esca-type-data {plasma}

ESCA type data

Description

The CombinedWeights object class merges the weight matrices for all data sets in a plasma object.

Usage

data(tfESCA)
data(mirESCA)

Format

Both tfData and mirESCA are data frames containng two columns. The first column is and ID column containing the TCGA sample barcode for an esophagela cancer sample. The second column, called Type identifies the sample as either "squamous" (for likely squamous cell carcinomas that cluster near head and neck cancers) or "adeno" (for likley adenocarcinomas that cluster near stomach cancers).

Author(s)

Kevin R. Coombes [e-mail], Kyoko Yamaguchi [e-mail]

Source

All data supplied here are based upon esophageal cancer data generated by the TCGA Research Network (https://www.cancer.gov/tcga).

The transcription factor classifications of 196 esophageal cancer into squamous cell carcinoma or adenocarcinoma are taken from work published by Abrams and colleaagues in BMC Genomics.

The microRNA classifications of 195 esophageal cancer samples into squamous cell carcinoma or adenocarcinoma are taken from work published by Asiaee and colleaagues in J Comput Biol.

References

Abrams ZB, Zucker M, Wang M, Asiaee Taheri A, Abruzzo LV, Coombes KR.
Thirty biologically interpretable clusters of transcription factors distinguish cancer type.
BMC Genomics. 2018 Oct 11;19(1):738. doi: 10.1186/s12864-018-5093-z.

Asiaee A, Abrams ZB, Nakayiza S, Sampath D, Coombes KR.
Explaining Gene Expression Using Twenty-One MicroRNAs.
J Comput Biol. 2020 Jul;27(7):1157-1170. doi: 10.1089/cmb.2019.0321.