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.
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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
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
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- Mi, H., & Thomas, P. (2009). PANTHER Pathway: An Ontology-Based Pathway Database Coupled with Data Analysis Tools. Methods in Molecular Biology. https://doi.org/10.1007/978-1-60761-175-2_7
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