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The BioRetis Database A tool for analysis and sharing of array data

The BioRetis Database A tool for analysis and sharing of array data. Objective. analysis of Affymetrix GeneChip data automation of group comparisons standards of analysis developed in the NGFN retrieval of candidate genes from single group comparisons from multiple group comparisons

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The BioRetis Database A tool for analysis and sharing of array data

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  1. The BioRetis DatabaseA tool for analysis and sharing of array data

  2. Objective • analysis of Affymetrix GeneChip data • automation of group comparisons • standards of analysis developed in the NGFN • retrieval of candidate genes • from single group comparisons • from multiple group comparisons • by predefined function • download of results for further analysis • integration of public data • restriction of access with options for sharing

  3. Affymetrix GeneChip data • hybridization with one sample and a single color • validation of detection by using • sets of several oligonucleotides per gene • mismatch oligonucleotides • statistical analysis of hybridisation based on the different oligonucleotides per probeset to provide • a measure for significance of detection • a signal intensity relative to whole chip intensity • statistical analysis of pairwise chip comparison based on the different oligonucleotides per probeset to provide • a measure for the significance of difference • a value for the magnitude of difference

  4. GeneChip data needed in BioRetis data for each array data for each pairwise comparisons Signal Detection call Signal log ratio Change call

  5. Chip E1 Chip B1 Chip E2 Chip B2 Chip E3 Chip B3 Pairwise comparisons needed for each group comparison Example: Experiment group E: n=3 chips compared to Baseline group B: n=3 chips number of pairwise comparisons: this results for 2x3=6 arrays in for 2x10=20 arrays in for 2x20=40 arrays in E vs E 3 45 190 E vs B 9 100 400 B vs B 3 45 190 total 15 190 780 comparisons comparisons comparisons

  6. Description of Array Experiments and Comparisons Names for each array reflect information to the following categories: array type kinetics stimulus tissue type donor number donor group 133A 4h LPS WBC 1 ND HG-U133 Plus 2.0 4 hours lipopolysacharide white blood cells first sample normal donor • Example for a group: ND_WBC_LPS_4h_133A • (Arrays from GEO dataset GSE3284: • healthy individuals were challenged with LPS and white blood cells were separated and analyzed • after 4 hours of challenge • on a HG-U133A GeneChip) • Example for a group comparison SPL_28:ND_WBC_LPS_4h_vs_ND_WBC_LPS_0h_133A • (4h challenge is compared to WBC before challenge)

  7. Gene Annotations • Affymetrix ID • GeneSymbol • Gene Ontology Biological Process • Gene Ontology Cellular Component • Gene Ontology Molecular Function • link to Entrez Gene

  8. Access and Rights • You may access • public data • own data • data owned by others and shared with you • You may share • only based on rights for accessing group comparisons • not based on rights for accessing chips

  9. Access and Rights You Colleague  Group A Group C Group B Group D If you allow access to a single or a group of your chips () to a colleague, the colleague would be able to perform comparisons with any of his own chips.

  10. You Colleague  Group A Group C Group B Group D Access and Rights You Colleague  Group A Group C Group B Group D To limit access to only one specific group comparison, for example group A vs group C, rights have to be limited to a single group comparison.

  11. rights array rights pairwise comparison rights group comparison rights description sample array description group comparison samples & comparisons signal values pairwise comparison values group comparison values values annotation probe set ID probe set ID array type genes Basic structure of the database

  12. Working with BioRetis: Access URL:http://www.acs-nett.de/bioretis • click on the appropriate card to • login • register for a personal account • access public data anonymously • get an introduction • see impressum when you register, you define your username, your e-mail, and you will receive a password to this e-mail address

  13. Change your profile you may also change the general settings of access to public data and to predefined gene list for retrieval to change to a new password, goto „account“ „settings“ … … and enter old and new password

  14. Starting to work Select from the drop down menu or click directly on the symbol to perform a new group comparison … … or to perform queries on single … … or multiple group comparisons

  15. Perform a new group comparison:select the Experiment group To perform a newgroup comparison you select the experiment group E from the list of all groups that are owned by you or that are shared with you by a colleague You may narrow in to the group of interest by specifying group parameters

  16. Select Experiment chips Select individual chips for the experiment group E

  17. Select Baseline group Select the baseline group B

  18. Select Baseline chips Select individual chips for the baseline group B … enter a description (optional) … and click „Start“

  19. Group comparison started The group comparison you have initiated is shown on the subsequent page … …and you may check the queue for newly initiated group comparisons still waiting for calculation

  20. See queue of initiated group comparisons The queue of group comparisons still waiting for calculation. The process of calculating a single group comparison takes 20 sec to 5 minutes, depending on the number and type of arrays.

  21. Querying a single group comparison Select from the drop down menu or click directly on the symbol to query a single group comparison

  22. Selecting the group comparison of interest Specify parameters to reduce the number of group comparisons displayed If necessary, specify parameters to reduce the number of group comparisons displayed Select the group comparison of interest … … and click the Next button Select the group comparison of interest … … and click the Next button

  23. Enter query parameters (1) You may click on the parameterset area … … to select default or your own saved parameters … … and fill the query form

  24. Enter query parameters (2) You may click on the columns area … … to change the number of columns in the query form… … and reload the query form to enter more query parameters

  25. Enter query parameters (3) You may click on the probesets area … … to select a list of probesets … … and Start the query in the search parameter area

  26. Enter query parameters (4) You may enter Affymetrix Probeset ID or GeneSymbol … Gene Ontology parameters … thresholds for statistical parameters of the Experiment group (EG) … results between columns are combined by „OR“ or „AND NOT“ or the Baseline group (BG) … Signal Log Ratio (SLR) or Fold Change (FC)… the percentage of change call increased or decreased in all of the pairwise comparisons between EG and BG all parameters in one column are combined by „AND“ p-value thresholds for the t-tests comparing log-transformed signals or SLREGvsBG compared to SLREGvsEG & SLRBGvsBG, SLREGvsBG compared to SLREGvsEG or SLREGvsBG compared to SLRBGvsBG percentage of no change

  27. Enter query parameters (5) You may click on the saveparametersets area … … enter a title and description … … and search and save the query

  28. Display of results symbols to click for switching to cards that display the arrays that were compared or to download results and signals Affymetrix Probeset IDs, symbol to link to the gene in Entrez Gene, the GeneSymbol and all statistical parameters of the group comparison

  29. Display details and download results click on the symbol to download results, … … to download parameters & results … to activate extraction of signals and to download parameters & results & signals in one single xls-file … or to activate extraction of signals and to download parameters & results & signals in one single xls-file

  30. Excel file for single group comparison query parameters results signals

  31. Querying multiple group comparison Select from the drop down menu or click directly on the symbol to query multiple group comparisons

  32. Selecting multiple group comparisons specify prameters, select multiple group comparison of interest and click the Next button specify prameters (optional)… …select multiple group comparison of interest… … and click the Next button

  33. Enter query parameters modify your selection of group comparisons if necessary, … … define Boolean operation between group comparisons, … … enter selection criteria and … … click next

  34. Display of results symbols to click for switching to cards that display the arrays that were compared or to download results and signals Group comparison, Affymetrix Probeset IDs, a symbol linking to the gene in Entrez Gene, the GeneSymbol and all statistical parameters of the group comparison

  35. Excel file for multiple group comparison query parameters results signals first comparison signals second comparison …

  36. Administration of rights to share click on rights and select user or analysis

  37. Select user to share with select user

  38. Give rights to access a comparison deny access (No Rights) or give access to query (May Read) or give access to query and to perform subanalyses (May Analyse) or give access to query, to perform subanalyses and to give rights for access by other users (Co-Owner) and confirm your selection

  39. Select comparison to share specify to reduce listed number of comparisons, … … select a comparison … and click on Next

  40. Administration of rights to share deny access (No Rights) … … or give access to query (May Read) … … or give access to query and to perform subanalyses (May Analyse) … … and confirm your selection … or give access to query, to perform subanalyses and to give rights for access by other users (Co-Owner) …

  41. Upload of gene lists for querying enter the title for the gene list … … and the description, … … select the txt-file on your computer (consisting of a single column of Affymetrix Probeset-IDs) … and start the upload

  42. Administration of gene lists goto settings … click on Probeset Lists …

  43. Display, update or delete gene lists enter the title to display the gene list … enter the title …to display the gene list you may delete … … or update the list

  44. Show Experiments to prospective collaborators Goto cooperation … … and show your experiments

  45. Select the experiments you want to show Activate the experiments that you want to show to the public … … and confirm This will only show your experiment to the public (see next slides) but NOT your expression data!

  46. Find Experiments of other users Goto cooperation … … and find experiments performed by others

  47. Find an experiment and contact the owner Specify the parameters … …to find and select experiments of interest (all your own experiments will be listed here that you have activated in „Show experiments“) Click Next … … to see the owner … … and to get in contact

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