The DOI matches its Crossref record; 13 of the 13 references it cites were found in a registry or an index.
VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
Open accessAbstract
Comparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name. Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/Shiny. The web app is named VolcaNoseR and it can be used to create, explore, label and share volcano plots ( https://huygens.science.uva.nl/VolcaNoseR ). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data. Therefore, VolcaNoseR increases the transparency and re-use of large comparative genome- and proteome-wide datasets.
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.
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
Statistical tests for differential expression in cDNA microarray experiments
Cui, X., & Churchill, G. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-4-210 · Cited by 896
PlotsOfData—A web app for visualizing data together with their summaries
Postma, M., & Goedhart, J. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000202 · Cited by 553
Self-citationVOLCANO PLOTS IN ANALYZING DIFFERENTIAL EXPRESSIONS WITH mRNA MICROARRAYS
LI, W. (2012) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720012310038 · Cited by 204
The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
van der Weegen, Y., Golan-Berman, H., Mevissen, T. E. T., Apelt, K., González-Prieto, R., Goedhart, J., Heilbrun, E. E., Vertegaal, A. C. O., van den Heuvel, D., Walter, J. C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15903-8 · Cited by 183
Self-citationCRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog
Pusapati, G. V., Kong, J. H., Patel, B. B., Krishnan, A., Sagner, A., Kinnebrew, M., Briscoe, J., Aravind, L., & Rohatgi, R. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.12.003 · Cited by 132
Gillingham, A. K., Bertram, J., Begum, F., & Munro, S. (2019) · eLife · doi:10.7554/elife.45916 · Cited by 97
G protein–coupled receptors control the sensitivity of cells to the morphogen Sonic Hedgehog
Pusapati, G. V., Kong, J. H., Patel, B. B., Gouti, M., Sagner, A., Sircar, R., Luchetti, G., Ingham, P. W., Briscoe, J., & Rohatgi, R. (2018) · Science Signaling · doi:10.1126/scisignal.aao5749 · Cited by 91
Impaired LXRα Phosphorylation Attenuates Progression of Fatty Liver Disease
Bécares, N., Gage, M., Voisin, M., Shrestha, E., Martin‐Gutierrez, L., Liang, N., Louie, R., Pourcet, B., Pello, Ó. M., Luong, T. V., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2018.12.094 · Cited by 75
PlotTwist: A web app for plotting and annotating continuous data
Goedhart, J. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000581 · Cited by 71
Self-citationDrainas, A. P., Lambuta, R. A., Ivanova, I., Serçin, Ö., Sarropoulos, I., Smith, M. L., Efthymiopoulos, T., Raeder, B., Stütz, A. M., Waszak, S. M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.03.029 · Cited by 34
Cited by
Stiff matrix induces exosome secretion to promote tumour growth
Wu, B., Liu, D.-A., Guan, L., Myint, P. K., Chin, L., Dang, H., Xu, Y., Ren, J., Li, T., Yu, Z., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01092-1 · Cited by 240
Autophagy enables microglia to engage amyloid plaques and prevents microglial senescence
Choi, I., Wang, M., Yoo, S., Xu, P., Seegobin, S. P., Li, X., Han, X., Wang, Q., Peng, J., Zhang, B., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01158-0 · Cited by 202
Daly, J. L., Danson, C. M., Lewis, P. A., Zhao, L., Riccardo, S., Di Filippo, L., Cacchiarelli, D., Lee, D., Cross, S. J., Heesom, K. J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-38719-8 · Cited by 45
Henningfield, C. M., Arreola, M. A., Soni, N., Spangenberg, E. E., & Green, K. N. (2022) · Glia · doi:10.1002/glia.24105 · Cited by 40
Peterson, P. P., Choi, J.-T., Fu, C., Cowen, L. E., Sun, S., Bahn, Y.-S., & Heitman, J. (2024) · PLOS Pathogens · doi:10.1371/journal.ppat.1012735 · Cited by 25
Metadata
- Authors
- Goedhart, J., & Luijsterburg, M. S.
- Venue
- Scientific Reports
- Published
- 2020-11-25
- Volume
- 10
- Issue
- 1
- Pages
- 20560-20560
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W3109082402
- Cited by
- 709
- References
- 13
- FWCI
- 17.98
- Type
- journal article
- Language
- en
- Open access
- gold
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. https://app.cochat.ai/papers/10.1038/s41598-020-76603-3
- The paper
- Goedhart, J., & Luijsterburg, M. S. (2020). VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. Scientific Reports. https://doi.org/10.1038/s41598-020-76603-3
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
