The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Analyzing biological network parameters with CentiScaPe
Open accessAbstract
Summary: The increasing availability of large network datasets along with the progresses in experimental high-throughput technologies have prompted the need for tools allowing easy integration of experimental data with data derived form network computational analysis. In order to enrich experimental data with network topological parameters, we have developed the Cytoscape plug-in CentiScaPe. The plug-in computes several network centrality parameters and allows the user to analyze existing relationships between experimental data provided by the users and node centrality values computed by the plug-in. CentiScaPe allows identifying network nodes that are relevant from both experimental and topological viewpoints. CentiScaPe also provides a Boolean logic-based tool that allows easy characterization of nodes whose topological relevance depends on more than one centrality. Finally, different graphic outputs and the included description of biological significance for each computed centrality facilitate the analysis by the end users not expert in graph theory, thus allowing easy node categorization and experimental prioritization. Availability: CentiScaPe can be downloaded via the Cytoscape web site: http://chianti.ucsd.edu/cyto_web/plugins/index.php. Tutorial, centrality descriptions and example data are available at: http://profs.sci.univr.it/∼scardoni/centiscape/centiscapepage.php Contact: giovanni.scardoni@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888
Gene 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
Statistical mechanics of complex networks
Albert, R., & Barabási, A.-L. (2002) · Reviews of Modern Physics · doi:10.1103/revmodphys.74.47 · Cited by 20,471
Network motifs: simple building blocks of complex networks.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002) · Science · doi:10.1126/science.298.5594.824 · Cited by 7,368
An automated method for finding molecular complexes in large protein interaction networks
Bader, G. D., & Hogue, C. W. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-2 · Cited by 6,072
The Large-Scale Organization of Metabolic Networks
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., & Barabási, A.-L. (2000) · Nature · doi:10.1038/35036627 · Cited by 4,972
Integration of biological networks and gene expression data using Cytoscape
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) · Nature Protocols · doi:10.1038/nprot.2007.324 · Cited by 2,507
Computing topological parameters of biological networks
Assenov, Y., Ramírez, F., Schelhorn, S.-E., Lengauer, T., & Albrecht, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm554 · Cited by 1,826
Wuchty, S., & Stadler, P. F. (2003) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(03)00071-7 · Cited by 406
Subnetwork hierarchies of biochemical pathways
Holme, P., Huss, M., & Jeong, H. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg033 · Cited by 367
Cited by
Topological analysis and interactive visualization of biological networks and protein structures
Doncheva, N. T., Assenov, Y., Domingues, F. S., & Albrecht, M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.004 · Cited by 503
The proteomic landscape of synaptic diversity across brain regions and cell types
van Oostrum, M., Blok, T. M., Giandomenico, S. L., tom Dieck, S., Tushev, G., Fürst, N., Langer, J. D., & Schuman, E. M. (2023) · Cell · doi:10.1016/j.cell.2023.09.028 · Cited by 135
Bari, E., Ferrarotti, I., Di Silvestre, D., Grisoli, P., Barzon, V., Balderacchi, A., Torre, M. L., Rossi, R., Mauri, P., Corsico, A. G., et al. (2019) · Cells · doi:10.3390/cells8090965 · Cited by 70
Huang, Y., Chen, H.-C., Chiang, C.-W., Yeh, C.-T., Chen, S.-J., & Chou, C.-K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks789 · Cited by 37
Presence and utility of intrinsically disordered regions in kinases
Kathiriya, J. J., Pathak, R. R., Clayman, E., Xue, B., Uversky, V. N., & Davé, V. (2014) · Molecular BioSystems · doi:10.1039/c4mb00224e · Cited by 30
Metadata
- Authors
- Scardoni, G., Petterlini, M., & Laudanna, C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-09-02
- Volume
- 25
- Issue
- 21
- Pages
- 2857-2859
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2112513984
- Cited by
- 543
- References
- 12
- FWCI
- 6.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
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: Analyzing biological network parameters with CentiScaPe. https://app.cochat.ai/papers/10.1093/bioinformatics/btp517
- The paper
- Scardoni, G., Petterlini, M., & Laudanna, C. (2009). Analyzing biological network parameters with CentiScaPe. Bioinformatics. https://doi.org/10.1093/bioinformatics/btp517
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.
