TY - JOUR
T1 - Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer
AU - Otálora-Otálora, Beatriz Andrea
AU - López-Kleine, Liliana
AU - Rojas, Adriana
N1 - Publisher Copyright:
© 2023 by the authors.
PY - 2023/1
Y1 - 2023/1
N2 - The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them the most frequently dysregulated transcription factors. Co-expression, gene regulatory, coregulatory, and transcriptional regulatory networks, along with fibration symmetries, were constructed to identify common connection patterns, alignments, main regulators, and target genes in order to analyze transcription factor complex formation, as well as its synchronized co-expression patterns in every type of lung cancer. The regulatory function of the most frequently dysregulated transcription factors over lung cancer deregulated genes was validated with ChEA3 enrichment analysis. A Kaplan–Meier plotter analysis linked the dysregulation of the top transcription factors with lung cancer patients’ survival. Our results indicate that lung cancer has unique and common deregulated genes and transcription factors with pulmonary arterial hypertension, co-expressed and regulated in a coordinated and cooperative manner by the transcriptional regulatory network that might be associated with critical biological processes and signaling pathways related to the acquisition of the hallmarks of cancer, making them potentially relevant tumor biomarkers for lung cancer early diagnosis and targets for the development of personalized therapies against lung cancer.
AB - The transcriptomic analysis of microarray and RNA-Seq datasets followed our own bioinformatic pipeline to identify a transcriptional regulatory network of lung cancer. Twenty-six transcription factors are dysregulated and co-expressed in most of the lung cancer and pulmonary arterial hypertension datasets, which makes them the most frequently dysregulated transcription factors. Co-expression, gene regulatory, coregulatory, and transcriptional regulatory networks, along with fibration symmetries, were constructed to identify common connection patterns, alignments, main regulators, and target genes in order to analyze transcription factor complex formation, as well as its synchronized co-expression patterns in every type of lung cancer. The regulatory function of the most frequently dysregulated transcription factors over lung cancer deregulated genes was validated with ChEA3 enrichment analysis. A Kaplan–Meier plotter analysis linked the dysregulation of the top transcription factors with lung cancer patients’ survival. Our results indicate that lung cancer has unique and common deregulated genes and transcription factors with pulmonary arterial hypertension, co-expressed and regulated in a coordinated and cooperative manner by the transcriptional regulatory network that might be associated with critical biological processes and signaling pathways related to the acquisition of the hallmarks of cancer, making them potentially relevant tumor biomarkers for lung cancer early diagnosis and targets for the development of personalized therapies against lung cancer.
KW - co-expression networks
KW - common connection patterns
KW - coregulatory network
KW - differentially expressed genes
KW - fibration symmetries
KW - gene regulatory network
KW - lung cancer
KW - lung cancer biomarkers
KW - patient’s survival
KW - pulmonary arterial hypertension
KW - transcription factors
KW - transcriptional regulatory network
KW - transcriptomics and bioinformatics
UR - http://www.scopus.com/inward/record.url?scp=85146742073&partnerID=8YFLogxK
U2 - 10.3390/cimb45010029
DO - 10.3390/cimb45010029
M3 - Article
AN - SCOPUS:85146742073
SN - 1467-3037
VL - 45
SP - 434
EP - 464
JO - Current Issues in Molecular Biology
JF - Current Issues in Molecular Biology
IS - 1
ER -