Reactome Functional Interaction (FI) Network

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25 Νοε 2013 (πριν από 3 χρόνια και 11 μήνες)

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www.reactome.org


Hinxton 30 March 2011

1

Reactome Functional
Interaction (FI) Network

Steve Jupe

www.reactome.org


Hinxton 30 March 2011

2

Motivation for Pathway and Network Analysis in Cancer



Exclusivity principle


in cancer.


once a gene is mutated in a pathway, the selective growth advantage
incurred by a second mutated gene in the same pathway is minimal.


rare for a single tumor to have multiple genes altered in the same
pathway.



Analyzing mutated genes in a pathway context.


reveals relationships among these genes.


facilitates hypothesis generation on roles of these genes in disease
phenotype.


identifies genes on the affected pathways as therapeutic targets.

www.reactome.org


Hinxton 30 March 2011

3

Analysis Workflow


Cancer Microarray

Experiment:
Gene expression profiling of pancreatic
tumour

(
vs

normal tissue).

Output:

list of genes that show significant changes in expression.

Downstream analysis:

1.
Validation of the top genes sorted by fold
-
change (or p
-
value):
artificial cut
-
off, information loss;

2.
Manual reviewing and gene classification based on literature, databases and own prior
experience:
time
-
consuming and bias;

3.
GO annotation and pathway analysis (e.g.
Reactome
):
what biological terms or functional
categories are represented in the gene list more often than expected by chance;

4.
Network
-
based analysis.
-

identify
markers not as individual genes but as
sub
-
networks
extracted from protein interaction
databases and the resulting sub
-
networks
provide novel
hypotheses for pathways involved
in cancer.


www.reactome.org


Hinxton 30 March 2011

4

What is the Functional Interaction Network?


A reliable interaction network based on manually curated pathways
extended with verified interactions


Covers almost 50% of human
Uniprot

proteins


A resource for construction of FI sub
-
networks based on gene sets


Tools that:


Provide the underlying evidence for FIs


B
uild and analyze network modules of highly
-
interacting groups


P
erform functional enrichment to annotate modules


Expand the network by finding genes related to the experimental data


display source pathway diagrams and overlay with a variety of information
sources such as cancer gene index annotations.


Method and practical application: A human functional protein
interaction network and its application to cancer data analysis,
Wu et
al. 2010 Genome Biology

www.reactome.org


Hinxton 30 March 2011

5

Pairwise Problem

Input
1
-
Input
2
,

Input
1
-
Catalyst,

Input
1
-
Activator,

Input
1
-

Inhibitor,

Input
2
-
Catalyst,

Input
2
-

Activator,

Input
2
-
Inhibtior,

Catalyst
-
Activator,

Catalyst
-

Inhibitor,

Activator
-
Inhibitor

Reaction Functional Interaction


Convert reactions in pathways into pair
-
wise relationships


Functional Interaction
: an interaction in which two proteins are involved in the
same reaction as input, catalyst, activator and/or inhibitor, or as components in a
complex

www.reactome.org


Hinxton 30 March 2011

6

Reactome Functional Interaction (FI) Network [15%]

Wu
et al. Genome Biology
2010

Construction of the Reactome FI Network

www.reactome.org


Hinxton 30 March 2011

7

Coverage after Prediction


10,956 proteins (9,542 genes)


209,988 FIs


5% of network shown here

www.reactome.org


Hinxton 30 March 2011

8

Reactome Pathway Diagram with FI Overlay

www.reactome.org


Hinxton 30 March 2011

9

Limitations of web FI overlay


Simple viewer


no extra tools


Not easy to produce networks


Not dynamic


you can

t move the pathway diagram
objects

www.reactome.org


Hinxton 30 March 2011

10

Projecting Experimental Data onto FI Network

www.reactome.org


Hinxton 30 March 2011

11

A FI Sub
-
Network Generated from Significant
Network Modules based on a TCGA OV
Expression Data Set

www.reactome.org


Hinxton 30 March 2011

12

Cytoscape


Cytoscape
-

open source platform for visualizing complex
-
networks and integrating these with any type of attribute
data.


Java
-
based


Plug
-
in development framework


First public release: July 2002, v0.8


Current release: 2.8.1


Website: http://www.cytoscape.org


www.reactome.org


Hinxton 30 March 2011

13

www.reactome.org


Hinxton 30 March 2011

14

Reactome FI Cytoscape Plug
-
In


Cytoscape v2.7.0 or later.


Reactome Homepage (see URL below)



Menu Bar
-
> Tools, FI Cytoscape Plugin


Save jar file
caBigR3.jar

into Cytoscape plugins folder,
restart.



http://reactomedev.oicr.on.ca:8080/caBigR3WebApp/Cytoscape/plugins/caBigR3.jar



Also available as Java Web Start:
Cytoscape.jnlp


http://reactomedev.oicr.on.ca:8080/caBigR3WebApp/Cytoscape/Cytoscape.jnlp

www.reactome.org


Hinxton 30 March 2011

15

FI Network Analysis Pipeline



Select gene list (mutated, over
-
expressed, down
-
regulated,

amplified or deleted genes)


Project genes of interest onto
Reactome F.I. Network


Identify Disease/Cancer Subnetwork


Apply Clustering Algorithms


Apply Pathway/GO Annotation to

each cluster


Generate Biological Hypothesis!

Predict Disease Gene Function

Classify Patients & Samples


T2D

OvCa

GBM

Breast

Prostate

TCGA

ICGC

www.reactome.org


Hinxton 30 March 2011

16

Using the Reactome FIs Plug
-
in


Choose Plugins, Reactome FIs.






FI plug
-
in supports three file formats:


Simple gene set: one line per gene.


Gene/sample number pair. Contains two required columns, gene
and number of samples having gene mutated, and an optional
third column listing sample names (delimited by semi
-
colon ;).


NCI MAF (mutation annotation file).

www.reactome.org


Hinxton 30 March 2011

17

File Formats

MSI2

PTPRT

PELO

SLC18A1

TACC2

FAM148B

PRC1

MSTN

ATP6V1G2

APOE

IMPA2

AGER

XPO5

MEST

RREB1

BAT1

WIPI1

CATSPERB

SSR1

VEGFA

EGFL8

Simple Gene List

Gene/Sample Number Pairs

NCI MAF (mutation annotation file)

www.reactome.org


Hinxton 30 March 2011

18

Loading a file


Choose file


Choose file format and parameters


Click OK


www.reactome.org


Hinxton 30 March 2011

19

Results Display


Constructed network is displayed in the Network View
panel using an FI specific visual style

www.reactome.org


Hinxton 30 March 2011

20

Pop
-
up menu


Right
-
click an empty space in the network view panel.

www.reactome.org


Hinxton 30 March 2011

21

Fetch FI annotations


Details information on selected
FIs. Three edge attributes are
created: FI Annotation, FI
Direction, and FI Score. Edges
display direction attribute values.


--
> for activating/catalyzing


--
| for inhibition



solid line for complexes or inputs


---

for predicted FIs.


VizMapper tab, Edge Source
Arrow Shape and Edge Target
Arrow Shape values give details.

www.reactome.org


Hinxton 30 March 2011

22

Analyze network functions


Pathway or GO term enrichment analysis for the displayed
network.


Use Data Panel to:


Filter enrichment results by FDR value.


Check

Hide nodes in not selected rows


to display only nodes
in the selected row or rows


To analyze an unlinked set of genes choose the "Show genes
not linked to others" option when importing data

www.reactome.org


Hinxton 30 March 2011

23

Cluster FI network


Runs spectral partition based network clustering
(
Newman, 2006
) on the displayed FI network.


Nodes in different network modules will be shown in
different colours (max 15 colours).

www.reactome.org


Hinxton 30 March 2011

24

Analyze module functions


Pathway or GO term enrichment analysis on individual
network modules.


Use filter to remove small network modules


Filter by FDR


Button selects nodes in the network corresponding to
selected row or rows in the Data Panel.

www.reactome.org


Hinxton 30 March 2011

25

Other features
-

Query FI source


Right
-
click edge, select "Reactome FI/Query FI
Source".


If the FI was extracted from a curated pathway the
original data source(s) is displayed


Double click a row in the table to show details


If the FI is predicted the evidence is displayed.

www.reactome.org


Hinxton 30 March 2011

26

Other features
-

Fetch FIs for node


Select node in the network panel, right click for pop
-
up
menu, select "Reactome FI, Fetch FIs"


FI partners for the selected node are displayed in two
sections: Partners that are displayed and partners that are
not displayed.


Select undisplayed partners and click Add

www.reactome.org


Hinxton 30 March 2011

27

Other features
-

Show pathway diagram (KEGG)


Select a pathway in "Pathways in Network/Modules" tabs, right click,
select "Show Pathway Diagram



KEGG pathways
-

diagram page is opened. Nodes listed in "Nodes"
column are highlighted in red.

www.reactome.org


Hinxton 30 March 2011

28

Other features
-

Show pathway diagram (Reactome)


Reactome pathway diagrams open in a separate window.


For human data the manually drawn pathway diagram is displayed.


For other species an automated layout is generated.


Nodes in the Cytoscape network are highlighted in blue on the diagram


Detailed information is viewed using a pop
-
up menu item "View
Instance".


Zoom slider bottom of the window.


Overview window top
-
right corner

www.reactome.org


Hinxton 30 March 2011

29

Cancer Gene Index annotations


Cancer Gene Index annotations can be added in two
ways:


popup menu "Load Cancer Gene Index" when no object is
selected (left)


popup menu "Fetch Cancer Gene Index" for a selected
node (right)

www.reactome.org


Hinxton 30 March 2011

30

Load Cancer Gene Index


This method loads the tree of NCI disease terms in the left
panel.


Select a disease term in the tree to select all diagram
objects that have this annotation or one of its sub
-
terms.

www.reactome.org


Hinxton 30 March 2011

31

Fetch Cancer Gene Index


This method is for viewing detailed annotations for the
selected gene or protein.


Annotations are sortable by PubMed ID, Cancer type,
status, and several other criteria.

www.reactome.org


Hinxton 30 March 2011

32

Cancer Gene Survival Analysis


Based on a server
-
side R script that runs
either coxph or Kaplan
-
Meyer survival
analysis.


Requires appropriate data file (see online).


Popup menu

Analyze Module Functions,
Survival Analysis...



Results are displayed with a tab "Survival
Analysis" (right).


You can display multiple analyses.


Only Kaplan
-
Meyer analysis will show a plot
file. You can click the file to view the actual
plot (far right).

www.reactome.org


Hinxton 30 March 2011

33

Summary


Reactome

is a highly reliable, human
-
curated database of biological pathways
and reactions.


Expanded the human curated
Reactome

pathways by importing pathways from
other databases and integrating predicted FIs: ~50% coverage.


Functional interaction network provides a powerful way to visualize cancer and
other disease genes to reveal functional relationships among these genes.


www.reactome.org


Hinxton 30 March 2011

34

Future


Implement multiple network clustering algorithms


Currently spectral partition only


Future: edge
-
betweenness, MCL, and hierarchical clustering


Integrate with other data types: gene expressions,
CNVs…


Seamless integration with Reactome pathway diagrams


Expand known cancer pathways by using FIs


Integrate miRNA/target interactions to study miRNA
activities on cancers



www.reactome.org


Hinxton 30 March 2011

35

Software Demo