4.6 Article

Exploring Core Genes by Comparative Transcriptomics Analysis for Early Diagnosis, Prognosis, and Therapies of Colorectal Cancer

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Medicine, General & Internal

Early detection and prognosis prediction for colorectal cancer by circulating tumour DNA methylation haplotypes: A multicentre cohort study

Shaobo Mo et al.

Summary: This study developed a noninvasive detection method for early detection and prognosis prediction of colorectal cancer based on circulating tumor DNA (ctDNA) methylation haplotype patterns. The analysis of plasma samples from 1138 individuals revealed the accuracy of ctDNA methylation patterns in distinguishing healthy individuals, advanced adenoma patients, and colorectal cancer patients. The method showed high accuracy and sensitivity, and high methylation levels were associated with poor prognosis.

ECLINICALMEDICINE (2023)

Article Biology

Robust identification of common genomic biomarkers from multiple gene expression profiles for the prognosis, diagnosis, and therapies of pancreatic cancer

Md Bayazid Hossen et al.

Summary: In this study, the authors identified 71 common differentially expressed genes (cDEGs) between pancreatic cancer and control samples. They further identified 8 key genes (KGs) as the drivers of pancreatic cancer using protein-protein interaction (PPI) network analysis. The expression patterns of KGs were validated using public databases. The study also revealed important molecular functions, biological processes, and pathways associated with KGs. Additionally, the authors identified repurposable drug molecules and a new molecule for the treatment of pancreatic cancer through molecular docking and molecular dynamic simulation.

COMPUTERS IN BIOLOGY AND MEDICINE (2023)

Article Biochemistry & Molecular Biology

Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer

Md Selim Reza et al.

Summary: Bioinformatics analysis is important in the diagnosis and treatment of cervical cancer. This study identified key genes and signaling pathways associated with cervical cancer, and found candidate drugs that can potentially target these genes. Furthermore, docking analysis and simulations were performed to determine the binding stability of the top-ranked drugs with their proposed receptors.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Multidisciplinary Sciences

Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing

Md. Parvez Mosharaf et al.

Summary: This study identified 10 hub genes/proteins related to SARS-CoV-2 infection through transcriptomics analysis. Functional and pathway enrichment analyses revealed important functions and signaling pathways associated with the infection. Docking analysis identified seven candidate drugs with strong binding affinities against COVID-19 causing receptor proteins. Stability simulations confirmed the stable performance of the top three drugs. These findings suggest the potential importance of these drugs in the treatment of different variants of SARS-CoV-2 infections.

SCIENTIFIC REPORTS (2022)

Article Biochemistry & Molecular Biology

Mechanisms of Cell Cycle Arrest and Apoptosis in Glioblastoma

Konstantinos Gousias et al.

Summary: Glioblastoma, a common malignant brain tumor, exhibits rapid growth and infiltration. It takes advantage of the patients' biological capacities to maintain its excessive proliferation and invasion, primarily through disrupting cell cycle regulation and apoptosis mechanisms. Molecular targeting therapies have been developed for glioblastoma, and promising therapeutic agents that induce cell cycle arrest and apoptosis are being studied.

BIOMEDICINES (2022)

Article Oncology

Integration of gene expression data identifies key genes and pathways in colorectal cancer

Hossein Hozhabri et al.

Summary: This study analyzed the gene expression profiles of CRC patients, identified 319 common differentially expressed genes, and found the most important dysregulated pathways in CRC through GO and KEGG pathway enrichment analysis. Several critical hub genes were identified, enhancing our understanding of the molecular mechanisms of CRC.

MEDICAL ONCOLOGY (2021)

Article Multidisciplinary Sciences

Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome

Eleonora Porcu et al.

Summary: Identification of gene expression changes between healthy and diseased individuals can reveal mechanistic insights and biomarkers. The bi-directional transcriptome-wide Mendelian Randomization approach was proposed to assess causal effects between gene expression and complex traits. Comparing transcript levels between healthy and diseased individuals allows for the identification of differentially expressed genes that may be causes, consequences or mere correlates of the disease under scrutiny.

NATURE COMMUNICATIONS (2021)

Article Oncology

A network pharmacology approach for investigating the multi-target mechanisms of Huangqi in the treatment of colorectal cancer

Xiao-Dong Chu et al.

Summary: This study systematically revealed the multitarget mechanism of HQ in CRC through a network pharmacology approach. We verified that HQ promotes CRC cell death via the IL-17 signaling pathway. This finding provides indications for further mechanistic studies and the development of HQ as a potential treatment for CRC patients.

TRANSLATIONAL CANCER RESEARCH (2021)

Article Oncology

Molecular Classification Based on Prognostic and Cell Cycle-Associated Genes in Patients With Colon Cancer

Zhiyuan Zhang et al.

Summary: Molecular classification of colon cancer patients based on cell cycle-associated genes can effectively identify different subgroups, providing new insights for diagnosis and treatment of patients.

FRONTIERS IN ONCOLOGY (2021)

Article Environmental Sciences

Identification of Hub Genes in Different Stages of Colorectal Cancer through an Integrated Bioinformatics Approach

Abhijeet R. Patil et al.

Summary: The study identified hub genes in different stages of CRC and their roles in key pathways, including the cell cycle and the p53 signaling pathway. Some of these genes were also related to stress-survival and apoptosis pathways. The hub DEGs may be used as biomarkers and contribute to understanding the mechanisms of CRC development and progression.

INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH (2021)

Article Oncology

Colorectal cancer statistics, 2020

Rebecca L. Siegel et al.

CA-A CANCER JOURNAL FOR CLINICIANS (2020)

Article Biochemistry & Molecular Biology

MELK Accelerates the Progression of Colorectal Cancer via Activating the FAK/Src Pathway

Guangming Liu et al.

BIOCHEMICAL GENETICS (2020)

Article Oncology

The prognosis analysis of RFWD2 inhibiting the expression of ETV1 in colorectal cancer

Wei Huang et al.

TRANSLATIONAL CANCER RESEARCH (2020)

Article Biochemistry & Molecular Biology

TIMER2.0 for analysis of tumor-infiltrating immune cells

Taiwen Li et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Medicine, General & Internal

miR-485-3p suppresses colorectal cancer via targeting TPX2

K. Taherdangkoo et al.

BRATISLAVA MEDICAL JOURNAL-BRATISLAVSKE LEKARSKE LISTY (2020)

Article Gastroenterology & Hepatology

Prognostic value of DLGAP5 in colorectal cancer

Vittorio Branchi et al.

INTERNATIONAL JOURNAL OF COLORECTAL DISEASE (2019)

Article Biochemistry & Molecular Biology

PubChem 2019 update: improved access to chemical data

Sunghwan Kim et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biotechnology & Applied Microbiology

Potential Prognostic and Diagnostic Values of CDC6, CDC45, ORC6 and SNHG7 in Colorectal Cancer

Yang Hu et al.

ONCOTARGETS AND THERAPY (2019)

Article Biochemistry & Molecular Biology

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions

Dimitra Karagkouni et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Aziz Khan et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors

Sarmistha Mitra et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2018)

Article Biochemical Research Methods

Identification of genes involved in the four stages of colorectal cancer: Gene expression profiling

Guiling Shi et al.

MOLECULAR AND CELLULAR PROBES (2018)

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Cell Biology

Targeting the cell cycle in breast cancer: towards the next phase

K. L. Thu et al.

CELL CYCLE (2018)

Article Chemistry, Medicinal

Manzamine A Exerts Anticancer Activity against Human Colorectal Cancer Cells

Li-Chun Lin et al.

MARINE DRUGS (2018)

Article Gastroenterology & Hepatology

Global patterns and trends in colorectal cancer incidence and mortality

Melina Arnold et al.

Article Biochemistry & Molecular Biology

Identification of Key Candidate Genes and Pathways in Colorectal Cancer by Integrated Bioinformatical Analysis

Yongchen Guo et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2017)

Review Biochemistry & Molecular Biology

FOXC1: an emerging marker and therapeutic target for cancer

B. Han et al.

ONCOGENE (2017)

Article Biotechnology & Applied Microbiology

Identification of differentially expressed genes and their upstream regulators in colorectal cancer

H. Y. Liu et al.

CANCER GENE THERAPY (2017)

Article Cell Biology

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Mohashin Pathan et al.

JOURNAL OF EXTRACELLULAR VESICLES (2017)

Article Pathology

Aurora Kinase A Is a Prognostic Marker in Colorectal Adenocarcinoma

Hyun Min Koh et al.

JOURNAL OF PATHOLOGY AND TRANSLATIONAL MEDICINE (2017)

Article Biochemistry & Molecular Biology

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Maxim V. Kuleshov et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

DSigDB: drug signatures database for gene set analysis

Minjae Yoo et al.

BIOINFORMATICS (2015)

Article Biotechnology & Applied Microbiology

Extracellular synthesis of gold bionanoparticles by Nocardiopsis sp and evaluation of its antimicrobial, antioxidant and cytotoxic activities

Panchanathan Manivasagan et al.

BIOPROCESS AND BIOSYSTEMS ENGINEERING (2015)

Article Biochemical Research Methods

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data

Jianguo Xia et al.

NATURE PROTOCOLS (2015)

Article

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

Katarzyna Tomczak et al.

Wspolczesna Onkologia-Contemporary Oncology (2015)

Article Mathematical & Computational Biology

cytoHubba: identifying hub objects and sub-networks from complex interactome

Chia-Hao Chin et al.

BMC SYSTEMS BIOLOGY (2014)

Article Chemistry, Physical

Lipid14: The Amber Lipid Force Field

Callum J. Dickson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Oncology

Cell Cycle Proteins Predict Recurrence in Stage II and III Colon Cancer

Eric J. Th Belt et al.

ANNALS OF SURGICAL ONCOLOGY (2012)

Review Oncology

The cell cycle and cancer

Gareth H. Williams et al.

JOURNAL OF PATHOLOGY (2012)

Article Gastroenterology & Hepatology

Emerging roles of the ribonucleotide reductase M2 in colorectal cancer and ultraviolet-induced DNA damage repair

Ai-Guo Lu et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2012)

Review Biochemistry & Molecular Biology

Hallmarks of Cancer: The Next Generation

Douglas Hanahan et al.

Article Cell Biology

Mitotic spindle misorientation in cancer - out of alignment and into the fire

Jillian C. Pease et al.

JOURNAL OF CELL SCIENCE (2011)

Article Biochemistry & Molecular Biology

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

Damian Szklarczyk et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Copy number increase of aurora kinase A in colorectal cancers: a correlation with tumor progression

Chao Zhang et al.

ACTA BIOCHIMICA ET BIOPHYSICA SINICA (2010)

Article Cell Biology

Role of cell cycle regulators in lung carcinogenesis

Beatrice Eymin et al.

CELL ADHESION & MIGRATION (2010)

Article Medicine, General & Internal

Association between colorectal cancer and urologic cancers

Audrey H. Calderwood et al.

ARCHIVES OF INTERNAL MEDICINE (2008)

Review Gastroenterology & Hepatology

Genomic and epigenetic instability in colorectal cancer pathogenesis

William M. Grady et al.

GASTROENTEROLOGY (2008)

Article Oncology

Mitotic Origins of Chromosomal Instability in Colorectal Cancer

W. Brian Dalton et al.

CURRENT COLORECTAL CANCER REPORTS (2007)

Article Biochemistry & Molecular Biology

Cell cycle control in breast cancer cells

CE Caldon et al.

JOURNAL OF CELLULAR BIOCHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Mechanistic and structural analysis of a family 31 α-glycosidase and its glycosyl-enzyme intermediate

AL Lovering et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Biochemical Research Methods

The Protein Data Bank

HM Berman et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field

E Krieger et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)

Article Multidisciplinary Sciences

Lethality and centrality in protein networks

H Jeong et al.

NATURE (2001)

Review Oncology

Genome changes and gene expression in human solid tumors

JW Gray et al.

CARCINOGENESIS (2000)