The road (taken) to designing/developing pathways - BiGCaT ...

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1 Οκτ 2013 (πριν από 4 χρόνια και 12 μέρες)

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Bioinformatics support for Focus Teams

By L. EIJSSEN, M.E. ADRIAENS, S.L.M. COORT and C.T.A. EVELO.
BiGCaT Bioinformatics,
Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
.


From withi
n NuGO
-
WP7 (Bioinformatics and System B
iology)
t
he BiGCAT group supports
the NUGO research focus teams with respect to Bioinformatics. Lars Eijssen and Susan Coort are
the
postdocs
that do most of this support work
.
Here
we
present

an overview of
our

activities d
uring
2007/8.

A first
major

goal of ou
r

w
ork is to support FT members with the analyses of their
genomics
experiments. For Affymetrix arrays, including the NuGO arrays that were developed at BiGCaT,
we
can
assist with

Quality Control

testing

and normalisation, using the NuGO R
pipel
ine as availab
le from
the NuGO R

server in Wageningen (Philip de Groot).
For other microarrays we have our own QC
workflow that makes intensive use of S
potfire

Decisionsite. W
e can assist
,
in further analysis of
microarray data,
by statistical evaluation of

the genes th
at are differentially regulated
, clustering and
multivariate analysis of groups
of
regulated genes showing the same pattern
. Analysis at pathway,
gene ontology
, or

biological proces
s level completes the spectrum. The newly acquired Genomatix
licence allows

integration
with

transcription factor analysis.
We can apply all of these

analyses

in
different genomics fields (transcriptomics, proteomics and metabolomics). Since the actual analysis is
often time consuming and requires intensive knowledge of the desig
n and purpose of the experiment
we prefer to do this together with the postdocs and PhD students from the FTs, and some exchange
grants for researchers visiting BiGCaT have been planned for this purpose.

In addition,

we support NuGO members in gathering mo
re knowledge on microarray data
analysis themselves, by offering an advanced hands
-
on microarray cour
s
e in Maastricht. This course is
held in July every year. Furthermore there will be a jamboree to discuss
and work on
analysis of
experiments between NuGO
FT
members

and WP7 bioinformaticians
, October this year

in Maastricht
.

Here we can learn from each other, and from the data analysis experts present.

Adjacent to this
meeting, we will host a Genomatix course for those interested (limited availa
bility!) and

probably a
NBX developers

meeting.

Further we support several other applications used within FT
s
, from a bioinforma
tics point of
view. These includ
e SNP technology and ep
igenomics technology. In the epigenomics field we are
developing an analytical approa
ch for high throughput DNA methylation assays which is in part also
applicable to ChIP data (see also Michiel Adri
a
ens
abstract

on this topic
).
W
e will write review papers
about the practical
analytical
approaches for SNP and DNA methylation analyses
.
Also

the
development of (improved or new) pathways for GenMAPP

and PathVisio

is one of our undertakings
(see also other abstract from Susan Coort).
Next to the earlier adaptations of the fat metabolism
pathways
,

a

car
o
tenoid/vitamin A metabolism and selenium p
athway
have
now
been

developed

and
are now available from the new community pathway wiki (www.wikipathways.org)
.



From a technical point of view, we are busy to get the NBX (NuGO blackboxes) up and
running to be used with microarray data. This also includ
es the use of Nutribase, the platform to store
and share your microarray and experimental data within NuGO (Philippe Rocca
-
Serra, Tony Travis).

Because

the availability of quality control, analysis and annotation tools in R and other environments
from the
NBX is under development, we will assist people in using this as soon as it is available.