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Enhanced evaluation of RNA expression in esophageal cancer tissues: combining microarray and RNA-sequence approaches

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Title: Enhanced evaluation of RNA expression in esophageal cancer tissues: combining microarray and RNA-sequence approaches
Authors: Otto, Nicola Miriam Elizabeth
Contributors: Tromp, Gerardus, Simba, Hannah, Stellenbosch University. Faculty of Science. Centre of Bioinformatics and Computational Biology.
Publisher Information: Stellenbosch University
Publication Year: 2026
Collection: Stellenbosch University: SUNScholar Research Repository
Subject Terms: Esophageal cancer, Esophageal squamous cell carcinoma -- Pathophysiology, Barrett's esophagus -- Molecular aspects, Gene expression -- Technique, RNA -- Data processing, DNA microarrays -- Data processing, UCTD
Description: Thesis (MSc)--Stellenbosch University, 2026. ; Otto, N. M. E. 2026. Enhanced evaluation of RNA expression in Esophageal Cancer tissues: Combining Microarray and RNA-Sequence approaches. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/9d3bec65-0b95-4f08-a355-bcb6ffb4089c ; ENGLISH ABSTRACT: Esophageal1 cancer (EC) is a serious global health challenge, associated with high mortality rates and limited advances in early detection. The two predominant malignant subtypes, esophageal1 squamous cell carcinoma (ESCC) and esophageal1 adenocarcinoma (EAC), arise through distinct biological and epidemiological pathways, yet both are associated with poor prognoses. Barrett’s esophagus1 (BE), a metaplastic transformation of the normal oesophageal epithelium driven primarily by chronic gastroesophageal reflux, is a recognised precursor lesion for EAC. Together, BE, EAC, and ESCC represent a complex disease spectrum characterised by extensive molecular and transcriptomic dysregulation. Many transcriptomic studies have investigated these conditions, but is often limited by small sample sizes, different methodologies and population-specific biases. This leads to limited reproducibility and biological interpretability, especially in areas like Africa where genomic research is still lacking. The objective of this study was to conduct a thorough integrative analysis of publicly available transcriptome data to discern molecular pathways linked to BE, EAC, and ESCC. To do this, microarray and bulk RNA-sequencing (RNA-seq) datasets were chosen from many independent studies and evaluated utilising, platform-specific techniques. For the microarray component, Affymetrix-based datasets were harmonised through rigorous preprocessing and subjected to a rank-based meta-analysis using a modified RankProd framework to accommodate large-scale data integration. Ranked gene lists were subsequently analysed using SetRank, a pathway enrichment approach designed to reduce bias ...
Document Type: thesis
File Description: xxiii, 78 pages : illustrations, maps; application/pdf
Language: English
Relation: https://scholar.sun.ac.za/handle/10019.1/135967
Availability: https://scholar.sun.ac.za/handle/10019.1/135967
Rights: Stellenbosch University
Accession Number: edsbas.9CC9BB35
Database: BASE
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PubType: Dissertation/ Thesis
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  Data: Enhanced evaluation of RNA expression in esophageal cancer tissues: combining microarray and RNA-sequence approaches
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  Data: Tromp, Gerardus<br />Simba, Hannah<br />Stellenbosch University. Faculty of Science. Centre of Bioinformatics and Computational Biology.
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  Data: Stellenbosch University
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  Data: 2026
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  Data: Stellenbosch University: SUNScholar Research Repository
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  Data: <searchLink fieldCode="DE" term="%22Esophageal+cancer%22">Esophageal cancer</searchLink><br /><searchLink fieldCode="DE" term="%22Esophageal+squamous+cell+carcinoma+--+Pathophysiology%22">Esophageal squamous cell carcinoma -- Pathophysiology</searchLink><br /><searchLink fieldCode="DE" term="%22Barrett's+esophagus+--+Molecular+aspects%22">Barrett's esophagus -- Molecular aspects</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression+--+Technique%22">Gene expression -- Technique</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+--+Data+processing%22">RNA -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+microarrays+--+Data+processing%22">DNA microarrays -- Data processing</searchLink><br /><searchLink fieldCode="DE" term="%22UCTD%22">UCTD</searchLink>
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  Label: Description
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  Data: Thesis (MSc)--Stellenbosch University, 2026. ; Otto, N. M. E. 2026. Enhanced evaluation of RNA expression in Esophageal Cancer tissues: Combining Microarray and RNA-Sequence approaches. Unpublished masters thesis. Stellenbosch: Stellenbosch University [online]. Available: https://scholar.sun.ac.za/items/9d3bec65-0b95-4f08-a355-bcb6ffb4089c ; ENGLISH ABSTRACT: Esophageal1 cancer (EC) is a serious global health challenge, associated with high mortality rates and limited advances in early detection. The two predominant malignant subtypes, esophageal1 squamous cell carcinoma (ESCC) and esophageal1 adenocarcinoma (EAC), arise through distinct biological and epidemiological pathways, yet both are associated with poor prognoses. Barrett’s esophagus1 (BE), a metaplastic transformation of the normal oesophageal epithelium driven primarily by chronic gastroesophageal reflux, is a recognised precursor lesion for EAC. Together, BE, EAC, and ESCC represent a complex disease spectrum characterised by extensive molecular and transcriptomic dysregulation. Many transcriptomic studies have investigated these conditions, but is often limited by small sample sizes, different methodologies and population-specific biases. This leads to limited reproducibility and biological interpretability, especially in areas like Africa where genomic research is still lacking. The objective of this study was to conduct a thorough integrative analysis of publicly available transcriptome data to discern molecular pathways linked to BE, EAC, and ESCC. To do this, microarray and bulk RNA-sequencing (RNA-seq) datasets were chosen from many independent studies and evaluated utilising, platform-specific techniques. For the microarray component, Affymetrix-based datasets were harmonised through rigorous preprocessing and subjected to a rank-based meta-analysis using a modified RankProd framework to accommodate large-scale data integration. Ranked gene lists were subsequently analysed using SetRank, a pathway enrichment approach designed to reduce bias ...
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RecordInfo BibRecord:
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    Languages:
      – Text: English
    Subjects:
      – SubjectFull: Esophageal cancer
        Type: general
      – SubjectFull: Esophageal squamous cell carcinoma -- Pathophysiology
        Type: general
      – SubjectFull: Barrett's esophagus -- Molecular aspects
        Type: general
      – SubjectFull: Gene expression -- Technique
        Type: general
      – SubjectFull: RNA -- Data processing
        Type: general
      – SubjectFull: DNA microarrays -- Data processing
        Type: general
      – SubjectFull: UCTD
        Type: general
    Titles:
      – TitleFull: Enhanced evaluation of RNA expression in esophageal cancer tissues: combining microarray and RNA-sequence approaches
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            NameFull: Otto, Nicola Miriam Elizabeth
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            NameFull: Tromp, Gerardus
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            NameFull: Simba, Hannah
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            NameFull: Stellenbosch University. Faculty of Science. Centre of Bioinformatics and Computational Biology.
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              Y: 2026
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