Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets
Summary: Understanding dysregulation of the eukaryotic initiation factor 4F (eIF4F) complex across tumor types is critical to cancer treatment development. We present a protocol and accompanying R package “eIF4F.analysis”. We describe analysis of copy number status, gene abundance and stoichiometry,...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722007602 |
| _version_ | 1797980349924376576 |
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| author | Su Wu Gerhard Wagner |
| author_facet | Su Wu Gerhard Wagner |
| author_sort | Su Wu |
| collection | DOAJ |
| description | Summary: Understanding dysregulation of the eukaryotic initiation factor 4F (eIF4F) complex across tumor types is critical to cancer treatment development. We present a protocol and accompanying R package “eIF4F.analysis”. We describe analysis of copy number status, gene abundance and stoichiometry, survival probability, expression covariation, correlating genes, mRNA/protein correlation, and protein co-expression. Using publicly available large multi-omics data, eIF4F.analysis permits computationally derived and statistically powerful inferences regarding initiation factor regulation in human cancers and clinical relevance of protein interactions within the eIF4F complex.For complete details on the use and execution of this protocol, please refer to Wu and Wagner (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T05:52:59Z |
| format | Article |
| id | doaj.art-4bbe8fbaf5474e0c8a8843c5efc03b40 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T05:52:59Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-4bbe8fbaf5474e0c8a8843c5efc03b402022-12-22T04:42:00ZengElsevierSTAR Protocols2666-16672022-12-0134101880Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasetsSu Wu0Gerhard Wagner1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Corresponding authorDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Corresponding authorSummary: Understanding dysregulation of the eukaryotic initiation factor 4F (eIF4F) complex across tumor types is critical to cancer treatment development. We present a protocol and accompanying R package “eIF4F.analysis”. We describe analysis of copy number status, gene abundance and stoichiometry, survival probability, expression covariation, correlating genes, mRNA/protein correlation, and protein co-expression. Using publicly available large multi-omics data, eIF4F.analysis permits computationally derived and statistically powerful inferences regarding initiation factor regulation in human cancers and clinical relevance of protein interactions within the eIF4F complex.For complete details on the use and execution of this protocol, please refer to Wu and Wagner (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166722007602BioinformaticsCancerRNAseqProteomics |
| spellingShingle | Su Wu Gerhard Wagner Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets STAR Protocols Bioinformatics Cancer RNAseq Proteomics |
| title | Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets |
| title_full | Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets |
| title_fullStr | Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets |
| title_full_unstemmed | Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets |
| title_short | Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets |
| title_sort | protocol to analyze dysregulation of the eif4f complex in human cancers using r software and large public datasets |
| topic | Bioinformatics Cancer RNAseq Proteomics |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722007602 |
| work_keys_str_mv | AT suwu protocoltoanalyzedysregulationoftheeif4fcomplexinhumancancersusingrsoftwareandlargepublicdatasets AT gerhardwagner protocoltoanalyzedysregulationoftheeif4fcomplexinhumancancersusingrsoftwareandlargepublicdatasets |