Molecular Networks – Representation and Analysis

Chapter

Abstract

Molecular networks, their representation and analysis have attracted increasing interest in recent years. Although the importance of molecular networks has been recognized for a long time, only the advent of new technologies during the last two decades has delivered the necessary data for a systematic study of molecular networks and their complex behavior. Especially the surge of genome-wide data as well as the increase in computational power have contributed to establishing network and systems biology as new paradigms. The conceptual framework is generally based on an integrated approach of computational and experimental methods. In this chapter, we introduce basic concepts and outline mathematical formalisms for representing and analyzing molecular networks. In particular, we review the study of transcriptional regulatory networks in prokaryotes and of protein interaction networks in humans as prime examples of network-orientated approaches to complex systems. The chapter is concluded with a discussion of current challenges and future directions of network biology.

Keywords

Bayesian Network Molecular Network Boolean Network Transcriptional Regulatory Network Human Protein Reference Database 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

BIND

biomolecular interaction network database

BLAST

basic local alignment search tool

BRCA

breast cancer-associated gene

BioGRID

biological general repository for interaction dataset

CLR

context likelihood of relatedness

ChIP

chromatin immunoprecipitation

Co-IP

coimmunoprecipitation

DBN

dynamic Bayesian network

DIP

database of interaction proteins

DNA

deoxyribonucleic acid

GTP

guanosine triphosphate

GTPBP

GTP binding protein

HMMR

hyaluronan-mediated motility

HPRD

human protein reference database

MI

molecular interaction

MPPI

Mammalian Protein–Protein Interaction Database

ORF

open reading frame

PAGE

polyacrylamide gel electrophoresis

PDB

protein data bank

PPI

protein–protein interaction

PROM

probabilistic regulation of metabolism

PSI

proteomics standard initiative

PTM

posttranslational modification

RNA

ribonucleic acid

ROS

reactive oxygen species

Rb

retinoblastoma

SDS

sodium dodecyl sulfate

STRING

search tool for the retrieval of interacting genes

TF

transcription factor

UniHI

Unified Human Interactome database

XML

extensible markup language

Y2H

yeast two hybrid

cDNA

complementary DNA

mRNA

messenger RNA

ncRNA

noncoding RNA

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Copyright information

© Springer-Verlag 2014

Authors and Affiliations

  1. 1.IBB/Centre for Biomedical and Structural BiomedicineUniversity of AlgarveFaroPortugal
  2. 2.DIBB/Centre for Biomedical and Structural BiomedicineUniversity of AlgarveFaroPortugal
  3. 3.IBB/Centre for Biomedical and Structural BiomedicineUniversity of AlgarveFaroPortugal

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