CNA2Subpathway: identification of dysregulated subpathway driven by copy number alterations in cancer

Transcriptional effects of copy number alterations in a large set of human cancers

(2020) Arkajyoti Bhattacharya et al.   Nature Communications

Autophagy, the innate immune response and cancer

(2020) Chelsea Gerada et al.   Molecular Oncology

Autophagic adaptation to oxidative stress alters peritoneal residential macrophage survival and ovarian cancer metastasis

(2020) Houjun Xia et al.   JCI Insight

Fumarate hydratase in cancer: A multifaceted tumour suppressor

(2019) Christina Schmidt et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Identification of Cancer Dysfunctional Subpathways by Integrating DNA Methylation, Copy Number Variation, and Gene-Expression Data

(2019) Siyao Liu et al.   Frontiers in Genetics

Fluid shear stress stimulates breast cancer cells to display invasive and chemoresistant phenotypes while upregulating PLAU in a 3D bioreactor

(2019) Caymen M. Novak et al.   BIOTECHNOLOGY AND BIOENGINEERING

Hypoxia-reprogrammed tricarboxylic acid cycle promotes the growth of human breast tumorigenic cells

(2019) Ke Tang et al.   ONCOGENE

Comprehensive Benchmarking and Integration of Tumor Microenvironment Cell Estimation Methods

(2019) Alejandro Jiménez-Sánchez et al.   CANCER RESEARCH

The Tricarboxylic Acid Cycle at the Crossroad Between Cancer and Immunity

(2019) Alessandra Scagliola et al.   ANTIOXIDANTS & REDOX SIGNALING

psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression

(2019) Junwei Han et al.   BIOINFORMATICS

Inference of patient-specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer

(2018) Junwei Han et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Recurrent copy number alterations in young women with breast cancer

(2018) Chen Chi et al.   Oncotarget

Fluid Shear Stress Promotes Autophagy in Hepatocellular Carcinoma Cells

(2018) Xiaoli Wang et al.   International Journal of Biological Sciences

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Systematic identification of mutations and copy number alterations associated with cancer patient prognosis

(2018) Joan C Smith et al.   eLife

Association Analysis of Somatic Copy Number Alteration Burden With Breast Cancer Survival

(2018) Linfan Zhang et al.   Frontiers in Genetics

MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data

(2017) Sangseon Lee et al.   METHODS

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

The cyclic GMP/protein kinase G pathway as a therapeutic target in head and neck squamous cell carcinoma

(2016) Traci R. Tuttle et al.   CANCER LETTERS

Estrogen Enhances the Cell Viability and Motility of Breast Cancer Cells through the ERα-ΔNp63-Integrin β4 Signaling Pathway

(2016) Jar-Yi Ho et al.   PLoS One

Non-invasive detection of genome-wide somatic copy number alterations by liquid biopsies

(2015) Ellen Heitzer et al.   Molecular Oncology

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways

(2014) J. Han et al.   Journal of the Royal Society Interface

Derailed Estrogen Signaling and Breast Cancer: An Authentic Couple

(2013) Bramanandam Manavathi et al.   ENDOCRINE REVIEWS

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Fluid shear stress sensitizes cancer cells to receptor-mediated apoptosis via trimeric death receptors

(2013) Michael J Mitchell et al.   NEW JOURNAL OF PHYSICS

Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways

(2013) Chunquan Li et al.   NUCLEIC ACIDS RESEARCH

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Targeting STAT3 inhibits growth and enhances radiosensitivity in head and neck squamous cell carcinoma

(2012) Makoto Adachi et al.   ORAL ONCOLOGY

Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis

(2011) Lisa Pham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hypoxia-inducible factor 1 is a master regulator of breast cancer metastatic niche formation

(2011) C. C.-L. Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Cytoprotective roles for autophagy

(2010) Kevin Moreau et al.   CURRENT OPINION IN CELL BIOLOGY

SubpathwayMiner: a software package for flexible identification of pathways

(2009) C. Li et al.   NUCLEIC ACIDS RESEARCH

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes

(2008) Hyunju Lee et al.   BIOINFORMATICS

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS