The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
The Molecular Signatures Database Hallmark Gene Set Collection
Open accessAbstract
The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.
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 cited source says what the claim attributes to it.
In the citing paper
“Performing gene set enrichment analysis using the MSigDB Hallmark gene sets (Liberzon et al. 2015), we observed that Myc target genes and DNA repair pathways were up-regulated, whereas TRP53 pathway genes were down-regulated (Fig. 4D).”
From Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging (2019) · cites this paper as Liberzon et al. 2015
The cited source says what the claim attributes to it.
In the citing paper
“Gene set enrichment analyses were performed according to standard procedures [39, 40] on two published RNA-seq datasets [31, 48]”
From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [40]
The cited source says what the claim attributes to it.
In the citing paper
“( F ) Hallmark gene set (81) enrichment plot for genes upregulated in control reactive astrocytes as compared to Ts21 reactive astrocytes (DEGs: adj. p<0.01, Wilcoxon Rank Sum test).”
From Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex (2026) · cites this paper as [81]
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Moreover, carriers of MNAT1 gene, which is one of the leading genes in the G2/M checkpoint pathway58, were linked to better treatment outcome of FOLFOX54.”
From Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer (2025) · cites this paper as [58]
Experimental — accuracy not yet measuredIn the citing paper
“Significant enrichment of hallmark gene sets (33) for inflammatory response and NF-κB signaling were found in the MDP-l,d dataset (Table S8).”
From Enterococcus peptidoglycan remodeling promotes checkpoint inhibitor cancer immunotherapy (2021) · cites this paper as [33]
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
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
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-citationSystematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108
Ostrom, Q. T., Gittleman, H. R., Farah, P., Ondracek, A., Chen, Y., Wolinsky, Y., Stroup, N. E., Kruchko, C., & Barnholtz‐Sloan, J. S. (2013) · Neuro-Oncology · doi:10.1093/neuonc/not151 · Cited by 12,063
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-citationThe basics of epithelial-mesenchymal transition
Kalluri, R., & Weinberg, R. A. (2009) · Journal of Clinical Investigation · doi:10.1172/jci39104 · Cited by 10,196
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950
Self-citationVerhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2009.12.020 · Cited by 7,575
Self-citationMolecular signatures database (MSigDB) 3.0
Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr260 · Cited by 7,111
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Items 301–400 of 1,112
Ferreira, D. P., da Silva, J. G., Wyss, T., Marraco, S. A. F., Scarpellino, L., Charmoy, M., Maas, R. R., Siddiqui, I., Tang, L., Joyce, J. A., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.09.005 · Cited by 200
Yang, Y., Sun, H., Zhang, Y., Zhang, T., Gong, J., Wei, Y., Duan, Y., Shu, M., Yang, Y., Wu, D., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109442 · Cited by 203
CRY2 and FBXL3 Cooperatively Degrade c-MYC
Huber, A., Papp, S. J., Chan, A. B., Henriksson, E., Jordan, S. D., Kriebs, A., Nguyen, M., Wallace, M., Li, Z., Metallo, C. M., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.012 · Cited by 203
The PTPN2/PTPN1 inhibitor ABBV-CLS-484 unleashes potent anti-tumour immunity
Baumgartner, C. K., Ebrahimi-Nik, H., Iracheta‐Vellve, A., Hamel, K. M., Olander, K. E., Davis, T. G. R., McGuire, K. A., Halvorsen, G. T., Avila, O. I., Patel, C. H., et al. (2023) · Nature · doi:10.1038/s41586-023-06575-7 · Cited by 204
Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer
Uhlitz, F., Bischoff, P., Peidli, S., Sieber, A., Obermayer, B., Blanc, E., Trinks, A., Lüthen, M., Ruchiy, Y., Sell, T., et al. (2021) · EMBO Molecular Medicine · doi:10.15252/emmm.202114123 · Cited by 195
Progressive plasticity during colorectal cancer metastasis
Moorman, A., Benitez, E. K., Cambuli, F., Jiang, Q., Mahmoud, A., Lumish, M., Hartner, S., Balkaran, S., Bermeo, J., Asawa, S., et al. (2025) · Nature · doi:10.1038/s41586-024-08150-0 · Cited by 229
“We performed differential expression analysis of ISC cells against all untreated tumour cells using MAST (v.1.16.0) and GSEA using relevant cell type gene sets from the literature (Supplementary Table 3) as well as all Hallmark 66 and KEGG 67 gene sets (Extended Data Fig.”
InfluentialMiguchi, M., Hinoi, T., Shimomura, M., Adachi, T., Saito, Y., Niitsu, H., Kochi, M., Sada, H., Sotomaru, Y., Ikenoue, T., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0166422 · Cited by 196
Crebbp Loss Drives Small Cell Lung Cancer and Increases Sensitivity to HDAC Inhibition
Jia, D., Augert, A., Kim, D. W., Eastwood, E., Wu, N., Ibrahim, A. H., Kim, K., Dunn, C. T., Pillai, S. P. S., Gazdar, A. F., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-0385 · Cited by 195
Ageing compromises mouse thymus function and remodels epithelial cell differentiation
Baran‐Gale, J., Morgan, M. D., Maio, S., Dhalla, F., Calvo‐Asensio, I., Deadman, M. E., Handel, A. E., Maynard, A., Chen, S., Green, F., et al. (2020) · eLife · doi:10.7554/elife.56221 · Cited by 191
Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia
Witkowski, M. T., Dolgalev, I., Evensen, N. A., Ma, C., Chambers, T. M., Roberts, K. G., Sreeram, S., Dai, Y., Tikhonova, A. N., Lasry, A., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.04.015 · Cited by 200
Wu, J., Liu, Q., Zhang, X., Tan, M., Li, X., Liu, P., Wu, L., Jiao, F., Lin, Z., Wu, X., et al. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05115-x · Cited by 211
Hypoxia inducible factor-1α drives cancer resistance to cuproptosis
Yang, Z., Su, W., Wei, X., Pan, Y., Xing, M., Niu, L., Feng, B., Kong, W., Ren, X., Huang, F., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.02.015 · Cited by 208
Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers
Kelso, T. W. R., Porter, D. K., Amaral, M. L., Shokhirev, M. N., Benner, C. W., & Hargreaves, D. C. (2017) · eLife · doi:10.7554/elife.30506 · Cited by 199
Hoang, S. A., Oseini, A. M., Feaver, R. E., Cole, B. K., Asgharpour, A., Vincent, R. J., Siddiqui, M. S., Lawson, M. J., Day, N., Taylor, J. M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-48746-5 · Cited by 195
Gabriel, S. S., Tsui, C., Chisanga, D., Weber, F., Llano-León, M., Gubser, P. M., Bartholin, L., Souza-Fonseca-Guimarães, F., Huntington, N. D., Shi, W., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.06.007 · Cited by 200
Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade
Nabet, B. Y., Hamidi, H., Lee, M. C., Banchereau, R., Morris, S., Adler, L., Gayevskiy, V., Elhossiny, A. M., Srivastava, M. K., Patil, N. S., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.01.010 · Cited by 196
Metastatic cancers promote cachexia through ZIP14 upregulation in skeletal muscle
Wang, G., Biswas, A. K., Ma, W., Kandpal, M., Coker, C., Grandgenett, P. M., Hollingsworth, M. A., Jain, R., Tanji, K., Lόpez-Pintado, S., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0054-2 · Cited by 188
ONECUT2 Is a Targetable Master Regulator of Lethal Prostate Cancer That Suppresses the Androgen Axis
Rotinen, M., You, S., Yang, J., Coetzee, S. G., Reis-Sobreiro, M., Huang, W., Huang, F., Pan, X., Yáñez, A., Hazelett, D. J., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0241-1 · Cited by 192
Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies
Yu, K., Hu, Y., Wu, F., Guo, Q., Qian, Z., Hu, W., Chen, J., Wang, K., Fan, X., Wu, X., et al. (2020) · National Science Review · doi:10.1093/nsr/nwaa099 · Cited by 190
Ravi, A., Hellmann, M. D., Arniella, M. B., Holton, M., Freeman, S. S., Naranbhai, V., Stewart, C., Leshchiner, I., Kim, J., Akiyama, Y., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01355-5 · Cited by 201
Tumour evolution and microenvironment interactions in 2D and 3D space
Mo, C.-K., Liu, J., Chen, S., Storrs, E. P., da Costa, A. L. N. T., Houston, A., Wendl, M. C., Jayasinghe, R. G., Iglesia, M. D., Ma, C., et al. (2024) · Nature · doi:10.1038/s41586-024-08087-4 · Cited by 198
Guedan, S., Madar, A., Casado‐Medrano, V., Shaw, C. E., Wing, A., Liu, F., Young, R. M., June, C. H., & Posey, A. D. (2020) · Journal of Clinical Investigation · doi:10.1172/jci133215 · Cited by 190
Kale, M. B., Wankhede, N. L., Pawar, R. S., Ballal, S., Kumawat, R., Goswami, M., Khalid, M., Taksande, B. G., Upaganlawar, A. B., Umekar, M. J., et al. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102497 · Cited by 208
High-Throughput Transcriptomics Platform for Screening Environmental Chemicals
Harrill, J., Everett, L. J., Haggard, D. E., Sheffield, T. Y., Bundy, J. L., Willis, C. M., Thomas, R. S., Shah, I., & Judson, R. (2021) · Toxicological Sciences · doi:10.1093/toxsci/kfab009 · Cited by 195
Balmus, G., Pilger, D., Coates, J., Demir, M., Sczaniecka-Clift, M., Barros, A. C., Woods, M., Fu, B., Yang, F., Chen, E. D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-07729-2 · Cited by 195
Rhee, S., Seo, S., & Kim, S. (2018) · International Joint Conference on Artificial Intelligence · doi:10.24963/ijcai.2018/490 · Cited by 191
Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors
Anderson, N. D., de Borja, R., Young, M. D., Fuligni, F., Rosic, A., Roberts, N. D., Hajjar, S., Layeghifard, M., Novokmet, A., Kowalski, P. E., et al. (2018) · Science · doi:10.1126/science.aam8419 · Cited by 191
Shin, B., Benavides, G. A., Geng, J., Koralov, S. B., Hu, H., Darley-Usmar, V. M., & Harrington, L. E. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.022 · Cited by 187
Transcriptional mediators of treatment resistance in lethal prostate cancer
He, M. X., Cuoco, M. S., Crowdis, J. P., Bosma-Moody, A., Zhang, Z., Bi, K., Kanodia, A., Su, M.-J., Ku, S., Garcia, M. M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01244-6 · Cited by 186
Wang, N., Zheng, J., Chen, Z., Yang, L., Dura, B., Kwak, M., Xavier-Ferrucio, J. M., Lu, Y.-C., Zhang, M., Roden, C., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-07981-6 · Cited by 185
Liu, H., Li, D., Sun, L., Qin, H., Fan, A., Meng, L., Graves‐Deal, R., Glass, S. E., Franklin, J. L., Liu, Q., et al. (2022) · Molecular Cancer · doi:10.1186/s12943-022-01555-3 · Cited by 182
A comprehensive analysis of breast cancer microbiota and host gene expression
Thompson, K. J., Ingle, J. N., Tang, X., Chia, N., Jeraldo, P. R., Walther-Antonio, M. R., Kandimalla, K. K., Johnson, S., Yao, J. Z., Harrington, S. C., et al. (2017) · PLOS ONE · doi:10.1371/journal.pone.0188873 · Cited by 183
Pala, F., Di Girolamo, D., Mella, S., Yennek, S., Chatre, L., Ricchetti, M., & Tajbakhsh, S. (2018) · Journal of Cell Science · doi:10.1242/jcs.212977 · Cited by 184
Harrod, A., Fulton, J., Nguyen, V. T. M., Periyasamy, M., Ramos-Garcia, L., Lai, C.-F., Metodieva, G., de Giorgio, A., WILLIAMS, R., Santos, D. B., et al. (2016) · Oncogene · doi:10.1038/onc.2016.382 · Cited by 180
Host blood RNA signatures predict the outcome of tuberculosis treatment
Thompson, E. G., Du, Y., Malherbe, S. T., Shankar, S., Braun, J., Valvo, J., Ronacher, K., Tromp, G., Tabb, D. L., Alland, D., et al. (2017) · Tuberculosis · doi:10.1016/j.tube.2017.08.004 · Cited by 182
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin
Sadeh, R., Sharkia, I., Fialkoff, G., Rahat, A., Gutin, J., Chappleboim, A., Nitzan, M., Fox-Fisher, I., Neiman, D., Meler, G., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00775-6 · Cited by 182
Phenotypic plasticity and genetic control in colorectal cancer evolution
Househam, J., Heide, T., Cresswell, G. D., Spiteri, I., Kimberley, C., Zapata, L., Lynn, C., James, C. T., Mossner, M., Fernández-Mateos, J., et al. (2022) · Nature · doi:10.1038/s41586-022-05311-x · Cited by 187
Jin, S., Zhang, L., & Nie, Q. H. (2020) · Genome biology · doi:10.1186/s13059-020-1932-8 · Cited by 181
Mutations disrupting neuritogenesis genes confer risk for cerebral palsy
Jin, S. C., Lewis, S. A., Bakhtiari, S., Zeng, X. Q., Sierant, M. C., Shetty, S., Nordlie, S. M., Elie, A., Corbett, M. A., Norton, B. Y., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0695-1 · Cited by 178
Chen, J. H., Nieman, L. T., Spurrell, M., Jorgji, V., Elmelech, L., Richieri, P. M., Xu, K. H., Madhu, R., Parikh, M., Zamora, I., et al. (2024) · Nature Immunology · doi:10.1038/s41590-024-01792-2 · Cited by 204
Tao, N., Li, H., Deng, L., Zhao, S., Ouyang, J., Wen, M., Chen, W., Zeng, K., Wei, C., & Liu, Y. (2021) · ACS Nano · doi:10.1021/acsnano.1c07504 · Cited by 179
Unterman, A., Sumida, T. S., Nouri, N., Yan, X., Zhao, A., Gasque, V., Schupp, J. C., Asashima, H., Liu, Y., Cosme, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27716-4 · Cited by 181
Apolipoprotein E induces pathogenic senescent-like myeloid cells in prostate cancer
Bancaro, N., Calì, B., Troiani, M., Elia, A. R., Arzola, R. A., Attanasio, G., Lai, P., Crespo, M., Gürel, B., Pereira, R., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.02.004 · Cited by 189
Roider, T., Seufert, J., Uvarovskii, A., Frauhammer, F., Bordas, M., Abedpour, N., Stolarczyk, M., Mallm, J., Herbst, S. A., Bruch, P., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0532-x · Cited by 186
Senescence Reprogramming by TIMP1 Deficiency Promotes Prostate Cancer Metastasis
Guccini, I., Revandkar, A., D'Ambrosio, M., Colucci, M., Pasquini, E., Mosole, S., Troiani, M., Brina, D., Sheibani-Tezerji, R., Elia, A. R., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2020.10.012 · Cited by 185
Iftekhar, A., Berger, H., Bouznad, N., Heuberger, J., Boccellato, F., Dobrindt, U., Hermeking, H., Sigal, M. J., & Meyer, T. F. (2021) · Nature Communications · doi:10.1038/s41467-021-21162-y · Cited by 188
Anadon, C. M., Yu, X., Hänggi, K., Biswas, S., Chaurio, R. A., Martin, A., Payne, K. K., Mandal, G., Innamarato, P., Harro, C. M., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.03.008 · Cited by 185
A comprehensive human embryo reference tool using single-cell RNA-sequencing data
Zhao, C., Reyes, Á. P., Schell, J. P., Weltner, J., Ortega, N. M., Zheng, Y., Björklund, Å. K., Baqué-Vidal, L., Sokka, J., Trokovic, R., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02493-2 · Cited by 185
“…construction, utilizing the top 4,500 variable genes and 50 PCs. Query datasets, including TLCs derived from naive and primed hPS cells and organoids derived from the first trimester 59 , were projected onto this extended reference following the same processing steps as for the original reference.”
Cui, M., Wang, Z., Chen, K., Shah, A. M., Tan, W. H., Duan, L., Sanchez‐Ortiz, E., Li, H. Z., Xu, L., Liu, N., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.02.019 · Cited by 180
Ditoro, D. F., Harbour, S. N., Bando, J. K., Benavides, G. A., Witte, S. J., Laufer, V. A., Moseley, C. E., Singer, J. R., Frey, B. F., Turner, H., et al. (2020) · Immunity · doi:10.1016/j.immuni.2020.03.013 · Cited by 178
Hu, Y., Xie, C., Yang, H., Ho, J. W. K., Wen, J., Han, L., Chiu, K. W.-H., Fu, J., & Vardhanabhuti, V. (2020) · JAMA Network Open · doi:10.1001/jamanetworkopen.2020.15927 · Cited by 174
Aberrant type 1 immunity drives susceptibility to mucosal fungal infections.
Break, T. J., Oikonomou, V., Dutzan, N., Desai, J. V., Swidergall, M., Freiwald, T., Chauss, D., Harrison, O. J., Alejo, J., Williams, D. W., et al. (2021) · Science · doi:10.1126/science.aay5731 · Cited by 175
Genetic associations for two biological age measures point to distinct aging phenotypes
Kuo, C., Pilling, L. C., Liu, Z., Atkins, J. L., & Levine, M. E. (2021) · Aging Cell · doi:10.1111/acel.13376 · Cited by 173
Rothchild, A. C., Olson, G. S., Nemeth, J., Amon, L. M., Mai, D., Gold, E. S., Diercks, A. H., & Aderem, A. A. (2019) · Science Immunology · doi:10.1126/sciimmunol.aaw6693 · Cited by 171
McFaline‐Figueroa, J. L., Hill, A. J., Qiu, X., Jackson, D. L., Shendure, J., & Trapnell, C. (2019) · Nature Genetics · doi:10.1038/s41588-019-0489-5 · Cited by 166
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma
Bakouny, Z., Braun, D. A., Shukla, S. A., Pan, W., Gao, X. Y., Hou, Y., Flaifel, A., Tang, S., Bosma-Moody, A., He, M. X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21068-9 · Cited by 174
Protein Amounts of the MYC Transcription Factor Determine Germinal Center B Cell Division Capacity
Finkin, S., Hartweger, H., Oliveira, T. Y., Kara, E. E., & Nussenzweig, M. C. (2019) · Immunity · doi:10.1016/j.immuni.2019.06.013 · Cited by 179
Necchi, A., Raggi, D., Andrea Gallina, A., Ross, J. S., Farè, E., Giannatempo, P., Marandino, L., Colecchia, M., Lucianò, R., Bianchi, M., et al. (2020) · European Urology · doi:10.1016/j.eururo.2020.02.028 · Cited by 172
RNAmod: an integrated system for the annotation of mRNA modifications
Liu, Q., & Gregory, R. I. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz479 · Cited by 170
Vandekerkhove, G. R., Lavoie, J., Annala, M., Murtha, A. J., Sundahl, N., Walz, S., Sano, T., Taavitsainen, S., Ritch, E. J., Fazli, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20493-6 · Cited by 174
Dissecting intratumoral myeloid cell plasticity by single cell RNA-seq
Song, Q., Hawkins, G. A., Wudel, L., Chou, P., Forbes, E., Pullikuth, A. K., Liu, L., Jin, G., Craddock, L., Topaloglu, U., et al. (2019) · Cancer Medicine · doi:10.1002/cam4.2113 · Cited by 168
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
Liu, N. Q., Maresca, M., van den Brand, T., Braccioli, L., Schijns, M. M. G. A., Teunissen, H., Bruneau, B. G., Nora, E. P., & de Wit, E. (2021) · Nature Genetics · doi:10.1038/s41588-020-00744-4 · Cited by 162
Occupancy maps of 208 chromatin-associated proteins in one human cell type
Partridge, E. C., Chhetri, S. B., Prokop, J. W., Ramaker, R. C., Jansen, C. S., Goh, S.-T., Mackiewicz, M., Newberry, K. M., Brandsmeier, L. A., Meadows, S. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2023-4 · Cited by 154
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
Kazer, S. W., Aicher, T. P., Muema, D., Carroll, S. L., Ordovás-Montañés, J., Miao, V. N., Tu, A. A., Ziegler, C. G. K., Nyquist, S. K., Wong, E. B., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0799-2 · Cited by 168
Mitochondrial integrated stress response controls lung epithelial cell fate
Han, S., Lee, M., Shin, Y., Giovanni, R., Chakrabarty, R. P., Herrerias, M. M., Dada, L. A., Flozak, A. S., Reyfman, P. A., Khuder, B., et al. (2023) · Nature · doi:10.1038/s41586-023-06423-8 · Cited by 163
Immune Landscape of Colorectal Cancer Tumor Microenvironment from Different Primary Tumor Location
Zhang, L., Zhao, Y., Dai, Y., Cheng, J., Gong, Z., Feng, Y., Sun, C., Jia, Q., & Zhu, B. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01578 · Cited by 172
Notch signaling and efficacy of PD-1/PD-L1 blockade in relapsed small cell lung cancer
Roper, N., Velez, M. J., Chiappori, A., Kim, Y. S., Wei, J. S., Sindiri, S., Takahashi, N., Mulford, D. A., Kumar, S., Ylaya, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24164-y · Cited by 166
Wang, Z., Xie, L., Ding, G., Song, S., Chen, L., Li, G., Xia, M., Han, D., Zheng, Y., Liu, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25771-5 · Cited by 163
Interferon-stimulated neutrophils as a predictor of immunotherapy response
Benguigui, M., Cooper, T. J., Kalkar, P., Schif‐Zuck, S., Halaban, R., Bacchiocchi, A., Kamer, I., Deo, A., Manobla, B., Rottem, M., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2023.12.005 · Cited by 179
Zhang, D. M., Navara, R., Yin, T., Szymanski, J. J., Goldsztejn, U., Kenkel, C., Lang, A., Mpoy, C., Lipovsky, C. E., Qiao, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25730-0 · Cited by 165
Newell, F., da Silva, I. P., Johansson, P. A., Menzies, A. M., Wilmott, J. S., Addala, V., Carlino, M. S., Rizos, H., Nones, K., Edwards, J. J., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.11.012 · Cited by 166
Diet-regulated production of PDGFcc by macrophages controls energy storage
Cox, N., Crozet, L., Holtman, I. R., Loyher, P.-L., Lazarov, T., White, J. B., Mass, E., Stanley, E. R., Elemento, O., Glass, C. K., et al. (2021) · Science · doi:10.1126/science.abe9383 · Cited by 172
Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state
Cerezo‐Wallis, D., Contreras-Alcalde, M., Troulé, K., Catena, X., Mucientes, C., Calvo, T. G., Cañón, E., Tejedo, C., Pennacchi, P. C., Hogan, S. A., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-1073-3 · Cited by 168
The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s
Tunbak, H., Enriquez-Gasca, R., Tie, C. H. C., Gould, P. A., Mlcochova, P., Gupta, R. K., Fernandes, L., Holt, J., van der Veen, A. G., Giampazolias, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19170-5 · Cited by 162
Brett, J. O., Arjona, M., Ikeda, M., Quarta, M., de Morrée, A., Egner, I. M., Perandini, L. A., Ishak, H. D., Goshayeshi, A., Benjamin, D. I., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0190-0 · Cited by 162
Kastenhuber, E. R., Lalazar, G., Houlihan, S. L., Tschaharganeh, D. F., Baslan, T., Chen, C.-C., Requena, D., Tian, S., Bosbach, B., Wilkinson, J. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716483114 · Cited by 163
A concerted neuron–astrocyte program declines in ageing and schizophrenia
Ling, E., Nemesh, J. C., Goldman, M., Kamitaki, N., Reed, N. M., Handsaker, R. E., Genovese, G., Vogelgsang, J. S., Gerges, S., Kashin, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07109-5 · Cited by 170
Dummer, R., Brase, J. C., Garrett, J., Campbell, C. D., Gasal, E., Squires, M. S., Gusenleitner, D., Santinami, M., Atkinson, V. G., Mandalà, M., et al. (2020) · The Lancet Oncology · doi:10.1016/s1470-2045(20)30062-0 · Cited by 162
Livanos, A. E., Jha, D., Cossarini, F., Gonzalez-Reiche, A. S., Tokuyama, M. A., Aydillo, T., Parigi, T. L., Ladinsky, M. S., Ramos, I., Dunleavy, K. A., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.02.056 · Cited by 163
Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID
Cortal, A., Martignetti, L., Six, E. M., & Rausell, A. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00896-6 · Cited by 165
Sun, K., Xu, R., Ma, F., Yang, N., Li, Y., Sun, X., Jin, P., Kang, W., Jia, L., Xiong, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32627-z · Cited by 163
Li, K., Tandurella, J. A., Gai, J., Zhu, Q., Lim, S. J., Thomas, D. L., Xia, T., Mo, G., Mitchell, J. T., Montagne, J. M., et al. (2022) · Cancer Cell · doi:10.1016/j.ccell.2022.10.001 · Cited by 160
Liu, Y., Ge, J., Chen, Y., Liu, T., Chen, L., Liu, C., Ma, D., Chen, Y., Cai, Y., Xu, Y., et al. (2023) · Advanced Science · doi:10.1002/advs.202205395 · Cited by 167
Macrophage correlates with immunophenotype and predicts anti-PD-L1 response of urothelial cancer
Zeng, D., Ye, Z., Wu, J., Zhou, R., Fan, X., Wang, G., Huang, Y., Wu, J., Sun, H., Wang, M., et al. (2020) · Theranostics · doi:10.7150/thno.46176 · Cited by 157
The RNA Atlas expands the catalog of human non-coding RNAs
Lorenzi, L., Chiu, H.-S., Avila Cobos, F., Gross, S., Volders, P.-J., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00936-1 · Cited by 163
Yang, C. G., Zhang, H., Chen, M., Wang, S., Qian, R., Zhang, L., Huang, X., Wang, J., Liu, Z., Qin, W., et al. (2022) · eLife · doi:10.7554/elife.71880 · Cited by 161
Qiu, X., Boufaied, N., Hallal, T., Feit, A. S., de Polo, A., Luoma, A., Alahmadi, W., Larocque, J., Zadra, G., Xie, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30257-z · Cited by 171
Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer
Chatila, W. K., Kim, J. K., Walch, H. S., Marco, M. R., Chen, C., Wu, F. H., Omer, D. M. R., Khalil, D. N., Ganesh, K., Qu, X., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01930-z · Cited by 163
Zagorulya, M., Yim, L., Morgan, D. M., Edwards, A. W., Torres-Mejia, E., Momin, N., McCreery, C. V., Zamora, I., Horton, B. L., Fox, J. G., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.01.010 · Cited by 160
Prognostic genome and transcriptome signatures in colorectal cancers
Nunes, L., Li, F., Wu, M., Luo, T., Hammarström, K., Torell, E., Ljuslinder, I., Mezheyeuski, A., Edqvist, P.-H. D., Löfgren‐Burström, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07769-3 · Cited by 179
“C T NND 1 [ 39 ] C T NN B 1 [ 27 ] B C L9L [ 101 ] B C L9 [ 82 ] AX I N 2 [ 62 ] AP C [ 107 ] A M E R 1 [ 62 ] W AS HC 2 C [ 35 ] S L C 46 A 3 [ 29 ] S L C 12 A 2 [ 25 ] SE T D 5 [ 51 ] R PS 16 [ 3 ] R PS 15 [ 5 ] R P L22 [ 141 ] R P L10 [ 16 ] R G M B [ 21 ] P R A C 2 [ 25 ] P I G W [ 10 ] M B D 6…”
InfluentialJaume, G., Vaidya, A. J., Chen, R. J., Williamson, D. F. K., Liang, P. P., & Mahmood, F. (2024) · IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · doi:10.1109/cvpr52733.2024.01100 · Cited by 184
An immunoproteomic approach to characterize the CAR interactome and signalosome
Ramello, M. C., Benzaïd, I., Kuenzi, B. M., Lienlaf, M., Kandell, W. M., Santiago, D. N., Pabón-Saldaña, M., Darville, L. N. F., Fang, B., Rix, U., et al. (2019) · Science Signaling · doi:10.1126/scisignal.aap9777 · Cited by 163
Müller, S., Bley, N., Busch, B., Glaß, M., Lederer, M., Misiak, C., Fuchs, T., Wedler, A., Haase, J., Bertoldo, J. B., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa653 · Cited by 159
Why All the Fuss about Oxidative Phosphorylation (OXPHOS)?
Xu, Y., Xue, D., Bankhead, A., & Neamati, N. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01013 · Cited by 173
Leng, K., Rose, I. V. L., Kim, H., Xia, W., Romero‐Fernandez, W., Rooney, B., Koontz, M., Li, E., Ao, Y., Wang, S., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01180-9 · Cited by 158
Inborn errors of OAS–RNase L in SARS-CoV-2–related multisystem inflammatory syndrome in children
Lee, D., Pen, J. L., Yatim, A., Dong, B., Aquino, Y., Ogishi, M., Pescarmona, R., Talouarn, E., Rinchai, D., Zhang, P., et al. (2022) · Science · doi:10.1126/science.abo3627 · Cited by 159
B lymphocytes directly contribute to tissue fibrosis in patients with IgG4-related disease
Della‐Torre, E., Rigamonti, E., Perugino, C. A., Sain, S. B., Sun, N., Kaneko, N., Maehara, T., Rovati, L., Ponzoni, M., Milani, R., et al. (2019) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2019.07.004 · Cited by 159
Yu, K., Chen, B., Aran, D., Charalel, J. K., Yau, C. S. F., Wolf, D. M., Veer, L. V. ‘., Butte, A. J., Goldstein, T. C., & Sirota, M. (2019) · Nature Communications · doi:10.1038/s41467-019-11415-2 · Cited by 165
p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis
Olivero, C. E., Martínez‐Terroba, E., Zimmer, J. T., Liao, C., Tesfaye, E., Hooshdaran, N., Schofield, J. A., Bendor, J., Fang, D., Simon, M. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.014 · Cited by 159
Gene Size Matters: An Analysis of Gene Length in the Human Genome
Lopes, I., Altab, G., Raina, P., & de Magalhães, J. P. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.559998 · Cited by 164
Metadata
- Authors
- Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Mesirov, Jill P.
- Tamayo, Pablo
- Venue
- Cell Systems
- Publisher
- Elsevier BV
- Published
- 2015-12
- Volume
- 1
- Issue
- 6
- Pages
- 417-425
- ISSN
- 2405-4712 (ISSN-L)
- PMC
- PMC4707969
- OpenAlex
- W2214074259
- Cited by
- 13,807
- References
- 37
- Citations by year
- 2026: 2174 · 2025: 2294 · 2024: 2415 · 2023: 1982 · 2022: 1708 · 2021: 1298 · 2020: 926 · 2019: 534 · 2018: 270 · 2017: 154 · 2016: 44
- FWCI
- 68.21
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Systems (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (R01CA154480, U54CA112962, R01CA121941)
- National Institute of General Medical Sciences (R01GM074024)
- 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
- Hallmark gene sets, gene set enrichment analysis, biological processes, cancer hallmarks
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
