4.8 Article

Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver

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 Biochemical Research Methods

monaLisa: an R/Bioconductor package for identifying regulatory motifs

Dania Machlab et al.

Summary: Proteins binding to specific nucleotide sequences, such as transcription factors, have significant roles in regulating gene expression. The monaLisa package, an R/Bioconductor package, provides methods to identify relevant transcription factors from experimental data. It allows seamless motif analyses without relying on software outside of R.

BIOINFORMATICS (2022)

Article Oncology

Ferroptosis Inducers Are a Novel Therapeutic Approach for Advanced Prostate Cancer

Ali Ghoochani et al.

Summary: The study found that mediators of ferroptosis are expressed in treatment-resistant prostate cancer, and treatment with ferroptosis inducers such as erastin and RSL3 can significantly reduce prostate cancer cell growth and migration, potentially serving as novel therapeutic strategies.

CANCER RESEARCH (2021)

Review Cell Biology

Ferroptosis: mechanisms, biology and role in disease

Xuejun Jiang et al.

Summary: Ferroptosis, as a form of regulated cell death driven by iron-dependent phospholipid peroxidation, has seen significant growth in research in recent years. Studies have focused on molecular mechanisms, regulation, and functions of ferroptosis, linking this cell death modality to various pathologies and proposing its roles in normal physiology and potential therapeutic targeting.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Multidisciplinary Sciences

Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis

Chunyang Li et al.

Summary: This study identified hub genes with diagnostic and therapeutic potential in gastric cancer through weighted gene co-expression network analysis and logistic regression, and successfully validated their discriminative ability in an independent testing set using artificial neural network algorithm.
Article Multidisciplinary Sciences

Pancancer survival analysis of cancer hallmark genes

Adam Nagy et al.

Summary: This study aimed to estimate the prognostic effect of cancer hallmark genes in multiple distinct cancer types. The results showed significant heterogeneity and tissue specificity in the correlation between these genes and survival, providing valuable information for future targeted therapy development in solid tumors.

SCIENTIFIC REPORTS (2021)

Article Cell Biology

Pan-cancer RNA-seq data stratifies tumours by some hallmarks of cancer

F. Graeme Frost et al.

JOURNAL OF CELLULAR AND MOLECULAR MEDICINE (2020)

Review Biochemistry & Molecular Biology

Effects of exosomes on pre-metastatic niche formation in tumors

Yaxin Guo et al.

MOLECULAR CANCER (2019)

Review Cell Biology

The multiple mechanisms that regulate p53 activity and cell fate

Antonina Hafner et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

Yuxing Liao et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

TCPA v3.0: An Integrative Platform to Explore the Pan-Cancer Analysis of Functional Proteomic Data

Mei-Ju May Chen et al.

MOLECULAR & CELLULAR PROTEOMICS (2019)

Article Biochemistry & Molecular Biology

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data

Galen F. Gao et al.

CELL SYSTEMS (2019)

Article Multidisciplinary Sciences

FSP1 is a glutathione-independent ferroptosis suppressor

Sebastian Doll et al.

NATURE (2019)

Article Multidisciplinary Sciences

The CoQ oxidoreductase FSP1 acts parallel to GPX4 to inhibit ferroptosis

Kirill Bersuker et al.

NATURE (2019)

Review Oncology

Exosomal tetraspanins as regulators of cancer progression and metastasis and novel diagnostic markers

Rama Rao Malla et al.

ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY (2018)

Article Biochemistry & Molecular Biology

Comprehensive Characterization of Cancer Driver Genes and Mutations

Matthew H. Bailey et al.

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biotechnology & Applied Microbiology

Disruption of Circulating Extracellular Vesicles as a Novel Therapeutic Strategy against Cancer Metastasis

Nao Nishida-Aoki et al.

MOLECULAR THERAPY (2017)

Article Multidisciplinary Sciences

A pathology atlas of the human cancer transcriptome

Mathias Uhlen et al.

SCIENCE (2017)

Review Biochemistry & Molecular Biology

Ferroptosis: process and function

Y. Xie et al.

CELL DEATH AND DIFFERENTIATION (2016)

Article Statistics & Probability

Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent

Noah Simon et al.

Journal of Statistical Software (2015)

Article Biochemical Research Methods

Application of fused lasso logistic regression to the study of corpus callosum thickness in early Alzheimer's disease

Sang H. Lee et al.

JOURNAL OF NEUROSCIENCE METHODS (2014)

Article Biochemical Research Methods

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

Linn Fagerberg et al.

MOLECULAR & CELLULAR PROTEOMICS (2014)

Article Genetics & Heredity

DawnRank: discovering personalized driver genes in cancer

Jack P. Hou et al.

GENOME MEDICINE (2014)

Editorial Material Genetics & Heredity

The Genotype-Tissue Expression (GTEx) project

John Lonsdale et al.

NATURE GENETICS (2013)

Letter Biochemical Research Methods

TCPA: a resource for cancer functional proteomics data

Jun Li et al.

NATURE METHODS (2013)

Article Biochemistry & Molecular Biology

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

Jianjiong Gao et al.

SCIENCE SIGNALING (2013)

Article Multidisciplinary Sciences

Comprehensive identification of mutational cancer driver genes across 12 tumor types

David Tamborero et al.

SCIENTIFIC REPORTS (2013)

Article Biochemistry & Molecular Biology

Mutual exclusivity analysis identifies oncogenic network modules

Giovanni Ciriello et al.

GENOME RESEARCH (2012)

Article Statistics & Probability

RANDOM LASSO

Sijian Wang et al.

ANNALS OF APPLIED STATISTICS (2011)

Review Biochemistry & Molecular Biology

Hallmarks of Cancer: The Next Generation

Douglas Hanahan et al.

Article Statistics & Probability

Regression shrinkage and selection via the lasso: a retrospective

Robert Tibshirani

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2011)

Article Biochemical Research Methods

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

Bruno M. Tesson et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

An Integrated Approach to Uncover Drivers of Cancer

Uri David Akavia et al.

Article Computer Science, Interdisciplinary Applications

Regularization Paths for Generalized Linear Models via Coordinate Descent

Jerome Friedman et al.

JOURNAL OF STATISTICAL SOFTWARE (2010)

Article Statistics & Probability

Stability selection

Nicolai Meinshausen et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2010)

Article Statistics & Probability

ON THE ADAPTIVE ELASTIC-NET WITH A DIVERGING NUMBER OF PARAMETERS

Hui Zou et al.

ANNALS OF STATISTICS (2009)

Article Biochemistry & Molecular Biology

Deficiency of the Tetraspanin CD63 Associated with Kidney Pathology but Normal Lysosomal Function

Jenny Schroeder et al.

MOLECULAR AND CELLULAR BIOLOGY (2009)

Article Biochemical Research Methods

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Steffen Durinck et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Article Oncology

Targeting von Hippel-Lindau pathway in renal cell carcinoma

Premal H. Patel et al.

CLINICAL CANCER RESEARCH (2006)

Article Statistics & Probability

The adaptive lasso and its oracle properties

Hui Zou

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION (2006)

Article Immunology

Anti-CD63 antibodies suppress IgE-dependent allergic reactions in vitro and in vivo

S Kraft et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2005)

Article Biochemistry & Molecular Biology

A general framework for weighted gene co-expression network analysis

Bin Zhang et al.

STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY (2005)

Article Statistics & Probability

Regularization and variable selection via the elastic net

H Zou et al.

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2005)

Article Oncology

Human agmatinase is diminished in the clear cell type of renal cell carcinoma

K Dallmann et al.

INTERNATIONAL JOURNAL OF CANCER (2004)