PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples | Zendy

Antti Häkkinen | Zendy; Kaiyang Zhang | Zendy; Amjad Alkodsi | Zendy; Noora Andersson | Zendy; Erdoğan Pekcan Erkan | Zendy; Jun Dai | Zendy; Katja Kaipio | Zendy; Tarja Lamminen | Zendy; Naziha Mansuri | Zendy; Kaisa Huhtinen | Zendy; Anna Vähärautio | Zendy; Olli Carpén | Zendy; Johanna Hynninen | Zendy; Sakari Hietanen | Zendy; Rainer Lehtonen | Zendy; Sampsa Hautaniemi | Zendy

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PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples

Author(s) -

Antti Häkkinen,

Kaiyang Zhang,

Amjad Alkodsi,

Noora Andersson,

Erdoğan Pekcan Erkan,

Jun Dai,

Katja Kaipio,

Tarja Lamminen,

Naziha Mansuri,

Kaisa Huhtinen,

Anna Vähärautio,

Olli Carpén,

Johanna Hynninen,

Sakari Hietanen,

Rainer Lehtonen,

Sampsa Hautaniemi

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab178

Subject(s) - transcriptome , rna seq , prism , rna , sample (material) , biology , computational biology , gene expression , genetics , gene , physics , chemistry , chromatography , optics

A major challenge in analyzing cancer patient transcriptomes is that the tumors are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a longitudinal, prospective ovarian cancer cohort and found that the sample composition changes systematically due to chemotherapy and between the anatomical sites, preventing direct comparison of treatment-naive and treated samples.

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