ArticleBioinformatics (Oxford, England)2018
TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers, 1 of them a synthesis 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
119 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Functional Gene Expression Differentiation of the Notch Signaling Pathway in Female Reproductive Tract Tissues-A Comprehensive Review With Analysis.Frontiers in cell and developmental biology · 2020Pooled it
- Helicobacter pylori infection activates the HIF-1α/ALS2/Rab5 signaling axis in gastric cells.Cell communication and signaling : CCS · 2026Article
- Identification of Clinically Relevant Genes Using Machine Learning Techniques.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Rapid Exploratory Data Visualization for Cancer Genomics.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Molecular typing of stage IB non-small-cell lung cancer for precision medicine.Frontiers in oncology · 2026Article
- An Interpretable Omics-to-Image Transformer Framework for Cancer Prognosis Prediction.Computational and structural biotechnology journal · 2026Article
- RNA/DNA-binding protein TDP43 regulates DNA mismatch repair genes with implications for genome stability.Nucleic acids research · 2025Article
- RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability.bioRxiv : the preprint server for biology · 2025Article
- Article
- A clustering approach to integrative analyses of multiomic cancer data.Journal of applied statistics · 2025Article
- Comprehensive single-cell pan-cancer atlas unveils IFI30+ macrophages as key modulators of intra-tumoral immune dynamics.Frontiers in immunology · 2025Article
- HNRNPC as a pan-cancer biomarker and therapeutic target involved in tumor progression and immune regulation.Oncology research · 2025Article
- Dysregulated miRNA Expression and Androgen Receptor Loss in Racially Distinct Triple-Negative Breast Cancer.International journal of molecular sciences · 2024Article
- GD-Net: An Integrated Multimodal Information Model Based on Deep Learning for Cancer Outcome Prediction and Informative Feature Selection.Journal of cellular and molecular medicine · 2024Article
- DeePathNet: A Transformer-Based Deep Learning Model Integrating Multiomic Data with Cancer Pathways.Cancer research communications · 2024Article
- A model-free and distribution-free multi-omics integration approach for detecting novel lung adenocarcinoma genes.Scientific reports · 2024Article
- Identifying the key hub genes linked with lung squamous cell carcinoma by examining the differentially expressed and survival genes.Molecular genetics and genomics : MGG · 2024Article
- Multi-omic analyses of m5C readers reveal their characteristics and immunotherapeutic proficiency.Scientific reports · 2024Article
- A gene-based score for the risk stratification of stage IA lung adenocarcinoma.Respiratory research · 2024Article
- Lactadherin immunoblockade in small extracellular vesicles inhibits sEV-mediated increase of pro-metastatic capacities.Biological research · 2024Article
59 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
6 authors.
Funding
Abstract
Motivation: The Cancer Genome Atlas (TCGA) program has produced huge amounts of cancer genomics data providing unprecedented opportunities for research. In 2014, we developed TCGA-Assembler, a software pipeline for retrieval and processing of public TCGA data. In 2016, TCGA data were transferred from the TCGA data portal to the Genomic Data Commons (GDCs), which is supported by a different set of data storage and retrieval mechanisms. In addition, new proteomics data of TCGA samples have been generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, which were not available for downloading through TCGA-Assembler. It is desirable to acquire and integrate data from both GDC and CPTAC. Results: We develop TCGA-assembler 2 (TA2) to automatically download and integrate data from GDC and CPTAC. We make substantial improvement on the functionality of TA2 to enhance user experience and software performance. TA2 together with its previous version have helped more than 2000 researchers from 64 countries to access and utilize TCGA and CPTAC data in their research. Availability of TA2 will continue to allow existing and new users to conduct reproducible research based on TCGA and CPTAC data. Availability and implementation: http://www.compgenome.org/TCGA-Assembler/ or https://github.com/compgenome365/TCGA-Assembler-2. Contact: zhuyitan@gmail.com or koaeraser@gmail.com. Supplementary information: Supplementary data are available at Bioinformatics online.
Indexed as
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.