Visualizing and interpreting cancer genomics data via the Xena platform
Open accessPublished version of a preprint
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
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?
TCGA datasets revealed no significant difference in Paneth-like gene signature expression between SMAD4 wild-type and mutant CRCs.
“Analysis of The Cancer Genome Atlas (TCGA) datasets revealed no significant difference in Paneth-like gene signature expression between SMAD4 wild-type and mutant CRCs (Figure S5M).54”
From Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer (2026) · cites this paper as [54]
The 'To the Editor' section says Xena hosts TCGA datasets and supports gene-expression and mutation data, consistent with its use as a resource for the citing authors’ analysis. It does not report a comparison of Paneth-like signature expression between SMAD4 wild-type and mutant colorectal cancers or the claimed nonsignificant result; the citing sentence points to its own Figure S5M for that finding. (LLM, conf=0.85)
Experimental — accuracy not yet measuredLower expression of IKZF2 was associated with poorer prognosis in AML (TCGA analysis).
“Analysis of the TCGA data showed that the lower expression of IKZF2 was associated with poorer prognosis in AML (Fig. 3d)33.”
From Subtype-specific 3D genome alteration in acute myeloid leukaemia (2022) · 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.
Cites
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455 · see citing works
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049 · see citing works
Genetic effects on gene expression across human tissues
GTEx Consortium (2017) · Nature · doi:10.1038/nature24277 · Cited by 4,036 · see citing works
Pan-cancer analysis of whole genomes
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature · doi:10.1038/s41586-020-1969-6 · Cited by 3,064 · see citing works
Self-citationHoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.022 · Cited by 2,546 · see citing works
Toward a Shared Vision for Cancer Genomic Data
Grossman, R. L., Heath, A. P., Ferretti, V., Varmus, H. E., Lowy, D. R., Kibbe, W. A., & Staudt, L. M. (2016) · New England Journal of Medicine · doi:10.1056/nejmp1607591 · Cited by 1,680 · see citing works
Toil enables reproducible, open source, big biomedical data analyses
Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., Novak, A., Pfeil, J., Narkizian, J., Deran, A. D., Musselman-Brown, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3772 · Cited by 1,365 · see citing works
Self-citationThe chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230 · see citing works
Self-citationPan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours
Ma, X., Liu, Y., Liu, Y., Alexandrov, L. B., Edmonson, M. N., Gawad, C., Zhou, X., Li, Y., Rusch, M. C., Easton, J., et al. (2018) · Nature · doi:10.1038/nature25795 · Cited by 901 · see citing works
The International Cancer Genome Consortium Data Portal
Zhang, J., Bajari, R., Andric, D., Gerthoffert, F., Lepsa, A., Nahal-Bose, H. K., Stein, L. D., & Ferretti, V. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0055-9 · Cited by 597 · see citing works
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
Gao, Q.-S., Liang, W.-W., Foltz, S., Mutharasu, G., Jayasinghe, R., Cao, S., Liao, W.-W., Reynolds, S., Wyczalkowski, M., Yao, L., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.050 · Cited by 557 · see citing works
DNA methylation loss in late-replicating domains is linked to mitotic cell division
Zhou, W., Dinh, H. Q., Ramjan, Z., Weisenberger, D. J., Nicolet, C. M., Shen, H., Laird, P. W., & Berman, B. P. (2018) · Nature Genetics · doi:10.1038/s41588-018-0073-4 · Cited by 405 · see citing works
Making sense of cancer genomic dataPreprint
Chin, L., Hahn, W. C., Getz, G. A., & Meyerson, M. M. (2011) · Genes & Development · doi:10.1101/gad.2017311 · Cited by 336 · see citing works
Cloud computing for genomic data analysis and collaboration
Langmead, B., & Nellore, A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.113 · Cited by 310 · see citing works
Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps
Perez-Llamas, C., & López-Bigas, N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019541 · Cited by 265 · see citing works
Cancer transcriptome profiling at the juncture of clinical translation
Cieslik, M. P., & Chinnaiyan, A. M. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.96 · Cited by 261 · see citing works
The UCSC Cancer Genomics Browser
Zhu, J., Sanborn, Z., Benz, S. C., Szeto, C. W., Hsu, F., Kuhn, R. M., Karolchik, D., Archie, J. G., Lenburg, M. E., Esserman, L. J., et al. (2009) · Nature Methods · doi:10.1038/nmeth0409-239 · Cited by 171 · see citing works
Self-citationWebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data
Wang, Y. E., Kutnetsov, L., Partensky, A., et al. (2017) · Cancer Research · doi:10.1158/0008-5472.can-17-0802 · Cited by 63 · see citing works
MAGI: visualization and collaborative annotation of genomic aberrations
Leiserson, M. D. M., Gramazio, C., Hu, J. C., Wu, H.-T., Laidlaw, D. H., & Raphael, B. J. (2015) · Nature Methods · doi:10.1038/nmeth.3412 · Cited by 27 · see citing works
Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples
Streit, M., Gratzl, S., Stitz, H., Wernitznig, A., Zichner, T., & Haslinger, C. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz009 · Cited by 21 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Conserved pan-cancer microenvironment subtypes predict response to immunotherapy
Bagaev, A., Kotlov, N., Nomie, K., Svekolkin, V., Gafurov, A., Isaeva, O., Osokin, N., Kozlov, I., Frenkel, F., Gancharova, O., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.04.014 · Cited by 1,302 · see citing works
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity
Griffin, G. K., Wu, J., Iracheta-Vellve, A., Patti, J. C., Hsu, J., Davis, T., Dele-Oni, D., Du, P. P., Halawi, A. G., Ishizuka, J. J., et al. (2021) · Nature · doi:10.1038/s41586-021-03520-4 · Cited by 370 · see citing works
Slow TCA flux and ATP production in primary solid tumours but not metastases
Bartman, C. R., Weilandt, D. R., Shen, Y., Lee, W. D., Han, Y., TeSlaa, T., Jankowski, C. S. R., Samarah, L., Park, N. R., da Silva-Diz, V., et al. (2023) · Nature · doi:10.1038/s41586-022-05661-6 · Cited by 299 · see citing works
Big data in basic and translational cancer research
Jiang, P., Sinha, S., Aldape, K., Hannenhalli, S., Sahinalp, C., & Ruppin, E. (2022) · Nature Reviews Cancer · doi:10.1038/s41568-022-00502-0 · Cited by 254 · see citing works
In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer
Dubrot, J., Du, P. P., Lane-Reticker, S. K., Kessler, E. A., Muscato, A. J., Mehta, A., Freeman, S. S., Allen, P. M., Olander, K. E., Ockerman, K. M., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01315-x · Cited by 218 · see citing works
Zhou, C., Peng, S., Lin, A., Jiang, A., Peng, Y., Gu, T., Liu, Z., Cheng, Q., Zhang, J., & Luo, P. (2023) · eClinicalMedicine · doi:10.1016/j.eclinm.2023.101967 · Cited by 213 · see citing works
Subtype-specific 3D genome alteration in acute myeloid leukaemia
Xu, J., Song, F., Lyu, H., Kobayashi, M., Zhang, B., Zhao, Z., Hou, Y., Wang, X., Luan, Y., Jia, B., et al. (2022) · Nature · doi:10.1038/s41586-022-05365-x · Cited by 208 · see citing works
CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer
Lin, A., Qi, C., Wei, T., Li, M., Cheng, Q., Liu, Z., Luo, P., & Zhang, J. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac129 · Cited by 152 · see citing works
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 · see citing works
EZH2-H3K27me3 mediated KRT14 upregulation promotes TNBC peritoneal metastasis
Verma, A., Singh, A., Singh, M. P., Nengroo, M. A., Saini, K. K., Satrusal, S. R., Khan, M. A., Chaturvedi, P., Sinha, A., Meena, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35059-x · Cited by 148 · see citing works
Ligon, J. A., Choi, W., Cojocaru, G., Fu, W., Hsiue, E. H.-C., Oke, T. F., Siegel, N., Fong, M. H., Ladle, B., Pratilas, C. A., et al. (2021) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-001772 · Cited by 124 · see citing works
A pan-cancer analysis of the prognostic and immunological role of β-actin (ACTB) in human cancers
Gu, Y., Tang, S., Wang, Z., Cai, L., Lian, H., Shen, Y., & Zhou, Y. (2021) · Bioengineered · doi:10.1080/21655979.2021.1973220 · Cited by 99 · see citing works
Interpretation of cancer mutations using a multiscale map of protein systems
Zheng, F., Kelly, M. R., Ramms, D. J., Heintschel, M. L., Tao, K., Tutuncuoglu, B., Lee, J. J., Ono, K., Foussard, H., Chen, M., et al. (2021) · Science · doi:10.1126/science.abf3067 · Cited by 81 · see citing works
Borràs, D. M., Verbandt, S., Ausserhofer, M., Sturm, G., Lim, J., Verge, G. A., Vanmeerbeek, I., Laureano, R. S., Govaerts, J., Sprooten, J., et al. (2023) · Cell Discovery · doi:10.1038/s41421-023-00605-4 · Cited by 67 · see citing works
Recent Updates on the Significance of KRAS Mutations in Colorectal Cancer Biology
László, L., Kurilla, A., Takács, T., Kudlik, G., Koprivanacz, K., Buday, L., & Vas, V. (2021) · Cells · doi:10.3390/cells10030667 · Cited by 58 · see citing works
Transcriptomics-Guided Slide Representation Learning in Computational Pathology
Jaume, G., Oldenburg, L., Vaidya, A., Chen, R. J., Williamson, D. F. K., Peeters, T., Song, A. H., & Mahmood, F. (2024) · 2024 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) · doi:10.1109/cvpr52733.2024.00920 · Cited by 51 · see citing works
Lin, J.-C., Liu, T.-P., & Yang, P.-M. (2020) · Journal of Clinical Medicine · doi:10.3390/jcm9124019 · Cited by 46 · see citing works
Benítez, S., Cordero, A., Santamaría, P. G., Redondo-Pedraza, J., Rocha, A. S., Collado-Solé, A., Jimenez, M., Sanz-Moreno, A., Yoldi, G., Santos, J. C., et al. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.04.022 · Cited by 41 · see citing works
Nepal, C., & Andersen, J. B. (2023) · Nature Communications · doi:10.1038/s41467-023-38272-4 · Cited by 39 · see citing works
Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer
Zhang, Y., Chen, J., She, Y., Fang, Z., Zhang, Y., Ruan, D., Guo, W., Liao, J., Zhou, W., Lao, J., et al. (2026) · Cancer Cell · doi:10.1016/j.ccell.2025.10.010 · Cited by 23 · see citing works
Wu, S., & Wagner, G. (2021) · Cell Systems · doi:10.1016/j.cels.2021.07.002 · Cited by 20 · see citing works
Detecting molecular subtypes from multi-omics datasets using SUMO
Sienkiewicz, K., Chen, J., Chatrath, A., Lawson, J. T., Sheffield, N. C., Zhang, L., & Ratan, A. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100152 · Cited by 18 · see citing works
Mills, L. J., Spector, L. G., Largaespada, D. A., & Williams, L. A. (2021) · Biology of Sex Differences · doi:10.1186/s13293-020-00347-y · Cited by 17 · see citing works
Ariyoshi, M., Yuge, R., Kitadai, Y., Shimizu, D., Miyamoto, R., Yamashita, K., Hiyama, Y., Takigawa, H., Urabe, Y., & Oka, S. (2024) · Cancers · doi:10.3390/cancers16183136 · Cited by 12 · see citing works
O-GlcNAcylation of FOXK1 orchestrates the E2F pathway and promotes oncogenesis
Masclef, L., Ahmed, O., Iannantuono, N., Gagnon, J., Gushul-Leclaire, M., Boulay, K., Estavoyer, B., Echbicheb, M., Poy, M., Ali Boubacar, K., et al. (2024) · doi:10.1101/2024.03.01.582838 · Cited by 6 · see citing works
Liu, T., Lin, Y.-C., Chang, P.-C., Hueng, D.-Y., & Li, Y.-F. (2025) · Discover Oncology · doi:10.1007/s12672-025-02662-5 · Cited by 4 · see citing works
Cheng, C. C. Y., Cheung, M. F., Lee, A. Y., Wu, Q., Chow, S. H.-C., Ang, J. Y. J., Riquelme Medina, I., Lo, G., Wu, H., Yang, W., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09154-w · Cited by 3 · see citing works
Yang, M., Li, S., Li, R., Dong, Y., Zhou, M., Zhao, J., Liu, M., & Tan, R. (2026) · New Biotechnology · doi:10.1016/j.nbt.2026.05.006
- Authors
- Goldman, M. J., Craft, B., Hastie, M., Repečka, K., McDade, F., Kamath, A., Banerjee, A., Luo, Y., Rogers, D., Brooks, A. N., Zhu, J., & Haussler, D.
- Affiliations
- University of California, Santa Cruz (US)
- Vilnius University (LT)
- Birla Institute of Technology and Science, Pilani - Goa Campus (IN)
- National Institute of Technology Durgapur (IN)
- Stanford University (US)
- Corresponding author
- Goldman, Mary J.
- Venue
- Nature Biotechnology
- Published
- 2020-05-22
- Volume
- 38
- Issue
- 6
- Pages
- 675-678
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7386072
- OpenAlex
- W3028304854
- Cited by
- 4,481
- References
- 20
- Citations by year
- 2026: 540 · 2025: 778 · 2024: 950 · 2023: 771 · 2022: 781 · 2021: 544 · 2020: 108 · 2019: 8
- FWCI
- 198.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health & Human Services | NIH | National Cancer Institute (5U24CA180951-04, 5U24CA210974-02)
- Silicon Valley Community Foundation (2018-182812)
- Google Summer of Code: https://summerofcode.withgoogle.com/
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- cancer genomics data, data visualization, data interpretation, genomic databases, cancer genomics
- MeSH terms
- Humans, Neoplasms, Software, Genomics, Databases, Genetic
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
