Transcript Powerpoint

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
3
enter your
password
4
click on
login
1
first register for a private login
and receive a password
by e-mail
Overview
select comparisons
of interest
perform new
group comparisons
analysis of single
group comparison
analysis of multiple
group comparison
select
experiment group
select
group comparison
select
baseline group
select
search parameters
select
combinations of
group comparison,
search parameters
and
output parameters
select
individual arrays
get list of
candidate genes
get list of
candidate genes
select
group comparisons
and sharing conditions
initiate comparison
view results of
individual genes
view results of
individual genes
activate your selection
of sharing conditions
sharing
select
the investigator
who shall
get access to
your comparison
change
password
enter
new password
and confirm
Naming of arrays and comparisons
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
Affymetrix
HG-U133 Plus 2.0
Example for a group:
ND_PBMC_LPS_4h_133A
Example for a comparison
with samples 1 to 3
of each group
SPL_28:ND_1_2_3_PBMC_LPS_4h_vs_ND_1_2_3_PBMC_LPS_0h_133A
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 panel
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
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.
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
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
6
select at least two
or more arrays of
the baseline
group
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
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
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
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
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
View and download results of a query
1
Affymetrix
probe sets identified
(not sorted!)
3
click on a probe set ID
to see the details of the results
for this probe set
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
2
click here to see the EntrezGene
information of the gene
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
the „mouse over“
function describes
each parameter
your selection criteria
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
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
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 subselections 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.
Administration of your own group
comparisons
1
click here to display all your
group comparisons
2
select the group comparison
you want to delete
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 !!!
3
confirm your decision and delete
this group comparison
or
go back and keep this
group comparison