The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Molecular signatures database (MSigDB) 3.0
Open accessAbstract
MOTIVATION: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. RESULTS: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. AVAILABILITY AND IMPLEMENTATION: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Transcription factor activities can be estimated using enrichment of their downstream targets26,27.”
From Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease (2023) · cites this paper as [27]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Ground truth is annotated according to Ensembl Release 110 [13], as collected in the MSigDB [29] C1 gene set (c1.all.v2023.2.Hs.symbols.gmt).”
From LAB-Bench: Measuring Capabilities of Language Models for Biology Research (2024) · cites this paper as [29]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Since transcription factor gene expression levels do not always reflect their functional importance, we chose those with the highest or lowest activities based on the induction or suppression of their downstream targets (See methods for details)26,27.”
From Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease (2023) · cites this paper as [27]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“which has a clear relationship to the diet phenotype”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Liberzon et al. 2011
Experimental — accuracy not yet measuredIn the citing paper
“The limma authors maintain mouse and human versions of the Molecular Signatures Database collections (64) in R binary format that can be conveniently used with camera, mroast or romer”
From limma powers differential expression analyses for RNA-sequencing and microarray studies (2015) · cites this paper as [64]
In the citing paper
“This OXTR/CD38 module was also enriched in genesets reported in the Molecular Signatures Database34 that are associated with several behavioral and cognitive state processes including feeding behavior (p = 5.83 × 10−3), cognition (p = 7.44 × 10−3), and behavioral response to stimuli (p = 1.05 × 10−2).”
From Oxytocin pathway gene networks in the human brain (2019) · cites this paper as [34]
In the citing paper
“Biological process labels are stored in databases such as MSigDB (Liberzon et al, 2011), the Gene Ontology (Ashburner et al, 2000; The Gene Ontology Consortium, 2017), or the pathway databases KEGG (Kanehisa et al, 2017) and Reactome (Fabregat et al, 2018).”
From Current best practices in single-cell RNA-seq analysis: a tutorial (2019) · cites this paper as Liberzon et al, 2011
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
Self-citationGene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197
Self-citationTRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
Matys, V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj143 · Cited by 2,142
NCBI GEO: archive for high-throughput functional genomic data
Barrett, T., Troup, D. B., Wilhite, S. E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I. F., Soboleva, A., Tomashevsky, M., Marshall, K. A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn764 · Cited by 1,043
Reactome knowledgebase of human biological pathways and processes
Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., de Bono, B., Garapati, P., Hemish, J., Hermjakob, H., Jassal, B., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn863 · Cited by 873
Parkinson, H., Kapushesky, M., Kolesnikov, N. N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Bérubé, H., Dyląg, M., Emam, I., Farne, A., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn889 · Cited by 418
A library of gene expression signatures to illuminate normal and pathological lymphoid biology
Shaffer, A. L., Wright, G. W., Yang, L., Powell, J. I., Ngo, V. N., Lamy, L., Lam, L. T., Davis, R. E., & Staudt, L. M. (2006) · Immunological Reviews · doi:10.1111/j.0105-2896.2006.00373.x · Cited by 227
Cahan, P., Rovegno, F., Mooney, D. L., Newman, J. C., Laurent, G. S., & McCaffrey, T. A. (2007) · Gene · doi:10.1016/j.gene.2007.06.016 · Cited by 129
GeneSigDB—a curated database of gene expression signatures
Culhane, A. C., Schwarzl, T., Sultana, R., Picard, K. C., Picard, S., Lu, T. H., Franklin, K. R., French, S. J., Papenhausen, G., Correll, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1015 · Cited by 96
CCancer: a bird's eye view on gene lists reported in cancer-related studies
Dietmann, S., Lee, W., Wong, P., Rodchenkov, I. V., & Antonov, A. V. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq515 · Cited by 27
Flagged first, then by citations
Cited by
Sorted by citations
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
The Molecular Signatures Database Hallmark Gene Set Collection
Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807
Self-citationnode2vec: Scalable Feature Learning for Networks
Grover, A., & Leskovec, J. (2016) · Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · doi:10.1145/2939672.2939754 · Cited by 10,926
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S. L., Jagodnik, K. M., Lachmann, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw377 · Cited by 10,799
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G. V., Clark, N. R., & Ma’ayan, A. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-128 · Cited by 7,814
Metadata
- Authors
- Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P.
- Affiliations
- Broad Institute (US)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-05
- Volume
- 27
- Issue
- 12
- Pages
- 1739-1740
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3106198
- OpenAlex
- W2010457001
- Cited by
- 7,111
- References
- 14
- Citations by year
- 2026: 675 · 2025: 1003 · 2024: 1086 · 2023: 942 · 2022: 825 · 2021: 774 · 2020: 602 · 2019: 374 · 2018: 203 · 2017: 151 · 2016: 141 · 2015: 117 · 2014: 102 · 2013: 64 · 2012: 38
- FWCI
- 27.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Cancer Institute (R01CA121941)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- MSigDB, gene sets, canonical pathways, experimental signatures, gene set annotation, biological process annotation, genomic data interpretation, molecular signatures
- MeSH terms
- Internet, Genomics, Databases, Genetic, Molecular Sequence Annotation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
