Abstract
Pathway annotation or enrichment is often used as the efficient tool to uncover the molecular mechanism of interesting gene sets from genome-wide research. Up to now, numerous pathway databases or web servers that integrated fragmented pathway maps have been published, such as KEGG, Reactome, NetPath, Pathway Commons, DAVID and PathwAX. However, all these data sources are not taking into account the pathway quantity or pathway topology information. Thus, to fill the gap, we developed ComPAT, which provides a web framework that enables users to perform pathway/subpathway enrichment analysis for interesting gene sets, browse and search detailed pathway annotation information. The current version of ComPAT contains a total of 2,881 pathways that were obtained from 10 pathway databases and extended gene interactions from 10 other gene interaction databases, including 10,760 genes and 1,136,971 interactive relationships. All pathways in ComPAT were converted into graphs. ComPAT provides comprehensive annotation for pathways, including network visualization and topology information, gene subcellular localization and gene–gene interaction strength. What's more, ComPAT integrated five types of subpathway algorithms to split pathways into 23,024 subpathways for small-scale gene sets enrichment. Users can input the interesting gene sets for pathway/subpathway annotation or enrichment analysis. Here, we performed the subpathway analysis for cardiac remodeling as a biological case. ComPAT also supports subpathway analysis pipeline for user-input networks. The server is freely available at http://bio.licpathway.net:8018/msg/ComPAT/index.do.
X. Su, C. Song and C. Feng—Contributed equally to this study.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Kanehisa, M., Goto, S.: KEGG: kyoto encyclopedia of genes and genomes. Nucl. Acids Res. 28(1), 27–30 (2000)
Brumby, A.M., Richardson, H.E.: Using Drosophila melanogaster to map human cancer pathways. Nat Rev Cancer 5(8), 626–639 (2005)
Evans, J.L., Goldfine, I.D., Maddux, B.A., Grodsky, G.M.: Oxidative stress and stress-activated signaling pathways: a unifying hypothesis of type 2 diabetes. Endocr. Rev. 23(5), 599–622 (2002)
Hunter, J.J., Chien, K.R.: Signaling pathways for cardiac hypertrophy and failure. N. Engl. J. Med. 341(17), 1276–1283 (1999)
Bracken, A.P., Pasini, D., Capra, M., Prosperini, E., Colli, E., Helin, K.: EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 22(20), 5323–5335 (2003)
Bader, G.D., Cary, M.P., Sander, C.: Pathguide: a pathway resource list. Nucleic Acids Res 34(Database issue) D504–506 (2006)
Joshi-Tope, G. et al.: Reactome: a knowledgebase of biological pathways. Nucleic Acids Res, 33(Database issue) D428–432 (2005)
Kandasamy, K., et al.: NetPath: a public resource of curated signal transduction pathways. Genome Biol. 11(1), R3 (2010)
Huang, D.W., Sherman, B.T., Lempicki, R.A.: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl. Acids Res. 37(1), 1–13 (2009)
Zhou, Y., Zhou, B., Pache, L., Chang, M., Khodabakhshi, A.H., Tanaseichuk, O., Benner, C., Chanda, S.K.: Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10(1), 1523 (2019)
Kuleshov, M.V., et al.: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucl. Acids Res. 44(W1), W90-97 (2016)
Cerami, E.G. et al.: Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 39(Database issue) D685–690 (2011)
Subramanian, A., et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 102(43), 15545–15550 (2005)
Antonov, A.V., Dietmann, S., Mewes, H.W.: KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. Genome Biol. 9(12), R179 (2008)
Sales, G., Calura, E., Cavalieri, D., Romualdi, C.: Graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinform. 13, 20 (2012)
Li, C. et al.: SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res. 37(19) e131 (2009)
Ogris, C., Helleday, T., Sonnhammer, E.L.: PathwAX: a web server for network crosstalk based pathway annotation. Nucl. Acids Res. 44(W1), W105-109 (2016)
Ma, J., Shojaie, A., Michailidis, G.: Network-based pathway enrichment analysis with incomplete network information. Bioinformatics 32(20), 3165–3174 (2016)
Li, C. et al.: Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways. Nucleic Acids Res. 41(9) e101 (2013)
Li, X., et al.: Dissection of human MiRNA regulatory influence to subpathway. Brief Bioinform. 13(2), 175–186 (2012)
UniProt C: UniProt: a hub for protein information. Nucl. Acids Res. 43(Database issue) D204–212 (2015)
Newman, M.E., Girvan, M.: Finding and evaluating community structure in networks. Phys. Rev. E Stat. Nonlin Soft Matter Phys. 69(2 Pt 2) 026113 (2004)
Clauset, A., Newman, M.E., Moore, C.: Finding community structure in very large networks. Phys. Rev. E Stat Nonlin Soft Matter Phys. 70(6 Pt 2) 066111 (2004)
Traag, V.A., Bruggeman, J.: Community detection in networks with positive and negative links. Phys. Rev. E. Stat. Nonlin. Soft Matter. Phys. 80(3 Pt 2) 036115 (2009)
Pons, P., Latapy, M.: Computing communities in large networks using random walks. Jof Graph Alg Appbf 10(2), 191–218 (2006)
Karp, P.D. et al.: Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 11(1) 40–79 (2010)
Feng, C., et al.: ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies. J. Cell Mol. Med. 23(2), 967–984 (2019)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this paper
Cite this paper
Su, X. et al. (2021). ComPAT: A Comprehensive Pathway Analysis Tools. In: Huang, DS., Jo, KH., Li, J., Gribova, V., Premaratne, P. (eds) Intelligent Computing Theories and Application. ICIC 2021. Lecture Notes in Computer Science(), vol 12838. Springer, Cham. https://doi.org/10.1007/978-3-030-84532-2_11
Download citation
DOI: https://doi.org/10.1007/978-3-030-84532-2_11
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-84531-5
Online ISBN: 978-3-030-84532-2
eBook Packages: Computer ScienceComputer Science (R0)