Guide to the SIPAGENE DataBase

Access to SIPAGENE

goto: https://www.sipagene.de

2enter your user name

2enter your user name

3enter your password

3enter your password

4click on

login

4click 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

1first register for a private login

and receive a password by e-mail

Overview

perform new group comparisons

analysis of single group comparison

analysis of multiple group comparison

changepassword

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 ofindividual genes

select combinations of

group comparison,search parameters

andoutput parameters

get list of candidate genes

view results ofindividual genes

select the investigator

who shall get access to

your comparison

selectgroup comparisons

and sharing conditions

activate your selection of sharing conditions

enter new password

and confirm

select comparisons of interest

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_133Awith 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 AffymetrixHG-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

First steps: Main page after login

navigation panelnavigation panel

change your password

1click on „Rights“ to

change your password or to manage sharing rights for

access to your data

1click on „Rights“ to

change your password or to manage sharing rights for

access to your data

2click here to change

your password

2click here to change

your password

3enter your old and

new password

3enter your old and

new password

4click here to confirm

4click here to confirm

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.

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Perform a group comparison

1select the

experiment group

1select the

experiment group

2confirm your

selection and go to the baseline selection

2confirm your

selection and go to the baseline selection

3select the

baseline group

3select the

baseline group

5select at least two or more arrays ofthe experiment

group

5select at least two or more arrays ofthe experiment

group

6select at least two or more arrays of

the baselinegroup

6select at least two or more arrays of

the baselinegroup

7start comparison

7start comparison

4confirm and go to the selection of individual

arrays

4confirm and go to the selection of individual

arrays

access to arrays of the experiment and baseline group is restricted by ownership and sharing rights

Search for existing group comparisons

2confirm your selection

2confirm your selection

1enter your keyword into global search,

any specific field, or select a description from one of the drop-down

menues

1enter your keyword into global search,

any specific field, or select a description from one of the drop-down

menues

Get experiment information for group comparisons

2for individual arrays, a short

description is provided

2for individual arrays, a short

description is provided

1the name of the group comparison provides abbreviated

information about donor, tissue, stimulus, kinetics,andarray type of the experiment group and the

baseline group

1the name of the group comparison provides abbreviated

information about donor, tissue, stimulus, kinetics,andarray type of the experiment group and the

baseline group

3extended information is

accessible from the publicrepositories by clicking

on the accession number for the array or the

experiment

3extended information is

accessible from the publicrepositories by clicking

on the accession number for the array or the

experiment

Define a selection of group comparisons for subsequent analysis

1individual comparisons may be

selected for furtheranalysis

1individual comparisons may be

selected for furtheranalysis

2a pre-selection of comparisons may be defined that will

be listed in the subsequent menus of comparisons

2a pre-selection of comparisons may be defined that will

be listed in the subsequent menus of comparisons

Search for candidate genes:1. Select an existing group comparison

1this menu shows the

comparisons that you have selected and that you are allowed

to access

1this menu shows the

comparisons that you have selected and that you are allowed

to access

2you may change your

selection if needed

2you may change your

selection if needed

3click „next“ to confirm and

start a query

3click „next“ to confirm and

start a query

1select pre-defined search criteria

(optimized criteria to select for „true positives“) or enter values for any parameter or

combination of parameters

1select pre-defined search criteria

(optimized criteria to select for „true positives“) or enter values for any parameter or

combination of parameters

2criteria in the same column are „AND“ selections;

to combine with „OR“ or „NOT“ select the next column and the appropriate operator

2criteria 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 orwithin each group

% change call of all pairwise

comparisons between EC versus BC orwithin 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

3start 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

View and download results of a query

Affymetrix probe sets identified

(not sorted!)

Affymetrix probe sets identified

(not sorted!)

1You may download the summary

of the group comparison or the list of signals of each individual gene and array for

further analysis like clustering

1You may download the summary

of the group comparison or the list of signals of each individual gene and array for

further analysis like clustering

2click here to see the EntrezGene

information of the gene

2click here to see the EntrezGene

information of the gene3

click on a probe set ID to see the details of the results

for this probe set

3click on a probe set ID

to see the details of the resultsfor this probe set

Details for a selected probe set

signals of eachexperiment chipsignals of eachexperiment chip

go to the„Entrez Gene“

information for this probe set

go to the„Entrez Gene“

information for this probe set

signals of eachbaseline chip

signals of eachbaseline chip

details of the statistical results for

each group comparison

details of the statistical results for

each group comparison

your selection criteriayour selection criteriathe „mouse over“ function describeseach parameter

the „mouse over“ function describeseach parameter

Queries from multiple group comparisons

1go to multiple group comparison

1go to multiple group comparison 2

select group comparisons

2select

group comparisons 3select

search parameters

3select

search parameters4

enter search criteria

4enter

search criteria

6select „AND/OR/NOT“

operator

6select „AND/OR/NOT“

operator

5select comparison for

display of results

5select comparison for

display of results

7start query7

start query

Result: list of selected probe sets Result: list of selected probe sets

How to share data

1click on „Rights“ to

manage sharing rights for access to your data

1click on „Rights“ to

manage sharing rights for access to your data

2select your collaboration

partner

2select your collaboration

partner 3confirm your

selection

3confirm your

selection

Define sharing rights

after you confirmed the selected investigator,

you will find all your comparisonsin this table

after you confirmed the selected investigator,

you will find all your comparisonsin this table

1select 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.

1select 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.

2confirm your selection

of rights

2confirm your selection

of rights

Administration of your own group comparisons

1click here to display all your

group comparisons

1click 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 !!!

3confirm your decision and delete

this group comparison

3confirm your decision and delete

this group comparison

orgo back and keep this

group comparison

orgo back and keep this

group comparison

2select the group comparison

you want to delete

2select the group comparison

you want to delete