The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools
Open accessAbstract
The availability of whole genome sequences from various model organisms and increasing experimental data and literatures stimulated the evolution of a systems approach for biological research. The development of computational tools and algorithms to study biological pathway networks has made great progress in helping analyze research data. Pathway databases become an integral part of such an approach. This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research. Next, we use PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display. Last, we describe the usage of such systems. We also describe the computational tools that utilize PANTHER Pathway information to analyze gene expression experimental data.
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
Using process diagrams for the graphical representation of biological networks
Kitano, H., Funahashi, A., Matsuoka, Y., & Oda, K. (2005) · Nature Biotechnology · doi:10.1038/nbt1111 · Cited by 483
Cited by
PANTHER : Making genome‐scale phylogenetics accessible to all
Thomas, P. D., Ebert, D., Muruganujan, A., Mushayahama, T., Albou, L., & Mi, H. (2022) · Protein Science · doi:10.1002/pro.4218 · Cited by 2,010
Self-citationNew genetic loci link adipose and insulin biology to body fat distribution
The ADIPOGen Consortium, Shungin, D., The CARDIOGRAMplusC4D Consortium, The CKDGen Consortium, The GEFOS Consortium, The GENIE Consortium, The, G. L. G. C., The, I. C. B. P., The International Endogene Consortium, Study, T. L. C., et al. (2015) · Nature · doi:10.1038/nature14132 · Cited by 1,580
Mi, H., Ebert, D., Muruganujan, A., Mills, C., Albou, L.-P., Mushayamaha, T., & Thomas, P. D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1106 · Cited by 1,332
Self-citationPANTHER version 10: expanded protein families and functions, and analysis tools
Mi, H., Poudel, S., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1194 · Cited by 770
Self-citationBioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082873 · Cited by 280
A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America
Greninger, A. L., Chen, E. C., Sittler, T., Scheinerman, A., Roubinian, N., Yu, G., Kim, E., Pillai, D. R., Guyard, C., Mazzulli, T., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013381 · Cited by 193
IFN-gamma-induced PD-L1 expression in melanoma depends on p53 expression
Thiem, A., Hesbacher, S., Kneitz, H., di Primio, T., Heppt, M. V., Hermanns, H. M., Goebeler, M., Meierjohann, S., Houben, R., & Schrama, D. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1403-9 · Cited by 153
Mabry, K. M., Payne, S. Z., & Anseth, K. S. (2016) · Biomaterials · doi:10.1016/j.biomaterials.2015.09.035 · Cited by 124
From Omics to Multi-Omics: A Review of Advantages and Tradeoffs
Hayes, C. N., Nakahara, H., Ono, A., Tsuge, M., & Oka, S. (2024) · Genes · doi:10.3390/genes15121551 · Cited by 119
Lehallier, B., Shokhirev, M. N., Wyss‐Coray, T., & Johnson, A. A. (2020) · Aging Cell · doi:10.1111/acel.13256 · Cited by 106
Cerebrospinal fluid proteomics implicates the granin family in Parkinson’s disease
Rotunno, M. S., Lane, M., Zhang, W., Wolf, P., Oliva, P., Viel, C., Wills, A.-M., Alcalay, R. N., Scherzer, C. R., Shihabuddin, L. S., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59414-4 · Cited by 94
Identification of genomic variants putatively targeted by selection during dog domestication
Cagan, A., & Blass, T. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0579-7 · Cited by 69
Ketkar, S., Verdoni, A. M., Smith, A. M., Bangert, C. V., Leight, E. R., Chen, D. Y., Brune, M. K., Helton, N. M., Hoock, M., George, D. R., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1918611117 · Cited by 35
Villar-Vesga, J., Henao-Restrepo, J., Voshart, D. C., Aguillon, D., Villegas, A., Castaño, D., Arias-Londoño, J. D., Zuhorn, I. S., Ribovski, L., Barazzuol, L., et al. (2020) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2020.587989 · Cited by 29
Metadata
- Authors
- Mi, H., & Thomas, P.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2009
- Volume
- 563
- Pages
- 123-140
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W74841586
- Cited by
- 744
- References
- 1
- FWCI
- 9.84
- Type
- book chapter
- Language
- en
- Open access
- green
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
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.
