Presentación de PowerPoint - Bioinformatics Core at CRG

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Oct 2, 2013 (4 years and 1 month ago)

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Galaxy

InCA

(In
tegration
of
C
ore’s
d
A
ta
)

Integration and
Automation


Guadalupe, Francesco, Ernesto, Toni, Luca

CRG CF
retreat
,
7
-
8
May

2012

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Trend in
Pubmed

Data Integration


Lu

et

al
.

(
2005
)
:

process

of

statistically

combining

data

from

different

sources

to

provide

a

unified

view

of

the

whole

genome

and

make

large
-
scale

statistical

inference
.



Hamid

et

al
.

(
2009
)
:

not

only

combining

data

using

statistical

approaches,

but

also

data

fusion

with

biological

domain

knowledge

using

a

variety

of

bioinformatics

and

computational

tools
.

*

'
Omics
'
-
data integration helps to address interesting
biological questions on the systems level.

Joyce A.R.,
Palsson

B.Ø.,
The model organism as a system: integrating
'
omics
' data sets,
Nature Reviews Molecular Cell Biology 2006

Main actors: semantic web (
i.e

MediaWiki
) & Galaxy

Semantic
Wiki

C.F.

results

Modeling, analysis,
correlation, …


Methylation array
pipeline

Proteomics

pipelines



Image

analysis

NGS

pipelines

Genomics

Microscopy

Proteomics

Bioinformatics

FACS

Histology

Protein

-
Standardize the output;

-
Project the “space” of the results;

-
Conceive the integrative analysis.

Effectors

-
Development of the
semantic web
interface and the
Galaxy;

-
Algorithm
development.

Ning

et

al,

The

utility

of

mass

spectrometry
-
based

proteomic

data

for

validation

of

novel

alternative

splice

forms

reconstructed

from

RNA
-
Seq

data
:

a

preliminary

assessment
,

BMC

Bioinformatics
.

2010


Examples of scientific outcome


Nagaraj

et al,
Deep proteome and
transcriptome

mapping of a
human cancer cell line
., Molecular Systems Biology 2011

Thanks for the attention!!

Hamid

J
.
S
.
,

Hu

P
.
,

Roslin

N
.
M
.
,

Ling

V
.
,

Greenwood

C
.
M
.
T
.
,

Beyene

J
.
,

Data

Integration

in

Genetics

and

Genomics
:

Methods

and

Challenges,

Human

Genomics

and

Proteomics

2009


Foundamental

aspects of data integration