cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer.

Journal article

Mahmoud Ahmed, Deok Ryong Kim
PeerJ, vol. 7, 2019, pp. e6509

Cite

APA Click to copy
Ahmed, M., & Kim, D. R. (2019). cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer. PeerJ, 7, e6509. https://doi.org/10.7717/peerj.6509

Chicago/Turabian Click to copy
Ahmed, Mahmoud, and Deok Ryong Kim. “CRegulome: an R Package for Accessing MicroRNA and Transcription Factor-Gene Expression Correlations in Cancer.” PeerJ 7 (2019): e6509.

MLA Click to copy
Ahmed, Mahmoud, and Deok Ryong Kim. “CRegulome: an R Package for Accessing MicroRNA and Transcription Factor-Gene Expression Correlations in Cancer.” PeerJ, vol. 7, 2019, p. e6509, doi:10.7717/peerj.6509.

BibTeX Click to copy

@article{mahmoud2019a,
  title = {cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer.},
  year = {2019},
  journal = {PeerJ},
  pages = {e6509},
  volume = {7},
  doi = {10.7717/peerj.6509},
  author = {Ahmed, Mahmoud and Kim, Deok Ryong}
}

Abstract

Background: Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions.

Implementation: Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data.

Availability: cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.