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Global Molecular and Cellular Measurement Technologies

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Book cover Cancer Systems Biology, Bioinformatics and Medicine

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Abstract

Measuring technologies in the field of molecular biology and cellular biology have developed rapidly over the recent years, most obviously in the sequencing field where capacity and throughput have increased by several orders of magnitude. This has been a major factor in systems biology research , which thrives on technologies facilitating efficient and relatively economical genome-wide readout on DNA, mRNA, protein, and metabolome level. With data generation increasing exponentially, we are faced with new challenges of transforming this data into useful models that help to predict the outcome of genomic aberrations and to develop novel diagnostic and therapeutic strategies. There is currently a technological and digital transition from many array-based assays to second-generation sequencing approaches that analyse gene expression , genotype, single nucleotide polymorphisms and methylation patterns. Sequencing technologies are developing rapidly, as are preparatory enrichment techniques, which include the amplification of sample signal or target enrichment to reduce sample complexity. Proteomics and functional assays have also been much advanced as a result of technological progress in mass spectrometry or automatic microscopy and image analysis. Nevertheless, we are still far away from routinely measuring whole proteome data, because of the complexity of different transcripts and post-translational modifications. In spite of this, numerous new or improved analytical techniques embedded in integrated systems approach frameworks will potentially generate clinical usefulness.

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Abbreviations

BRET:

bioluminescence resonance energy transfer

BS:

bisulfite

CDK:

cyclin dependent kinases

CGH:

comparative genome hybridization

CGP:

cancer genome project

CNVs:

copy number variations

DIGE:

differential-in-gel-electrophoresis

ds:

double stranded

esiRNA:

endoribonuclease-derived short interference RNAs

FISH:

fluorescence in situ hybridizations

FFPE:

formalin-fixed and paraffin-embedded

FRET:

fluorescence resonance energy transfer

GC:

gas chromatography

HPR:

Human Protein Atlas

HRG:

Histidine rich glycoprotein

ICGC:

international cancer genome consortia

IEF:

isoelectric focusing

IHC:

immuno-histo chemistry

IMAC:

immobilized metal affinity chromatography

InDel:

insertions/deletions

IPG:

immobilized pH gradient

ICAT:

isotope encoded affinity tags

LC-MS:

liquid chromatography MS

LUMIER:

luminescence-based mammalian interactome mapping

MBP:

methyl-binding protein

MeDIP:

methylated DNA immuno-precipitation

MGS:

microarray -based genomic selection

MS:

mass spectrometry

MSCC:

Methyl-Seq and methyl-sensitive cut counting

NGS:

next-generation sequencing

NMR:

nuclear magnetic resonance

NSL:

non-small lung cancer

ORF:

open reading frame

PAC:

phosphoramidate chemistry

PGP:

personal genome project

PLA:

proximity ligation assay

PPI:

protein-protein interaction

PSA:

prostate specific antigen

PTM:

posttranslational modification

QQQ:

triple quadrupole

RISC:

RNA-induced silencing complex

RNAi:

RNA interferences

RPPA:

reverse phase protein array

RRBS:

reduced representation BS sequencing

SBGN:

Systems Biology Graphical Notation

SBML:

Systems Biology Markup Language

SNPs:

single nucleotide polymorphisms

SILAC:

stable-isotope labelling by amino acids in cell culture

TAP:

tandem affinity purification

TCGA:

The Cancer Genome Atlas

Y2H:

yeast-two-hybrid

4sU:

4-thiouridine

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Acknowledgments

We thank our colleagues for comments on text and discussions, in particular M. Ralser for his extensive comments and suggestions on the MS part of the manuscript and C. Wierling for contributing Fig. 3.2. Our work is funded through: BL: NGFN IG Cellular Systems Biology, IG Neuronet, IG Mutanom; MS: IG Mutanom, IG Intestinal Modifiers; HL: Max Planck Society

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  1. Department of Vertebrate Genomics, Max-Planck Institute for molecular Genetics, Ihnestrasse 73, 14195, Berlin, Deutschland

    PD. Dr. Bodo M. H. Lange, Dr. Dr. Michal R. Schweiger & Prof. Dr. Hans Lehrach

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  1. PD. Dr. Bodo M. H. Lange
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  2. Dr. Dr. Michal R. Schweiger
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  3. Prof. Dr. Hans Lehrach
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Correspondence to Bodo M. H. Lange .

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  1. Via vi Valcannuta 247, Rome, 00166, Italy

    Alfredo Cesario

  2. Rue Ed. Dereume 72, Rixensart, 1330, Belgium

    Frederick Marcus

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Lange, B., Schweiger, M., Lehrach, H. (2011). Global Molecular and Cellular Measurement Technologies. In: Cesario, A., Marcus, F. (eds) Cancer Systems Biology, Bioinformatics and Medicine. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1567-7_3

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