ArticleNucleic acids research2012
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 3 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
67 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020Pooled it
- The Role of Proliferation in Determining Response to Neoadjuvant Chemotherapy in Breast Cancer: A Gene Expression-Based Meta-Analysis.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Pooled it
- iBBiG: iterative binary bi-clustering of gene sets.Bioinformatics (Oxford, England) · 2012Pooled it
- Transposable Element Is Predictive of Chemotherapy- and Immunotherapy-Related Overall Survival in Glioma.Biomedicines · 2025Article
- BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.Nature biotechnology · 2024Article
- Article
- Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients.Journal of translational medicine · 2023Article
- Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology.Cancers · 2022Review
- Declined expressions of vast mitochondria-related genes represented by CYCS and transcription factor ESRRA in skeletal muscle aging.Bioengineered · 2021Article
- Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.PLoS computational biology · 2021Article
- Linking clinotypes to phenotypes and genotypes from laboratory test results in comprehensive physical exams.BMC medical informatics and decision making · 2021Article
- Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors.Neuroscience bulletin · 2021Article
- Amadis: A Comprehensive Database for Association Between Microbiota and Disease.Frontiers in physiology · 2021Article
- signatureSearch: environment for gene expression signature searching and functional interpretation.Nucleic acids research · 2020Article
- An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier.Cancers · 2020Article
- The transcription factor C/EBPβ orchestrates dendritic cell maturation and functionality under homeostatic and malignant conditions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification and Analysis of Glioblastoma Biomarkers Based on Single Cell Sequencing.Frontiers in bioengineering and biotechnology · 2020Article
- Identification of a Transcriptomic Prognostic Signature by Machine Learning Using a Combination of Small Cohorts of Prostate Cancer.Frontiers in genetics · 2020Article
- Gene Set Analysis: Challenges, Opportunities, and Future Research.Frontiers in genetics · 2020Review
- Dissection of gene expression datasets into clinically relevant interaction signatures via high-dimensional correlation maximization.Nature communications · 2019Article
7 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
16 authors.
Funding
Abstract
GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a 'basket' feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org.
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.