SET THE ADVANCED OPTIONS AND RETURN TO THE MAIN PAGE TO FETCH Select the PQTL type to display only those eQTLs that are within PQTLS of this type CTRitclick to muitivie select PROBESET OPTIONS Al Enter probeset s separated by commas in the text box or upload a file LT Display only these PQTLs Select fetch to return eQTLs associated with these probesets OR highlight to indicate these probesets within all eQTLs Search by probeset wil OR upload a file that contains probeset names separ mmas eQTL Explorer Software User Guide Probeset Options If you are interested in specific probesets or a list of probesets you can enter them as a comma separated list or upload a file that contains the probeset names separated by commas on one line It is then possible to either e Highlight eQTLs that contain these probesets This option will highlight eQTLs that contain this probeset with a red circle e Fetch only eQTLs that contain these probesets This option will display only those eQTLs that contain the required probesets Please click on Fetch button again after entering the probeset list pQTL Options Selecting a pQTL type or several pQTL types will display only those eQTLs that are within the bounds of a pQTL of that type It is also possible to display only the pQTLs of a specific type and eQTLs withi
4. left clicking on the eQTL or pQTL eQTLs link to information for probesets and markers A pop up box will appear having links to Ensembl RGD Entrez databases Please select any of the options to view information about that particular eQTL pQTL from the database eQTL Explorer Software User Guide For eQTLs probeset information And Marker information For pQTLs Entrez Query Ensembl Contigview Plot gtl reaper results Him qui R qzi F probeset i Ensembl Contigview of Marker Position Query RGD For Marker Query RGD For OTL Ensembl Contigview of QTL Position 10 eQTL Explorer Software User Guide For eQTL probesets the Plot gtl reaper results option gives a Genome wide plot of the linkage for that particular probeset in that particular tissue Probeset 1379594_at Overview Click on chromosome plot to enlarge Chromosome 8 LRS additive coefficient This shows the p value LRS and additive coefficient across the whole genome The linkage plot panel is subdivided into chromosomes and clicking each chromosome will give a zoom view panel of the data for that chromosome 11 eQTL Explorer Software User Guide 8 Troubleshooting a clicked on the option Show Table and the table does not appear Please be patient The software extracts all the information from the database and populates the table The number of eQTLs it has to fetch governs the t
5. 70871735 1 3519 0 002472171 1 0E 7 158396007 158 0 DiRat47 158590090 158 0 CIS kidney 1374907 _at 97 34960938 78 64306641 1 2379 0 004008932 1 0E 6 158396007 158 0 DiRat47 158590090 158 0 CIS kidney 1374675_at 316 1055603 4 266 63848877 1 1855 0 048675142 8 0E 6 167465181 167 0 DiRat356 1173621619 173 0 CIS fat 1375927 _at 131 14907837 178 35380554 1 3599 0002237257 1 223E 5 84966638 184 0 DiRat212 36588680 86 0 CIS kidney 1371085_at 94 96022797 124 07952881 1 3066 7 57184E 4 1 0E 6 167456059 167 0 DiRat356 173621619 1 173 0 CIS fat 1374675 _at 302 23251343 251 22325134 1 203 0 008401122 5 53E 5 167465181 167 0 IDIRat356 1173621619 173 0 CIS fat 1371085 _at l47 84555435 98 28238678 2 0542 0 001040156 1 0E 6 167456059 167 0 DiRat356 173621619 173 0 TRANS fat 1383734_at 155 76190186 170 90608215 1 0972 0 032257681 8 0E 6 4651292 4 4 0 IDiCebrp137s2 1248300192 245 0 CIS kidney 1371615_at 411 98822021 268 03704834 1 5371 0 012872642 3 548E 5 156525993 156 0 IDiRat47 158590090 158 0 CIS kidney 1377534_at
6. e implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details 12
7. eQTL Explorer Software USER GUIDE Version 4 0 september 2005 2005 MRC 1 Logging In eQTL Explorer Software User Guide When eQTL Explorer is launched you are presented with the following login window Log On to eQTLexplorer User name eqtl_guest Password By default the guest login details appear in the window Click connect or press enter to start the database connection 2 The Main Screen When eQTL Explorer has loaded and retrieved experiment information from the database you will be presented with the main screen from which you can fetch the detailed information eQTL explorer File Display Help Experiment huebner_aitman_pravenec Y QTL reaper analysis ID Tissue Date May 26 2004 May 26 2004 Comments Enrico Petretto 2 kidney Herbert Schulz How to fetch data Cis Trans Window Colour p Value cut off 1 0E 4 plot by marker location v show cis trans undefined e Choose an experiment from the drop down list e Click on the tissue s you are interested in If you wish to visualise eQTL information for all tissues click and drag on all tissue rows under the QTL reaper analysis heading Choose the value of the max eQTL size between 0 toi By default the p value is 1 0E 4 You can change the p value to any number eQTL Explorer Software User Guide e Select one of the plot by options By default it is by marker location e C
8. eQTLs fetched for each analysis tissue type is displayed in the information bar at the bottom of the genome panel 7 Chromosome Panels The chromosome panel is a detailed view of a chromosome Chromosome 1 File Table eQTL Count 26 cis 0 not plottable eQTLs pQTLs iN lf the eQTLs appear to reach the extreme left boundary of the chromosome panel please click on the chromosome anywhere within the black boundary to zoom in that chromosome You can scroll towards the left using the scroll bar provided on the bottom of the chromosome panel Zooming in a particular chromosome minimizes the main window of the software After closing the zoomed chromosome panel you will have to restore the main software window There is a slider provided on the right side of the chromosome panel and dragging the slider upwards will zoom in the chromosome further along its y axis eQTL Explorer Software User Guide Visualising eQTL information in table format The chromosome panel has an option in the menu bar as Table There are two sub menus under this option One is to visualise eQTL data in table format Show Table Other option is to import data in an Excel file to local disk Save Table 2 undefined 32 total 0 not plottable pQTLs If you click the Show Table option the software imports all the relevant data from the database and populates the table After it has populated the table
9. hoose any of the options in the show block By default all options cis trans and undefined are selected After all parameters are selected press the Fetch button The software will fetch the data from the database and display it on the Genome panel below Changing cis trans undefined and plot by parameters Once the eQTLs are displayed on the Genome panel you can change the cis trans and undefined checkboxes or plot by option and see the desired eQTLs WITHOUT clicking on the Fetch button again Changing p value tissue parameters If you wish to change the tissue p value parameters then please change these parameters and click on Fetch button Without clicking on Fetch button there will be no changes on the Genome panel Note that if you select a p value of greater than 0 01 a warning will appear and you will have to press Fetch again to confirm the p value This feature has been incorporated as using a p value of greater than 0 01 may return many data points and take a long time Changing max eQTL size By default the window size for defining cis and trans is set to 10 Mb You can change this window size by clicking on the drop down icon and change the window size to 5 or 15 Mb After changing the max eQTL size please click on the Fetch button again to make changes in the graphical output 3 Advanced Options It is possible to filter the information that is retrieved
10. ime it will take to populate the table b I clicked on Fetch button and it appears that the software is not doing anything lt depends on the internet speed amount of data to be fetched from the database and number of people using this database at the same time If it takes a lot of time please close the application and re run it c closed the zoomed image of the chromosome and when I maximize the main window of the software the images don t appear There is probably less of graphics memory Please click on File menu button to refresh the main window d click on Fetch button and I don t see all the pQTLs or eQTLs It is probably because the text field in the advanced options is not clear and still has a list of Affymetrix probeset ids Similarly some of the pQTLs may be selected in the previous Fetch Click on the Reset button to deselect the entire pQTLs list and click on Fetch again 9 Additional Information Please contact jon mangion csc mrc ac uk for any problems or suggestions System Requirements Minimum system requirements are 256Mb RAM and the ability to run Java 1 4 2 The software has been tested on Windows XP Linux 2 4 and Mac OS X Licence The eQTL Explorer software is distributed under the GNU Public Licence It is freely available for non commercial use Disclaimer eQTL Explorer is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even th
11. it displays it on screen The last 4 columns have links to external database Clicking on any of the cells will take you to the respective website Cis_Trans Tissue ProbesetId Probeset Probeset Probeset Probeset RI Fold C RIP Value Probeset Probeset Probeset PeakMark PeakMark PeakMark PeakMark UNDEFINED kidney null Probes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Dicebr21s2 175894688 175 0 CIS kidney 1389650_at 129 83169556 229 10592651 1 7646 0 001443013 15 0E 6 135945648 135 0 DiRat42 135496587 135 0 CIS kidney 1372093_at 796 27679443 540 52416992 1 4732 6 6E 5 1 437E 5 259800723 259 0 DiRat225 261391206 261 0 TRANS fat 1374996 _at 202 77272034 177 55444336 1 142 0 428835167 1 483E 5 109823620 109 0 DiRat47 158590090 158 0 CIS fat 1389650 _at 86 22306824 137 18231201 1 591 0 0012248 6 0E 6 135945648 135 0 DiRat42 135496587 135 0 UNDEFINED kidney null Probes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Dicebrp137s2 248300192 248 0 CIS kidney 1374831_at 112 18357086 85 60999298 1 3104 0 001200225 1 0E 7 201276888 201 0 DiCcebr10s3 198323072 198 0 CIS fat 1374907 _at 119 92453003 88
12. ments May 26 2004 Enrico Petretto 2 kidney May 26 2004 Herbert Schulz _ Cis Trans Win Colour Select a specific region hp Probeset Id mieParent Strain average SHR Parent Strain average Brown Norway Parentstrain Probeset Fold Change Start cis trans 1 0E 4 undefined As with the Fetch on the Main Page e Choose an experiment from the drop down list e Click on the tissue you are interested in If you wish to visualise eQTL information for all three tissues click and drag on all three tissue rows under the QTL reaper analysis heading Figure 1 Choose the value of the max eQTL size e By default the p value is 1 0E 4 You can change the p value to any number between 0 toi e Select one of the plot by options By default it is by marker location e Choose any of the options in the show block By default all options cis trans and undefined are selected e You can select a single chromosome or multiple chromosomes using CTRL click or the ALL option which is at the end of the list e It is also possible to select a specific bp region for one chromosome or the same region on several all chromosomes eQTL Explorer Software User Guide e By default all columns will be exported but it is possible to select which columns you want to be written to the file Selection is in a similar manner to the chromosomes
13. n those pQTLs pQTLs are displayed on the genome panel Please click on the Fetch button after selecting specific pQTL s 4 Warnings Any information about the retrieval of data will be displayed in this pane eQTL explorer File Display Help For example if a probeset is selected to be fetched and this is not present in an eQTL of the required criteria this will be reported in the warnings window Similarly if a probeset is entered to be highlighted and it is not present amongst the eQTLs this is reported In addition probeset identifiers that are not of the required format DIGITS letters are reported as warnings eQTL Explorer Software User Guide eQTL explorer File Display Help Main Page Advanced Options Warnings Export Affy Id not found in eQTLs list 12345678_at for l tissue Affy Id not found in eQTLs list INVALID NAME FORMAT PROBESET at for l tissue Affy Id not found in eQTLs list 12345678 at for 2 tissue Affy Id not found in eQTLs list INVALID NAME FORMAT PROBESET at for 2 tissue An example of the warnings display 5 Export The export tab gives the option to export information from particular chromosomes all chromosomes or specific chromosome regions eQTL explorer File Display Help Choose which chromosome s Choose the columns to output Experiment huebner_aitman_pravenec vi ses a TE Cis Trans Definition QTL reaper analysis Tissue D Tissue Date Com
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