GS2PATH: A web-based integrated Analysis Tool for Finding ...

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22 Οκτ 2013 (πριν από 3 χρόνια και 7 μήνες)

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>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


GS2PATH:

Linking Gene Ontology
and Pathways

Jin Ok Yang

Korean BioInformation Center

6
th

InCoB 2007

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


KOBIC (
Korean BioInformation Center)



The national bioinformatics center of Korea



Integration of diverse biological information



Genome information



Biodiversity information



Bioresource information



Bioinformatics training



International exchange program



Collaborative Development of bioinformatic tools


Bioportal (Biowiki)


Biopipeline (Bioworkflow engine)

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


BioWiki


Wiki



a web technology that enables anyone to create and
update website contents



suited for developing online knowledge bases (e.g.,
Wikipedia )



BioWiki



To adopt the wiki paradigm in biology



Collaborative development of biological knowledge
bases



BioWiki Contest (
http://biowiki.net

)


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology



BioPipe (http://www.biopipe.net)

Design View

Ontology View

Monitoring View

Toolbar

Drag the module from the list and drop it into the design view.


BioWorkFlow Engine


No installation required


Drag & Drop, and then Connect



BioPipe Contest !!


Aug 15th ~ Sep 20
th


Open free Web 2.0


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


GS2PATH:

Linking Gene Ontology and
Pathways

Jin Ok Yang

Korean BioInformation Center

6
th

InCoB 2007

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Background





Efforts on analyzing functional relationships among gene sets
with GO term and pathways


Gene Ontology (GO) Term based analysis


䅮慬祳楳
景捵獥搠潮 晵湣瑩潮


GO term related pathways


䵯牥r畳u晵氠楮景牭慴楯i

How do you
interpret
the gene set ?

GO &

Pathways


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Gene set enrichment


Enrichment Test


Means test to investigate which specific GO term the given gene set has


P
-
value for GO term was calculated by using hyper
-
geometric
probability


Gene set enrichment


Derives its power by focusing on gene sets, that is, groups
of genes that share common biological function,
chromosomal location, or regulation


Evaluates microarray data at the level of gene sets which
are defined based on prior biological knowledge


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Introduction: GO


GO databases and tools


GO term
was used mostly to analyze
data sets to identify
significant
biological changes


Pathways also can be exploited to find
functional relationships in genes

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Introduction: Pathways

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


GS2PATH


A system

to find gene set enrichment in
each
Gene Ontology
(GO)
terms

and map the part
of gene set on GO term into
biological
pathways
(KEGG

and BioCarta)


An integrated search tool
for analyzing the
functional relationships

in gene sets and for
providing comprehensive results

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Features


Functional relationships between GO term and
pathways


Hyper
-
geometric test for gene set enrichment


Dual search for up
-

and down
-

regulation gene set


Various filtering options for GO terms


the number of descendant node, evidence of GO terms
and statistical values mapping gene set in

each GO term


User
-
specified coloring for genes onto pathways

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Implementation

(1/3)


GS2Path consists of


one internal database (mapping database)


four components


Query Processor, GO Accessor, KEGG Accessor,
and BioCarta Accessor

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Schema of internal mapping DB

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Architecture

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Implementation

(2/3)


Query Processor


receives a user query


Converts query into gene related information


distributes it to the other components, waiting for receiving results


from them


GO Accessor



retrieves statistical values mapping gene set in

each GO terms to KEGG
and BioCarta Pathways


Calculates P
-
value using cumulative hyper
-
geometric distribution


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Implementation

(3/3)


BioCarta and KEGG Accessor



retrieve results from BioCarta and KEGG databases,
respectively


To support
user
-
specified coloring
,


For KEGG, exploiting the web service API (SOAP/WSDL) of KEGG


For BioCarta, no supporting user
-
defined coloring API. Thus, after
retrieving the image of a pathway from BioCarta database, we color
genes in the image on
-
the
-
fly.

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


GO Term based Pathways Analysis

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Search


Gene set enrichment test in organism total
profile:
GO, KEGG and BioCarta


Single or two parts analysis (up and down
regulation)


Pathway viewer for KEGG and BioCarta

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Input


Database


GO category


Biological Process


Molecular Function


Cellular Component


Pathways: KEGG and BioCarta



Organism


Human, Mouse, Rat, and Yeast



Gene ID list

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Test



Enrichment test


P
-
value: Hyper
-
geometric probability



FDR (False Discovery Rate)


Adjustment of p
-
value


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Filtering


GO Term


Evidence


Slim


Number of genes in term


P
-
value



Pathways: KEGG and Biocarta


Number of genes in term


P
-
value

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Example: microarray clustering data

Part A

Part B

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Interface

Select Organism

Put the gene set

Select GO category
or Pathways

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Click

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Retaining only
GO terms
having at least
5 genes

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Select customized
colors

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Genes colored in KEGG and BioCarta

>>> Korean BioInformation Center

>>>
KRIBB

Korea Research institute of Bioscience and Biotechnology


Conclusion


Using Gs2path, users


Get the integrated Gene Ontology terms and
pathways information together


Filter the results with various conditions


Capture relationships between Gene Ontology
terms and Pathways



Available at
http://array.kobic.re.kr:8080/arrayport/gs2path/