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