/merlin-p_inferred_networks

The original repository is accessible here

Condition specific inferred networks:

Heat stress:

  • heat_All.txt (All inferred edges)
  • heat_3more.txt (Edges with frequency of 3 or more)

Osmotic stress:

  • osmotic_All.txt (All inferred edges)
  • osmotic_3more.txt (Edges with frequency of 3 or more)

Skeleton network:

  • merlin_M_K_C_All.txt (All inferred edges)
  • merlin_M_K_C_30K.txt (Top 30K inferred edges)

All predictions in yeast:

  • yeast_networks/inferred/ (All inferred networks, from 8 methods and 3 expression datasets)
  • yeast_networks/gold/ (The gold standard networks (filtered to include only genes from specific datasets))
  • yeast_networks/priors/ (The prior networks)

All predictions in human LCL:

  • LCL_networks/inferred (Inferred networks using PGG, on 4 expression datasets and 3 prior setting (no prior, beta=3, and beta=4))
  • LCL_networks/gold (The two gold standards)
  • LCL_networks/prior (The prior network)

Description of the datasets:

The full description of the datasets can be found in the original paper:

A prior-based integrative framework for functional transcriptional regulatory network inference

Siahpirani and Roy, Nucl Acids Res, 2016.

https://academic.oup.com/nar/article/doi/10.1093/nar/gkw963/2333925/A-prior-based-integrative-framework-for-functional

Yeast datasets:

Prior networks:

  • Motif prior:
    • Gordân et al. Genome Biol. 2011
    • YeTFaSCo (de Boer and Hughes Nucleic Acids Res. 2012)
  • ChIP network:
    • Harbison et al. Nature 2004
    • Venters et al. Mol. Cell. 2011*
  • KO network:
    • Hu et al. Nat. Genet. 2007
    • Reimand et al. Nucleic Acids Res. 2010*

Expression datasets:

  • Natural variation:
    • Brem and Kruglyak Proc. Natl. Acad. Sci. U.S.A. 2005
    • Smith and Kruglyak PLoS Biol. 2008
    • Zhu et al. PLoS Biol. 2012
  • Knockout:
    • Chua et al. Proc. Natl. Acad. Sci. U.S.A. 2006
    • Hu et al. Nat. Genet. 2007
  • Stress response:
    • Gasch et al. Mol. Biol. Cell. 2000

Human datasets:

Prior networks:

  • Motif prior: Cis-BP (Weirauch et al. Cell 2014)

Expression datasets:

  • Natural variation:
    • Geuvadis (Lappalainen et al. Nature 2013
    • Niu et al. Genome Res. 2010
  • Stress response:
    • Benton et al. BMC Genomics. 2011
    • Junaid et al. Biochem. Biophys. Res. Commun. 2011
    • Forrester et al. PLoS One. 2012
    • Luca et al. PLoS One. 2013
    • Su et al. PLoS Genet. 2015
    • Glover et al. PLoS One. 2015
    • GSE22639 and GSE51454