Protocol Exchange

Author Information

Subject Terms

Keywords

Abstract

Introduction & Materials

Procedures

Outcomes

Conflicting Financial Interests

Associated Publications

Supplementary Files

Figures

Giovanni Coppola

Kellen Winden

Genevieve Konopka

Fuying Gao

Daniel Geschwind

Expression and network analysis of Illumina microarray data

Microarrays are commonly used tools for assessing changes in gene expression between two populations.  Many algorithms exist for analyzing the hybridization signals from theses arrays.  Here, we present our code for assessing changes in expression from samples hybridized to Illumina whole genome microarrays.  We also include our code for building weighted gene coexpression networks.  Finally, we present how we determined the overlap from two independent microarray studies.

1.  Requires a personal computer running R/Bioconductor.

Smyth, G.K., Gentleman, R., Carey, V., Dudoit, S., Irizarry, R., and Huber, W. \(2005). Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor \(Springer), pp. 397-420.





Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. \(2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol, 5.





Zhang, B., and Horvath, S.  \(2005)  A general framework for weighted gene co-expression network analysis.  Stat Appl Genet Mol Biol, 4: Article 17.





Langfelder, P., Zhang, B., and Horvath, S.  \(2008)  Defining clusters from a hierarchical cluster tree:  the Dynamic Tree Cut package for R.  Bioinformatics, 24\(5): 719-20.

None

Biotechnology

Biochemistry

Method Article

Giovanni Coppola, Kellen Winden, Genevieve Konopka, Fuying Gao, Daniel Geschwind

Giovanni Coppola

UCLA

Kellen Winden

UCLA

Genevieve Konopka

UCLA

Fuying Gao

UCLA

Daniel Geschwind

UCLA

DOI:

10.1038/nprot.2009.215

Download PDF

Introduction

Equipment

Procedure

References

Comments

Version History

CURRENT STATUS: Posted

Version 1

No community comments so far

Metrics

Comments: 0

HTML Views: ...

Subject Areas

Biotechnology

Biochemistry

Associated Publications

Human-specific transcriptional regulation of CNS development genes by FOXP2

by Genevieve Konopka, Jamee M. Bomar, Kellen Winden, +6

Nature (20 October, 2009)

Method Article

Giovanni Coppola, Kellen Winden, Genevieve Konopka, Fuying Gao, Daniel Geschwind

Giovanni Coppola

UCLA

Kellen Winden

UCLA

Genevieve Konopka

UCLA

Fuying Gao

UCLA

Daniel Geschwind

UCLA

Badges

Peer Review Timeline

Version History

CURRENT STATUS: Posted

Version 1

No community comments so far

Metrics

Metrics

Comments: 0

HTML Views: ...

Subject Areas

Subject Areas

Biotechnology

Biochemistry

DOI & PDF

DOI:

10.1038/nprot.2009.215

Download PDF

License

Declarations

Introduction

Equipment

Procedure

References

Comments

Related Articles

Associated Publications

Human-specific transcriptional regulation of CNS development genes by FOXP2

by Genevieve Konopka, Jamee M. Bomar, Kellen Winden, +6

Nature (20 October, 2009)

Privacy Policy

Terms of Service