Detecting Network Motifs in Gene Co-expression Networks Xinxia Peng - - PowerPoint PPT Presentation

Detecting “Network Motifs” in Gene Co-expression Networks

Xinxia Peng

Genome Science & Technology Program The University of Tennessee – Oak Ridge Natl. Lab

Motivation

Modularity of Biological Networks

Co-expression Network

Cutoff: 0.8 Correlation Matrix* Adjacency Matrix

*Pearson’s R

Genes of Similar Function Cluster Together

Densely connected subgraphs

Protein complexes Pathways …

Clique

maximally connected subgraph

Gene Duplication

Paralogs “Paralogous pathways”: pathways with duplicated proteins and interactions

co-expression duplication

1dxy

Protein Domain (or Motif)

Evolutionary unit Functional unit Reiterated use of domains

“Network Motifs”

II and III are

• verlapping,

I and II are non-

• verlapping

Materials and Methods

Protein Domain Annotation

Protein Sequences

PlasmoDB http://plasmodb.org

HMM Library

Pfam http://www.sanger.ac.uk /Software/Pfam

HMMER

http://hmmer.wustl.edu

OIT Cluster

http://icl.cs.utk.edu/si nrg/index.html

Domain Annotations

Network Motif Discovery (1)

< G, k, f > Enumeration of k-vertex cliques Groups of cliques Network motifs Protein domain f: # of non-overlapping cliques

Network Motif Discovery (2)

p-value: fraction of times putative network motifs found in randomized networks

Randomize the real network by randomly

permuting the protein domain labels

Repeat 1,000 times

Network Motif Discovery (3)

Domain Matching Level 2 Domain Matching Level 4

1 1’ A B C A B C 2 2’ A D A D A

Protein Interaction Network and Data Visualization

Protein Interaction Network (PPI)

BIND (http://www.blueprint.org/bind/bind.php) Vertices: genes/proteins Edges: binary protein interactions Protein complex: “matrix” model

Visualization

ALIVE (http://mouse.ornl.gov/alive) R (http://www.r-project-org)

Results

Co-expression Network

• Complete Dataset
• R >= 0.95
• 2,292 ORFs
• 93% ( 2124) with strong

periodic behavior

• cover 78% (2124/2714)
• f Overview Dataset

Prediction of Network Motifs

k: size of network motif. f: min. number of non-overlapping instances # of network motifs having at least one instance in yeast PPI # of network motifs found

↑ k or f , ↑ % in yeast PPI

Percentage of network motifs having instance in yeast PPI network by Freq. x Size. Domain matching level 2

25/88 2/3 11/18 5/6 1/1 0/0 0/0 0/0

↑ k ↑ f

↑ k or f , ↑ % in yeast PPI

Percentage of network motifs having instance in yeast PPI network by Freq. x Size. Domain matching level 4

0/0 0/0 0/0 0/0 6/9 17/32 0/0 6/6 29/87 53/197 13/17 5/5

↑ f ↑ k

Example 1

Functional Annotations

DEAD/DEAH box helicase (PF00270) and Helicase conserved C- terminal domain (PF00271), WD domains, G-beta repeats (PF00400), Brix domain (PF04427), GTPase of unknown function (PF01926).

Supported by Yeast Protein Interactions

Prediction of Complementary Functional Units

Example 2

Functional Annotations

Protein kinase domain (PF00069), Calcineurin-like phosphoesterase (PF00149), AhpC/TSA family (PF00578), it contains Peroxiredoxins (Prxs), a ubiquitous family of antioxidant enzymes, and Prxs can be regulated by phosphorylation.

Differential Temporal Expression

More Results

http://mouse.ornl.gov/~xpv/camda04/index.html

Conclusion

New strategy for microarray data analysis Data integration

Gene expression, sequence, protein interaction, …

Easier for experimental verification

Small clusters Implication about relationships among members

Biological hypothesis

Modularity of biological networks

Acknowledgements

• Dr. Jay Snoddy (Genome Science &

Technology, UT-ORNL)

Adam Tebbe, Suzanne Baktash, …

• Dr. Michael Langston (Computer Science,

UT)

Nicole Baldwin

• Dr. Arnold Saxton (Animal Science, UT)

References

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[3] Chang, L. and Karin, M. Mammalian MAP kinase signalling cascades. Nature, 410 (6824). 37-40. [4] Chang, T.S., Jeong, W., Choi, S.Y., Yu, S., Kang, S.W. and Rhee, S.G. Regulation of peroxiredoxin I activity by Cdc2-mediated

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