Integration of Online Omics-Data Resources for Cancer Research

Pan-cancer analysis of whole genomes

(2020)   NATURE

Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia

(2020) Robersy Sanchez et al.   Scientific Reports

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

(2020) Michael A. Gillette et al.   CELL

Genomic and Transcriptomic Landscape of Triple-Negative Breast Cancers: Subtypes and Treatment Strategies

(2019) Yi-Zhou Jiang et al.   CANCER CELL

NEMO: cancer subtyping by integration of partial multi-omic data

(2019) Nimrod Rappoport et al.   BIOINFORMATICS

CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts

(2019) Po-Jung Huang et al.   BMC Medical Genomics

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

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

(2019) Galen F. Gao et al.   Cell Systems

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

(2019) Farhana R. Pinu et al.   Metabolites

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Applications of liquid biopsies for cancer

(2019) Austin K. Mattox et al.   Science Translational Medicine

DriverDBv3: a multi-omics database for cancer driver gene research

(2019) Shu-Hsuan Liu et al.   NUCLEIC ACIDS RESEARCH

Quantifying the impact of public omics data

(2019) Yasset Perez-Riverol et al.   Nature Communications

Harnessing the tissue and plasma lncRNA-peptidome to discover peptide-based cancer biomarkers

(2019) Sajib Chakraborty et al.   Scientific Reports

Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers

(2019) Fengju Chen et al.   Nature Communications

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data

(2018) Zhuo Zhang et al.   BRIEFINGS IN BIOINFORMATICS

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

COSMIC-3D provides structural perspectives on cancer genetics for drug discovery

(2018) Harry C. Jubb et al.   NATURE GENETICS

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

(2018) Wei Tang et al.   Genome Medicine

Onco-Multi-OMICS Approach: A New Frontier in Cancer Research

(2018) Sajib Chakraborty et al.   Biomed Research International

Protein abundance of AKT and ERK pathway components governs cell type‐specific regulation of proliferation

(2017) Lorenz Adlung et al.   Molecular Systems Biology

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

Ki67 assessment in breast cancer: an update

(2017) Frederique Penault-Llorca et al.   PATHOLOGY

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Genome-wide prediction of DNase I hypersensitivity using gene expression

(2017) Weiqiang Zhou et al.   Nature Communications

Comprehensive analysis of normal adjacent to tumor transcriptomes

(2017) Dvir Aran et al.   Nature Communications

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

(2017) Kuan-lin Huang et al.   Nature Communications

UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses

(2017) Darshan S. Chandrashekar et al.   NEOPLASIA

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

(2016) Haiyang Guo et al.   NATURE GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer

(2016) Jeanne Tie et al.   Science Translational Medicine

Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer

(2016) Yunee Kim et al.   Nature Communications

Inhibition of the autocrine IL-6–JAK2–STAT3–calprotectin axis as targeted therapy for HR−/HER2+breast cancers

(2015) Ruth Rodriguez-Barrueco et al.   GENES & DEVELOPMENT

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

(2015) Nathan J. Edwards et al.   JOURNAL OF PROTEOME RESEARCH

moCluster: Identifying Joint Patterns Across Multiple Omics Data Sets

(2015) Chen Meng et al.   JOURNAL OF PROTEOME RESEARCH

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

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

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer

(2015) Anna Díez-Villanueva et al.   Epigenetics & Chromatin

Oncogenomic portals for the visualization and analysis of genome-wide cancer data

(2015) Katarzyna Klonowska et al.   Oncotarget

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes

(2015) Yuanshuai Zhou et al.   PLoS One

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Cancer Systems Biology: a peek into the future of patient care?

(2014) Henrica M. J. Werner et al.   Nature Reviews Clinical Oncology

Group sparse canonical correlation analysis for genomic data integration

(2013) Dongdong Lin et al.   BMC BIOINFORMATICS

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

Pattern discovery and cancer gene identification in integrated cancer genomic data

(2013) Qianxing Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) J. Gao et al.   Science Signaling

Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome

(2013) Debraj GuhaThakurta et al.   Expert Review of Clinical Pharmacology

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Aberrant Epigenetic Landscape in Cancer: How Cellular Identity Goes Awry

(2010) María Berdasco et al.   DEVELOPMENTAL CELL

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS