tigre - Transcription factor Inference through Gaussian process Reconstruction of Expression

Description

This package implements the method of Gao et al. (2008) and Honkela et al. (2010) for Gaussian process modelling single input motif regulatory systems with time-series expression data. The method can be used to rank potential targets of transcription factors based on such data.

Details

For details of using the package please refer to the Vignette.

Author(s)

Antti Honkela, Pei Gao, Jonatan Ropponen, Miika-Petteri Matikainen, Magnus Rattray, Neil D. Lawrence

Maintainer: Antti Honkela <antti.honkela@hiit.fi>

References

A.~Honkela, P.~Gao, J.~Ropponen, M.~Rattray, and N.~D.~Lawrence. tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression for Bioconductor. Bioinformatics 27(7):1026-1027, 2011. DOI: 10.1093/bioinformatics/btr057.

P.~Gao, A.~Honkela, M.~Rattray, and N.~D.~Lawrence. Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities. Bioinformatics 24(16):i70–i75, 2008. DOI: 10.1093/bioinformatics/btn278.

A.~Honkela, C.~Girardot, E.~H. Gustafson, Y.-H. Liu, E.~E.~M. Furlong, N.~D. Lawrence, and M.~Rattray. Model-based method for transcription factor target identification with limited data. Proc Natl Acad Sci USA 107(17):7793-7798, 2010. DOI: 10.1073/pnas.0914285107.

See Also

puma

Examples

## Not run: 
  # Load a mmgmos preprocessed fragment of the Drosophila developmental
  # time series
  data(drosophila_gpsim_fragment)

  # Get the target probe names
  library(annotate)
  aliasMapping <- getAnnMap("ALIAS2PROBE",
                    annotation(drosophila_gpsim_fragment))
  twi <- get('twi', env=aliasMapping)
  fbgnMapping <- getAnnMap("FLYBASE2PROBE",
                   annotation(drosophila_gpsim_fragment))
  targetProbe <- get('FBgn0035257', env=fbgnMapping)

  # Learn the model
  model <- GPLearn(drosophila_gpsim_fragment,
                   TF=twi, targets=targetProbe,
                   useGpdisim=TRUE, quiet=TRUE)

  # Plot it
  GPPlot(model, nameMapping=getAnnMap("FLYBASE",
                   annotation(drosophila_gpsim_fragment)))

## End(Not run)