atlas of miRNA-gene correlations in cancer
Nina Hauptman (Author), Jože Pižem (Author), Daša Jevšinek Skok (Author)

Abstract

The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.

Keywords

miRNA;gene;expression;cancer;correlation;gene prioritization;

Data

Language: English
Year of publishing:
Typology: 1.01 - Original Scientific Article
Organization: KIS - Agricultural Institute of Slovenia
UDC: 577.2
COBISS: 198138371 Link will open in a new window
ISSN: 2001-0370
Views: 28
Downloads: 8
Average score: 0 (0 votes)
Metadata: JSON JSON-RDF JSON-LD TURTLE N-TRIPLES XML RDFA MICRODATA DC-XML DC-RDF RDF

Other data

Secondary language: Slovenian
Secondary keywords: miRNA;gen;izražanje;rak (medicina);korelacija;prednostno določanje genov;
Type (COBISS): Article
Source comment: Nasl. z nasl. zaslona; Opis vira z dne 7. 6. 2024;
Pages: str. 2277-2288
Issue: ǂVol. ǂ23
Chronology: 2024
DOI: 10.1016/j.csbj.2024.05.030
ID: 25762706