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Guide to the SIPAGENE DataBase Access to SIPAGENE goto: https://www.sipagene.de navigation bar to select individual areas for - login - generating a personal account - login as anonymous public user -introduction -contact information 2 enter your user name 3 enter your password 4 click on login 1 first register for a private login and receive a password by e-mail Overview select comparisons of interest perform new group comparisons analysis of single group comparison analysis of multiple group comparison select experiment group select group comparison select baseline group select search parameters select combinations of group comparison, search parameters and output parameters select individual arrays get list of candidate genes get list of candidate genes select group comparisons and sharing conditions initiate comparison view results of individual genes view results of individual genes activate your selection of sharing conditions sharing select the investigator who shall get access to your comparison change password enter new password and confirm Naming of arrays and comparisons donor group donor number tissue type stimulus kinetics array type ND_ 1_ PBMC_ LPS_ 4h_ 133A normal donor first sample peripheral blood mononuclear cells lipopolysacharide 4 hours Affymetrix HG-U133 Plus 2.0 Example for a group: ND_PBMC_LPS_4h_133A Example for a comparison with samples 1 to 3 of each group SPL_28:ND_1_2_3_PBMC_LPS_4h_vs_ND_1_2_3_PBMC_LPS_0h_133A user = SPL (SIPAGENE public library) comparison number of user SPL = 28 arrays of the experiment group arrays of the baseline group arrays type First steps: Main page after login navigation panel change your password 1 click on „Rights“ to change your password or to manage sharing rights for access to your data 2 click here to change your password 3 enter your old and new password 4 click here to confirm Group comparisons Definitions: The order of a comparison is important and is pre-defined by the order of the pairwise comparisons. Experiment Chips (EC) are compared to Baseline Chips (BC). If experiment chips present higher expression levels than baseline chips, the signal log ratio and the fold change values are positive, otherwise both are negative. You may not change this order, but you can always retrieve for decreased expression by using the negative values. Perform a group comparison 3 select the baseline group 1 select the experiment group 5 select at least two or more arrays of the experiment group 2 confirm your selection and go to the baseline selection 4 confirm and go to the selection of individual arrays access to arrays of the experiment and baseline group is restricted by ownership and sharing rights 7 start comparison 6 select at least two or more arrays of the baseline group Search for existing group comparisons 1 enter your keyword into global search, any specific field, or select a description from one of the drop-down menues 2 confirm your selection Get experiment information for group comparisons 1 the name of the group comparison provides abbreviated information about donor, tissue, stimulus, kinetics,and array type of the experiment group and the baseline group 2 for individual arrays, a short description is provided 3 extended information is accessible from the public repositories by clicking on the accession number for the array or the experiment Define a selection of group comparisons for subsequent analysis 2 a pre-selection of comparisons may be defined that will be listed in the subsequent menus of comparisons 1 individual comparisons may be selected for further analysis Search for candidate genes: 1. Select an existing group comparison 2 you may change your selection if needed 1 this menu shows the comparisons that you have selected and that you are allowed to access 3 click „next“ to confirm and start a query Search for candidate genes: 2. Define the selection criteria name of the comparison the „mouse over“ function describes the parameter 1 select pre-defined search criteria (optimized criteria to select for „true positives“) or enter values for any parameter or combination of parameters parameters of the experiment chips (EC) 2 criteria in the same column are „AND“ selections; to combine with „OR“ or „NOT“ select the next column and the appropriate operator parameters of the baseline chips (BC) fold change and signal log ratio % change call of all pairwise comparisons between EC versus BC or within each group p-values of the t-tests when applying signals or signal log ratios 3 start your retrieval View and download results of a query 1 Affymetrix probe sets identified (not sorted!) 3 click on a probe set ID to see the details of the results for this probe set You may download the summary of the group comparison or the list of signals of each individual gene and array for further analysis like clustering 2 click here to see the EntrezGene information of the gene Details for a selected probe set go to the „Entrez Gene“ information for this probe set signals of each experiment chip signals of each baseline chip details of the statistical results for each group comparison the „mouse over“ function describes each parameter your selection criteria Queries from multiple group comparisons 1 go to multiple group comparison 2 select group comparisons 3 select search parameters 4 enter search criteria 5 select comparison for display of results 6 select „AND/OR/NOT“ operator 7 start query Result: list of selected probe sets How to share data 1 click on „Rights“ to manage sharing rights for access to your data 2 select your collaboration partner 3 confirm your selection Define sharing rights after you confirmed the selected investigator, you will find all your comparisons in this table 2 confirm your selection of rights 1 select one of the following levels of sharing rights: - no rights: to deny access to this comparison. - read results: to permit analysis of this comparison. - right to analyze: to perform new comparisons of subselections of arrays from this comparison. - give rights …: to permit further distribution of rights to access the selected comparison. ! The Owner may always revoke any sharing rights. Administration of your own group comparisons 1 click here to display all your group comparisons 2 select the group comparison you want to delete Please administrate your group comparisons regularly to avoid overload of the database. Keep only those that are essential, avoid unnecessary redundancy and delete outdated subgroup analyses. This will help to keep retrieval time as short as possible !!! 3 confirm your decision and delete this group comparison or go back and keep this group comparison