1. Guide to the SIPAGENE DataBase

2. Access to SIPAGENE goto: https://www.sipagene.de 2 enter your user name 2 enter your user name 3 enter your password 3 enter your password 4 click on login 4 click on login navigation bar to select individual areas for - login - generating a personal account - login as anonymous public user -introduction -contact information 1 first register for a private login and receive a password by e-mail 1 first register for a private login and receive a password by e-mail

3. Overview perform new group comparisons analysis of single group comparison analysis of multiple group comparison change password sharing select experiment group select baseline group select individual arrays initiate comparison select group comparison select search parameters get list of candidate genes view results of individual genes select combinations of group comparison, search parameters and output parameters get list of candidate genes view results of individual genes select the investigator who shall get access to your comparison select group comparisons and sharing conditions activate your selection of sharing conditions enter new password and confirm select comparisons of interest

4. Naming of arrays and comparisons Example for a group:ND_PBMC_LPS_4h_133A Example for a comparison SPL_28:ND_1_2_3_PBMC_LPS_4h_vs_ND_1_2_3_PBMC_LPS_0h_133A with samples 1 to 3 of each group 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 user = SPL (SIPAGENE public library) comparison number of user SPL = 28 arrays of the experiment group arrays of the baseline group arrays type

5. First steps: Main page after login navigation panel

6. change your password 1 click on „Rights“ to change your password or to manage sharing rights for access to your data 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 2 click here to change your password 3 enter your old and new password 3 enter your old and new password 4 click here to confirm 4 click here to confirm

7. 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.

8. Perform a group comparison 1 select the experiment group 1 select the experiment group 2 confirm your selection and go to the baseline selection 2 confirm your selection and go to the baseline selection 3 select the baseline group 3 select the baseline group 5 select at least two or more arrays of the experiment group 5 select at least two or more arrays of the experiment group 6 select at least two or more arrays of the baseline group 6 select at least two or more arrays of the baseline group 7 start comparison 7 start comparison 4 confirm and go to the selection of individual arrays 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

9. Search for existing group comparisons 2 confirm your selection 2 confirm your selection 1 enter your keyword into global search, any specific field, or select a description from one of the drop-down menues 1 enter your keyword into global search, any specific field, or select a description from one of the drop-down menues

10. Get experiment information for group comparisons 2 for individual arrays, a short description is provided 2 for individual arrays, a short description is provided 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 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 3 extended information is accessible from the public repositories by clicking on the accession number for the array or the experiment 3 extended information is accessible from the public repositories by clicking on the accession number for the array or the experiment

11. Define a selection of group comparisons for subsequent analysis 1 individual comparisons may be selected for further analysis 1 individual comparisons may be selected for further analysis 2 a pre-selection of comparisons may be defined that will be listed in the subsequent menus of comparisons 2 a pre-selection of comparisons may be defined that will be listed in the subsequent menus of comparisons

12. Search for candidate genes: 1. Select an existing group comparison 1 this menu shows the comparisons that you have selected and that you are allowed to access 1 this menu shows the comparisons that you have selected and that you are allowed to access 2 you may change your selection if needed 2 you may change your selection if needed 3 click „next“ to confirm and start a query 3 click „next“ to confirm and start a query

13. 1 select pre-defined search criteria (optimized criteria to select for „true positives“) or enter values for any parameter or combination of parameters 1 select pre-defined search criteria (optimized criteria to select for „true positives“) or enter values for any parameter or combination of parameters 2 criteria in the same column are „AND“ selections; to combine with „OR“ or „NOT“ select the next column and the appropriate operator 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 experiment chips (EC) parameters of the experiment chips (EC) name of the comparison name of the comparison fold change and signal log ratio fold change and signal log ratio % change call of all pairwise comparisons between EC versus BC or within each group % 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 p-values of the t-tests when applying signals or signal log ratios 3 start your retrieval 3 start your retrieval parameters of the baseline chips (BC) parameters of the baseline chips (BC) the „mouse over“ function describes the parameter the „mouse over“ function describes the parameter Search for candidate genes: 2. Define the selection criteria

14. View and download results of a query Affymetrix probe sets identified (not sorted!) Affymetrix probe sets identified (not sorted!) 1 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 1 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 2 click here to see the EntrezGene information of the gene 3 click on a probe set ID to see the details of the results for this probe set 3 click on a probe set ID to see the details of the results for this probe set

15. Details for a selected probe set signals of each experiment chip signals of each experiment chip go to the „Entrez Gene“ information for this probe set go to the „Entrez Gene“ information for this probe set signals of each baseline chip signals of each baseline chip details of the statistical results for each group comparison details of the statistical results for each group comparison your selection criteria the „mouse over“ function describes each parameter the „mouse over“ function describes each parameter

16. Queries from multiple group comparisons 1 go to multiple group comparison 1 go to multiple group comparison 2 select group comparisons 2 select group comparisons 3 select search parameters 3 select search parameters 4 enter search criteria 4 enter search criteria 6 select „AND/OR/NOT“ operator 6 select „AND/OR/NOT“ operator 5 select comparison for display of results 5 select comparison for display of results 7 start query 7 start query Result: list of selected probe sets

17. How to share data 1 click on „Rights“ to manage sharing rights for access to your data 1 click on „Rights“ to manage sharing rights for access to your data 2 select your collaboration partner 2 select your collaboration partner 3 confirm your selection 3 confirm your selection

18. Define sharing rights after you confirmed the selected investigator, you will find all your comparisons in this table after you confirmed the selected investigator, you will find all your comparisons in this table 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 sub- selections 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. 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 sub- selections 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. 2 confirm your selection of rights 2 confirm your selection of rights

19. Administration of your own group comparisons 1 click here to display all your group comparisons 1 click here to display all your group comparisons 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 3 confirm your decision and delete this group comparison or go back and keep this group comparison or go back and keep this group comparison 2 select the group comparison you want to delete 2 select the group comparison you want to delete