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BITS2007 Meeting
BITS2007 Meeting



26-28 April 2007 Napoli, Italy

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Identification of cancer signaling pathways from published gene expession signatures using PubLiME
 
Motivation
Gene expression technology has become a routine application
in many laboratories and
has provided large amounts of gene expression signatures
that have been identified in
a variety of cancer types. Interpretation of gene expression
signatures would profit
from the availability of a procedure capable of assigning
differentially regulated
genes or entire gene signatures to defined cancer signaling
pathways. Here we
describe a graph based approach that identifies cancer
signaling pathways from
published gene expression signatures.

Methods
Published gene expression signatures are collected in a
database (PubLiME: Published
Lists of Microarray Experiments) enabled for cross-platform
gene annotation.
Significant co-occurrence modules composed of up to ten
genes in different gene
expression signatures are identified. Significantly
co-occurring genes are linked by
an edge in an undirected graph. Edge betweenness and
k-clique clustering combined
with graph modularity as a quality measure are used to
identify communities in the
resulting graph. 

Results
The identified communities consist of cell cycle, apoptosis,
phosphorylation cascade,
extra cellular matrix, interferon and immune response
regulators as well as
communities of unknown function. The genes constituting
different communities are
characterized by common genomic features and strongly
enriched cis-regulatory modules
in their upstream regulatory regions that are consistent
with pathway assignment of
those genes.
 
Id: 97
Place: Napoli, Italy
Centro Congressi "Federico II"
Via Partenope 36
Napoli
Starting date:
28-Apr-2007   10:20
Duration: 05'
Contribution type: Poster
Primary Authors: MULLER, Heiko (FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, 20139 Milan, Italy; European Institute of Oncology (IEO), Via Ripamonti 435, 20141 Milan, Italy)
Co-Authors: MANCUSO FRANCESCO, Mattia (FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, 20139 Milan, Italy; European Institute of Oncology (IEO), Via Ripamonti 435, 20141 Milan, Italy)
CITTARO, Davide (FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, 20139 Milan, Italy)
FINOCCHIARO, Giacomo (FIRC Institute of Molecular Oncology Foundation (IFOM), Via Adamello 16, 20139 Milan, Italy; European Institute of Oncology (IEO), Via Ripamonti 435, 20141 Milan, Italy)
Presenters: MULLER, Heiko
 
Included in session: Spot Presentations
Included in track: Gene expression and system biology
 




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