The BioRetis DatabaseA 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– by predefined function
• download of results for further analysis
• integration of public data
• restriction of access with options for sharing
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
GeneChip data needed in BioRetis
Signal
Detection call
Signal log ratio
Change call
data for each array
data for each pairwise comparisons
Pairwise comparisons needed for each group comparison
E vs E3
45190
E vs B9
100400
B vs B3
45190
this resultsfor 2x3=6 arrays infor 2x10=20 arrays infor 2x20=40 arrays in
total15
190780
Example: Experiment group E: n=3 chips compared to Baseline group B: n=3 chips
number of pairwise comparisons:
Chip E1
Chip E2
Chip E3
Chip B1
Chip B2
Chip B3
comparisonscomparisonscomparisons
Description of Array Experiments and Comparisons
donor group donor number tissue type stimulus kinetics array type
ND 1 WBC LPS 4h 133A
normal donor first sample white blood cells lipopolysacharide 4 hours HG-U133 Plus 2.0
Example for a group: ND_WBC_LPS_4h_133A (Arrays from GEO dataset GSE3284:healthy individuals were challenged with LPS andwhite 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)
Names for each array reflect information to the following categories:
Gene Annotations
• Affymetrix ID• GeneSymbol• Gene Ontology Biological Process• Gene Ontology Cellular Component• Gene Ontology Molecular Function• link to Entrez Gene
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
Access and Rights
Group A
Group B
Group C
Group D
You Colleague
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.
Access and Rights
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.
Group A
Group B
Group C
Group D
You Colleague
Group A
Group B
Group C
Group D
You Colleague
probe set ID
arraydescription
sample
signalvalues
pairwise comparisonvalues
group comparisonvalues
descriptiongroup comparison
annotationprobe set ID
array type
rightsarray
rightspairwise comparison
rightsgroup comparisonrights
samples & comparisons
values
genes
Basic structure of the database
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
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, andyou will receive a password to this e-mail address
when you register, you define your username, your e-mail, andyou will receive a password to this e-mail address
Change your profile
you may also change the general settings of access to public data andto predefined gene list for retrieval
you may also change the general settings of access to public data andto predefined gene list for retrieval
to change to a new password, goto„account“ „settings“ …
… and enter old and new password
to change to a new password, goto„account“ „settings“ …
… and enter old and new password
Starting to work
Select from the drop down menu or click directly on the symbol to perform a new group comparison …
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 to perform queries on single …
… or multiple group comparisons… or multiple group comparisons
Perform a new group comparison:
select the Experiment groupTo perform a new group comparisonyou select the experiment group E fromthe list of all groups that are owned by you orthat are shared with youby a colleague
To perform a new group comparisonyou select the experiment group E fromthe list of all groups that are owned by you orthat are shared with youby a colleague
You may narrow in to the group of interest by specifying group parameters
You may narrow in to the group of interest by specifying group parameters
Select Experiment chips
Select individual chips for the experiment group ESelect individual chips for the experiment group E
Select Baseline group
Select the baseline group BSelect the baseline group B
Select Baseline chips
Select individual chips for the baseline group B …
enter a description (optional) …
and click „Start“
Select individual chips for the baseline group B …
enter a description (optional) …
and click „Start“
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 stillwaiting for calculation
The group comparison you have initiated is shown on the subsequent page ……and you may check the queue for newly initiated group comparisons stillwaiting for calculation
See queue of initiated group comparisons
The queue of group comparisons still waiting for calculation.
The process of calculatinga single group comparison takes 20 sec to 5 minutes,depending on the numberand type of arrays.
The queue of group comparisons still waiting for calculation.
The process of calculatinga single group comparison takes 20 sec to 5 minutes,depending on the numberand type of arrays.
Querying a single group comparison
Select from the drop down menu or click directly on the symbol to query a single group comparison
Select from the drop down menu or click directly on the symbol to query a single group comparison
Select the group comparison of interest …
… and click the Next button
Select the group comparison of interest …
… and click the Next button
Selecting the group comparison of interest
Specify parameters to reduce the number of group comparisons displayed
Specify parameters to reduce the number of group comparisons displayed
If necessary, 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
Enter query parameters (1)
You may click on the parameterset area …
… to select default or your own saved parameters …
… and fill the query form
You may click on the parameterset area …
… to select default or your own saved parameters …
… and fill the query form
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
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
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
You may click on the probesets area …
… to select a list of probesets …
… and Start the query in the search parameter area
the percentage of change call increased or decreased in all of the pairwise comparisons between EG and BG
the percentage of change call increased or decreased in all of the pairwise comparisons between EG and BG
Enter query parameters (4)
You may enter Affymetrix Probeset ID orGeneSymbol …
You may enter Affymetrix Probeset ID orGeneSymbol …
Gene Ontology parameters …Gene Ontology parameters …
thresholds for statistical parameters of the Experiment group (EG) …
thresholds for statistical parameters of the Experiment group (EG) …
Signal Log Ratio (SLR) or Fold Change (FC) …Signal Log Ratio (SLR) or Fold Change (FC) …
p-value thresholds for the t-testscomparing log-transformed signals or SLREGvsBG compared to SLREGvsEG & SLRBGvsBG, SLREGvsBG compared to SLREGvsEG
or SLREGvsBG compared to SLRBGvsBG
p-value thresholds for the t-testscomparing log-transformed signals or SLREGvsBG compared to SLREGvsEG & SLRBGvsBG, SLREGvsBG compared to SLREGvsEG
or SLREGvsBG compared to SLRBGvsBG
percentage of no changepercentage of no change
all parameters in one column are combinedby „AND“
all parameters in one column are combinedby „AND“
results betweencolumns are combinedby „OR“ or„AND NOT“
results betweencolumns are combinedby „OR“ or„AND NOT“
or the Baseline group (BG) …or the Baseline group (BG) …
Enter query parameters (5)
You may click on the save parametersets area …
… enter a title and description …
… and search and save the query
You may click on the save parametersets area …
… enter a title and description …
… and search and save the query
Display of results
symbols to click for switching to cards that display the arrays that were compared orto download results and signals
symbols to click for switching to cards that display the arrays that were compared orto download results and signals
Affymetrix Probeset IDs,symbol to link to the gene in Entrez Gene,the GeneSymbol andall statistical parameters of the group comparison
Affymetrix Probeset IDs,symbol to link to the gene in Entrez Gene,the GeneSymbol andall statistical parameters of the group comparison
Display details and download results
click on the symbolto download results, …click on the symbolto download results, …
… to download parameters & results …… to download parameters & results …
to activate extraction of signals and to download parameters & results & signals in one single xls-file
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
… or to activate extraction of signals and to download parameters & results & signals in one single xls-file
Excel file for single group comparison
query parametersquery parameters
resultsresults
signalssignals
Querying multiple group comparison
Select from the drop down menu or click directly on the symbol to query multiple group comparisons
Select from the drop down menu or click directly on the symbol to query multiple group comparisons
specify prameters,select multiple group comparison of interestand click the Next button
specify prameters,select multiple group comparison of interestand click the Next button
Selecting multiple group comparisons
specify prameters (optional)…
… 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
Enter query parameters
… click next… click next
modify your selection of group comparisons if necessary, …
… define Boolean operation between group comparisons, …
… enter selection criteria and …
modify your selection of group comparisons if necessary, …
… define Boolean operation between group comparisons, …
… enter selection criteria and …
Display of results
symbols to click for switching to cards that display the arrays that were compared orto download results and signals
symbols to click for switching to cards that display the arrays that were compared orto download results and signals
Group comparison,Affymetrix Probeset IDs,a symbol linking to the gene in Entrez Gene,the GeneSymbol andall statistical parameters of the group comparison
Group comparison,Affymetrix Probeset IDs,a symbol linking to the gene in Entrez Gene,the GeneSymbol andall statistical parameters of the group comparison
Excel file for multiple group comparison
query parametersquery parameters
resultsresults
signalsfirst comparison
signalsfirst comparison
signalssecondcomparison …
signalssecondcomparison …
Administration of rights to share
click on rights and select user or analysisclick on rights and select user or analysis
Select user to share with
select userselect user
Give rights to access a comparison
deny access (No Rights)deny access (No Rights)
or give access to query (May Read)or give access to query (May Read)
or give access to query and to perform subanalyses (May Analyse)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)
or give access to query,to perform subanalyses and to give rights for access by other users (Co-Owner)
and confirm your selectionand confirm your selection
Select comparison to share
specify to reduce listednumber of comparisons, …
… select a comparison …
and click on Next
specify to reduce listednumber of comparisons, …
… select a comparison …
and click on Next
Administration of rights to share
deny access (No Rights) …deny access (No Rights) …
… or give access to query (May Read) …… or give access to query (May Read) …
… or give access to query and to perform subanalyses (May Analyse) …… 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) …
… or give access to query,to perform subanalyses and to give rights for access by other users (Co-Owner) …
… and confirm your selection… and confirm your selection
Upload of gene lists for querying
enter the title for the gene list … enter the title for the gene list …
… and the description, … … and the description, …
and start the uploadand start the upload
… select the txt-file on your computer (consisting of a single column of Affymetrix Probeset-IDs) …
… select the txt-file on your computer (consisting of a single column of Affymetrix Probeset-IDs) …
Administration of gene lists
goto settings … goto settings …
click on Probeset Lists … click on Probeset Lists …
Display, update or delete gene lists
enter the title to display the gene list … enter the title to display the gene list … enter the title … to display the gene listenter the title … to display the gene list
you may delete …you may delete …
… or update the list… or update the list
Show Experiments to prospective collaborators
Goto cooperation …
… and show your experiments
Goto cooperation …
… and show your experiments
Select the experiments you want to show
Activate the experiments thatyou want to show to the public …
… and confirm
Activate the experiments thatyou 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!
Find Experiments of other users
Goto cooperation …
… and find experiments performed by others
Goto cooperation …
… and find experiments performed by others
Find an experiment and contact the owner
Specify the parameters …
…to find and select experiments of interest
(all your own experiments will be listed herethat you have activated in „Show experiments“)
Specify the parameters …
…to find and select experiments of interest
(all your own experiments will be listed herethat you have activated in „Show experiments“)
Click Next …
… to see the owner …
… and to get in contact
Click Next …
… to see the owner …
… and to get in contact