Whole-Transcriptome Causal Network Inference with Genomic and Transcriptomic Data

  • Lingfei WangEmail author
  • Tom Michoel
Part of the Methods in Molecular Biology book series (MIMB, volume 1883)


Reconstruction of causal gene networks can distinguish regulators from targets and reduce false positives by integrating genetic variations. Its recent developments in speed and accuracy have enabled whole-transcriptome causal network inference on a personal computer. Here, we demonstrate this technique with program Findr on 3000 genes from the Geuvadis dataset. Subsequent analysis reveals major hub genes in the reconstructed network.

Key words

Causal gene network Whole-transcriptome network Causal inference Genome–transcriptome variation 



Development of Findr was supported by grants from the BBSRC [BB/J004235/1, BB/M020053/1].


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Division of Genetics and Genomics, The Roslin InstituteThe University of EdinburghMidlothianUK
  2. 2.Current address: Computational Biology Unit, Department of InformaticsUniversity of BergenBergenNorway

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