ArticleNucleic acids research2010
GeneSigDB--a curated database of gene expression signatures.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 5 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
68 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma.Genome medicine · 2015Pooled it
- A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer.PloS one · 2013Pooled it
- Expression profiling of archival tumors for long-term health studies.Clinical cancer research : an official journal of the American Association for Cancer Research · 2012Pooled it
- iBBiG: iterative binary bi-clustering of gene sets.Bioinformatics (Oxford, England) · 2012Pooled it
- A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database.BMC genomics · 2010Pooled it
- Exclusive functional signatures for gene annotation with vast OpenOrd layout.Algorithms for molecular biology : AMB · 2025Article
- Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Structural and Phylogenetic Analysis ofVaccines · 2023Article
- Constitutive Activation of the Tumor Suppressor p53 in Hepatocytes Paradoxically Promotes Non-Cell Autonomous Liver Carcinogenesis.Cancer research · 2022Article
- Application of weighted gene co-expression network analysis to identify the hub genes in H1N1.International journal of physiology, pathophysiology and pharmacology · 2021Article
- A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition.Life science alliance · 2020Article
- A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions.Journal of cheminformatics · 2020Review
- netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis.Genome research · 2020Article
- HGNChelper: identification and correction of invalid gene symbols for human and mouse.F1000Research · 2020Article
- A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine.International journal of molecular sciences · 2019Article
- Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.Radiology · 2018Article
- Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response.EBioMedicine · 2018Article
- Drug repurposing for the treatment of glioblastoma multiforme.Journal of experimental & clinical cancer research : CR · 2017Review
- The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms.Scientific reports · 2017Article
- annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.Bioinformatics (Oxford, England) · 2017Article
8 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
11 authors.
Funding
Abstract
The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats.
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.