Integrative Transcriptomic Profiling of Lung Adenocarcinoma

Obtain the FPKM expression matrix for lung adenocarcinoma from the Genomic Data Commons (GDC) repository (https://portal.gdc.cancer.gov/ ). Gene expression profiles of lung adenocarcinoma were queried from the GEO Gene Expression Dataset (https://www.ncbi.nlm.nih.gov/geo/ ) and microarray and high-throughput sequencing transcriptome data GSE42127, GSE72094, GSE26939, GSE31547, GSE19188, GSE14814, GSE37745, GSE5828 (BULK transcriptome data for validation), GSE135222, PRJEB23709, phs000452 (BULK transcriptome data for validation of impact on immunotherapy); we applied a text-mining-based data parsing workflow to collect the TISCH2 database (http://tisch.compgenomics.org/ ) of GSE117570 lung adenocarcinoma single-cell dataset, with all genes expressed in at least 3 cells, at least 200 genes per cell, UMIs retaining reads in the range 500-6500 depending on distribution, and percentage of mitochondrial reads < 80%; single-cell data as UMI transcript matrices as well as cellular information matrices, merged into Seraut objects required for analysis, using LogNormalize to normalise the data and check for batch effects between samples by UMAP and found no significant batch effects between samples.

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He N., Xi Y., Yu D., Yu C, & Shen W. (2023). Construction of IL-1 signalling pathway correlation model in lung adenocarcinoma and association with immune microenvironment prognosis and immunotherapy: Multi-data validation. Frontiers in Immunology, 14, 1116789.

Publication 2023

Bulk Cancer Cell Cell matrices Cellular matrices Gene expression Genes Genomic Immunotherapy Lung adenocarcinoma Microarray Mitochondrial Tisch Transcriptome

Corresponding Organization : Ningbo University

Other organizations : Nankai University

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Variable analysis

independent variables

Lung adenocarcinoma gene expression profiles obtained from the GEO Gene Expression Dataset (GSE42127, GSE72094, GSE26939, GSE31547, GSE19188, GSE14814, GSE37745, GSE5828, GSE135222, PRJEB23709, phs000452)
Lung adenocarcinoma single-cell dataset from the TISCH2 database (GSE117570)

dependent variables

FPKM expression matrix for lung adenocarcinoma from the Genomic Data Commons (GDC) repository

control variables

Genes expressed in at least 3 cells
At least 200 genes per cell
UMIs retaining reads in the range 500-6500 depending on distribution
Percentage of mitochondrial reads < 80%

controls

Positive controls: Not explicitly mentioned
Negative controls: Not explicitly mentioned

Annotations

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