Decosus: An R Framework for Universal Integration of Cell Proportion Estimation Methods.

Journal article

Anene, C.A., Taggart, E., Harwood, C., Pennington, D.J. and Wang, J. (2022). Decosus: An R Framework for Universal Integration of Cell Proportion Estimation Methods. Frontiers in genetics. 13, p. 802838. https://doi.org/10.3389/fgene.2022.802838
AuthorsAnene, C.A., Taggart, E., Harwood, C., Pennington, D.J. and Wang, J.
AbstractThe assessment of the cellular heterogeneity and abundance in bulk tissue samples is essential for characterising cellular and organismal states. Computational approaches to estimate cellular abundance from bulk RNA-Seq datasets have variable performances, often requiring benchmarking matrices to select the best performing methods for individual studies. However, such benchmarking investigations are difficult to perform and assess in typical applications because of the absence of gold standard/ground-truth cellular measurements. Here we describe Decosus, an R package that integrates seven methods and signatures for deconvoluting cell types from gene expression profiles (GEP). Benchmark analysis on a range of datasets with ground-truth measurements revealed that our integrated estimates consistently exhibited stable performances across datasets than individual methods and signatures. We further applied Decosus to characterise the immune compartment of skin samples in different settings, confirming the well-established Th1 and Th2 polarisation in psoriasis and atopic dermatitis, respectively. Secondly, we revealed immune system-related UV-induced changes in sun-exposed skin. Furthermore, a significant motivation in the design of Decosus is flexibility and the ability for the user to include new gene signatures, algorithms, and integration methods at run time.
KeywordsGene Expression; R Package; Cell Deconvolution; Method Integration; Immuno-biology
Year2022
JournalFrontiers in genetics
Journal citation13, p. 802838
PublisherFrontiers Media
ISSN1664-8021
Digital Object Identifier (DOI)https://doi.org/10.3389/fgene.2022.802838
Web address (URL)https://www.frontiersin.org/articles/10.3389/fgene.2022.802838/full
Funder/ClientAcademy of Medical Sciences
Publication dates
Online01 Apr 2022
Print01 Jan 2022
Publication process dates
Deposited16 Jun 2022
Accepted author manuscript
License
File Access Level
Open
LicenseCC BY
Permalink -

https://openresearch.lsbu.ac.uk/item/8zy9y

Download files

Accepted author manuscript
Anene, C.A., Taggart, E., Harwood, C.A., Pennington, D.J. and Wang, J., 2022.pdf
License: CC BY 4.0
File access level: Open

  • 51
    total views
  • 38
    total downloads
  • 0
    views this month
  • 0
    downloads this month

Export as

Related outputs

Cumulative incidence and risk factors for cutaneous squamous-cell carcinoma metastases in organ transplant recipients: the SCOPE-ITSCC metastases study, a prospective multi-center study.
de Jong, E., Genders, R., Harwood, C.A, Green, A.C., Plasmeijer, E.I., Proby, C., Geissler, E., Ferrándiz-Pulido, C., Ducroux, E., Euvrard, S., Geusau, A., Jahn-Bassler, K., Borik-Heil, L., Rácz, E., Nägeli, M., Hofbauer, G.F., Piaserico, S., Russo, I., Mackintosh, L., Borges-Costa, J., Angeliki-Gkini, M., Zavattaro, E., Savoia, P., Imko-Walszuk, B., Dębska-Slizień, A., Garmyn, M., van Kelst, S., Ricar, J., Cetkovska, P., Matin, R., Güleç, A.T., Seçkin, D., Anene, C.A., Oliveira, W.R.P., Rademaker, M., Goeman, J., van Geloven, N., Ruiz, E., Murad, F., Karn, E., Schmults, C.D. and Bouwes Bavinck, J.N. (2024). Cumulative incidence and risk factors for cutaneous squamous-cell carcinoma metastases in organ transplant recipients: the SCOPE-ITSCC metastases study, a prospective multi-center study. Journal of the American Academy of Dermatology. https://doi.org/10.1016/j.jaad.2024.01.040
Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis.
Wang J, Harwood CA, Bailey E, Bewicke-Copley F, Anene, C., Thomson J, Qamar MJ, Laban R, Nourse C, Schoenherr C, Treanor-Taylor M, Healy E, Lai C, Craig P, Moyes C, Rickaby W, Martin J, Proby C, Inman GJ and Leigh IM (2023). Transcriptomic analysis of cutaneous squamous cell carcinoma reveals a multi-gene prognostic signature associated with metastasis. Journal of the American Academy of Dermatology. 89 (6), pp. 1159-1166. https://doi.org/10.1016/j.jaad.2023.08.012
Dysregulation of the miR-30c/DLL4 axis by circHIPK3 is essential for KSHV lytic replication
Harper, K.L., Mottram, T.J., Anene, C., Foster, B., Patterson, M.R., McDonnell, E., Macdonald, A., Westhead, D. and Whitehouse, A. (2022). Dysregulation of the miR-30c/DLL4 axis by circHIPK3 is essential for KSHV lytic replication. EMBO Reports. (e54117). https://doi.org/10.15252/embr.202154117
The Genomic Landscape of Actinic Keratosis
Thomson, J., Bewicke-Copley, F., Anene, C., Gulati, A., Nagano, A., Purdie, K., Inman, G.J., Proby, C.M., Leigh, I.M., Harwood, C.A. and Wang, J. (2021). The Genomic Landscape of Actinic Keratosis. The Journal of Investigative Dermatology. https://doi.org/10.1016/j.jid.2020.12.024
ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles
Anene, C., Khan F., Bewicke-Copley, F., Maniati, E. and Wang, J. (2021). ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profiles. Patterns. 2 (6), p. 100270. https://doi.org/10.1016/j.patter.2021.100270
SFPQ promotes an oncogenic transcriptomic state in melanoma
Bi, O., Anene, C., Nsengimana, J., Roberts, W., Newton-Bishop, J. and Boyne, J.R. (2021). SFPQ promotes an oncogenic transcriptomic state in melanoma. Oncogene. 40, pp. 5192-5203. https://doi.org/10.1038/s41388-021-01912-4
Systematic Evaluation of Somatic Cis-Regulatory Mutations in Follicular Lymphoma
Firat U., Bewicke-Copley, F., Anene, C., Schlesner, M., Icgc MMML-Seq Project3, Siebert, R., Okosun, J., Fitzgibbon, J. and Wang, J (2020). Systematic Evaluation of Somatic Cis-Regulatory Mutations in Follicular Lymphoma. American Society of Hematology. https://doi.org/10.1182/blood-2020-142623
The role of CAF derived exosomal microRNAs in the tumour microenvironment of melanoma
Shelton, M., Anene, C., Nsengimana, J., Roberts, W., Newton-Bishop, J. and Boyne, J.R. (2020). The role of CAF derived exosomal microRNAs in the tumour microenvironment of melanoma. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer. 1875 (1), p. 188456. https://doi.org/10.1016/j.bbcan.2020.188456
Merkel cell polyomavirus small tumour antigen activates the p38 MAPK pathway to enhance cellular motility
Dobson, S.J., Anene, C., Boyne, J.R., Mankouri, J., Macdonald, A. and Whitehouse, A (2020). Merkel cell polyomavirus small tumour antigen activates the p38 MAPK pathway to enhance cellular motility. Biochemical Journal. 477 (14), pp. 2721-2733. https://doi.org/10.1042/BCJ20200399
Platelet microparticle delivered microRNA-Let-7a promotes the angiogenic switch
Anene, C., Graham, A.M., Boyne, J. and Roberts, W. (2018). Platelet microparticle delivered microRNA-Let-7a promotes the angiogenic switch. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. https://doi.org/10.1016/j.bbadis.2018.04.013
Platelet induced hepatocellular carcinoma HEPG2 cell proliferation and angiogenic potential is integrin IIb3 dependent.
Rashed, Al-Hammad, Anene, C., Graham, A.M. and Roberts, W. (2015). Platelet induced hepatocellular carcinoma HEPG2 cell proliferation and angiogenic potential is integrin IIb3 dependent. Taylor & Francis. https://doi.org/10.3109/09537104.2015.1115703