title: Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression.
abstract: Massively Parallel Signature Sequencing (MPSS), a recently developed high-throughput transcription profiling technology, has the ability to profile almost every transcript in a sample without requiring prior knowledge of the sequence of the transcribed genes. As is the case with DNA microarrays, effective data analysis depends crucially on understanding how noise affects measurements. We analyze the sources of noise in MPSS and present a quantitative model describing the variability between replicate MPSS assays. We use this model to construct statistical hypotheses that test whether an observed change in gene expression in a pair-wise comparison is significant. This analysis is then extended to the determination of the significance of changes in expression levels measured over the course of a time series of measurements. We apply these analytic techniques to the study of a time series of MPSS gene expression measurements on LPS-stimulated macrophages. To evaluate our statistical significance metrics, we compare our results with published data on macrophage activation measured by using Affymetrix GeneChips.
authors.affiliation: IBM Computational Biology Center, PO Box 218, Yorktown Heights, NY 10598, USA. gustavo@us.ibm.com
authors.forename: G A
authors.initials: GA
authors.lastname: Stolovitzky
authors.forename: A
authors.initials: A
authors.lastname: Kundaje
authors.forename: G A
authors.initials: GA
authors.lastname: Held
authors.forename: K H
authors.initials: KH
authors.lastname: Duggar
authors.forename: C D
authors.initials: CD
authors.lastname: Haudenschild
authors.forename: D
authors.initials: D
authors.lastname: Zhou
authors.forename: T J
authors.initials: TJ
authors.lastname: Vasicek
authors.forename: K D
authors.initials: KD
authors.lastname: Smith
authors.forename: A
authors.initials: A
authors.lastname: Aderem
authors.forename: J C
authors.initials: JC
authors.lastname: Roach
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms; D045744:Cell Line, Tumor; D002478:Cells, Cultured; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000737:chemistry; D005260:Female; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D008070:Lipopolysaccharides / Q000494:pharmacology*; D008262:Macrophage Activation / Q000187:drug effects / Q000502:physiology*; D008264:Macrophages / Q000187:drug effects / Q000502:physiology*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D018076:DNA, Complementary; D008070:Lipopolysaccharides