ArticleF1000Research2016
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 207 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
207 citing papers in PubMed, 2 syntheses or guidelines pooled it, 229 citations in OpenAlex.
- Visualizing genomic characteristics across an RNA-Seq based reference landscape of normal and neoplastic brain.Scientific reports · 2023Pooled it
- The applications of DNA methylation as a biomarker in kidney transplantation: a systematic review.Clinical epigenetics · 2022Pooled it
- Intratumoral B cell and interferon signatures in newly diagnosed glioblastoma are associated with longer survival in patients treated with SurVaxM.Cancer immunology, immunotherapy : CII · 2025Trial
- Article
- Expanding the molecular grading criteria in IDH-mutant astrocytoma.Neuro-oncology · 2026Article
- RepurNet: A network medicine framework for systematic drug repurposing and disease vulnerability discovery.iScience · 2026Article
- Integrative in silico and clinical validation of urinary lncRNAs (SNHG7 & LINC00675) and β-catenin mRNA as molecular markers for early bladder cancer detection.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2026Article
- Identification of pyroptosis and hypoxia related molecular subtypes and a prognostic signature in colorectal cancer.Discover oncology · 2026Article
- Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.Nature communications · 2026Article
- Protein buffering of aneuploidy is driven by coordinated factors identified through machine learning.Molecular systems biology · 2026Article
- Subtype-Stratified Consensus Gene Signatures: Bridging Tumor Cell Biology, Immune Microenvironment, and Clinical Prognosis in Breast Cancer.International journal of molecular sciences · 2026Article
- Aging Associated Transcriptomic Signatures in Tumor and Tumor Adjacent Lung Tissues Associated with Recurrence Following Resection of Stage I Lung Adenocarcinoma.Research square · 2026Article
- MVGAE: A Multi-View Graph Auto-Encoder Model for Drug Prediction of Non-Small Cell Lung Cancer Based on Synthetic Lethality.Current issues in molecular biology · 2026Article
- ATRX loss in sarcomas is associated with dysregulated gene and transposable element expression, loss of DNA methylation, and worse survival.ESMO rare cancers · 2026Article
- Genomic biomarkers of immunotherapy plus chemotherapy in patients with advanced NSCLC: Insights from the phase 3 ORIENT-11 study.iScience · 2026Article
- GNAL-driven calcium signaling reshapes the spatiotemporal immune landscape in ERTranslational cancer research · 2026Article
- Elevated Tumor-Associated Androgen Receptor Activity Correlates with Poor Immune Infiltration and Immunotherapy Response across Cancer Types.Cancer research communications · 2026Article
- CEACAM7 Expression and DNA Methylation: Prognostic Biomarkers for Lung Adenocarcinoma in African Americans.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2026Article
- G-protein coupled estrogen receptor 1Frontiers in endocrinology · 2026Article
- Revisiting differential expression analysis: An updated six-dimensional comparative study.PloS one · 2026Article
147 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 5 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, most packages are designed for specific data types (e.g. expression, epigenetics, genomics) and there is no one comprehensive tool that provides a complete integrative analysis of the resources and data provided by all three public projects. A need to create an integration of these different analyses was recently proposed. In this workflow, we provide a series of biologically focused integrative analyses of different molecular data. We describe how to download, process and prepare TCGA data and by harnessing several key Bioconductor packages, we describe how to extract biologically meaningful genomic and epigenomic data. Using Roadmap and ENCODE data, we provide a work plan to identify biologically relevant functional epigenomic elements associated with cancer. To illustrate our workflow, we analyzed two types of brain tumors: low-grade glioma (LGG) versus high-grade glioma (glioblastoma multiform or GBM). This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, MINET, RTCGAToolbox, TCGAbiolinks.
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Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.