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Guide to the SIPAGENE DataBase

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. 1

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Guide to the SIPAGENE DataBase

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  1. Guide to the SIPAGENEDataBase

  2. 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 1 first register for a private login and receive a password by e-mail 3 enter your password 4 click on login

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

  4. array type kinetics stimulus tissue type donor number donor group 133A 4h_ LPS_ PBMC_ 1_ ND_ Affymetrix HG-U133 Plus 2.0 4 hours lipopolysacharide peripheral blood mononuclear cells first sample normal donor 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 user = SPL (SIPAGENE public library) comparison number of user SPL = 28 arrays of the experiment group arrays type arrays of the baseline group

  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 2 click here to change your password 3 enter your old and new password 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 3 select the baseline group 1 select 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 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. View and download results of a query 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 Affymetrix probe sets identified (not sorted!) 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

  15. 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 your selection criteria the „mouse over“ function describes each parameter

  16. 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

  17. 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

  18. 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 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.

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

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