Gene network interconnectedness and the generalized topological overlap measure
<p>Abstract</p> <p>Background</p> <p>Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the...
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| Format: | Article |
| Language: | English |
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BMC
2007-01-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/22 |
| _version_ | 1818067902602936320 |
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| author | Horvath Steve Yip Andy M |
| author_facet | Horvath Steve Yip Andy M |
| author_sort | Horvath Steve |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz <it>et al</it>. <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> can be interpreted as a measure of agreement between the <it>m </it>= 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness.</p> <p>Results</p> <p>We generalize the topological overlap measure from <it>m </it>= 1 step neighborhoods to <it>m </it>≥ 2 step neighborhoods. This allows us to define the <it>m</it>-th order generalized topological overlap measure (GTOM) by (i) counting the number of <it>m</it>-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis.</p> <p>Conclusion</p> <p>Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The <it>m</it>-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules.</p> |
| first_indexed | 2024-12-10T15:31:04Z |
| format | Article |
| id | doaj.art-93a18d33653d4e0b8285963900c9b69a |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T15:31:04Z |
| publishDate | 2007-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-93a18d33653d4e0b8285963900c9b69a2022-12-22T01:43:24ZengBMCBMC Bioinformatics1471-21052007-01-01812210.1186/1471-2105-8-22Gene network interconnectedness and the generalized topological overlap measureHorvath SteveYip Andy M<p>Abstract</p> <p>Background</p> <p>Network methods are increasingly used to represent the interactions of genes and/or proteins. Genes or proteins that are directly linked may have a similar biological function or may be part of the same biological pathway. Since the information on the connection (adjacency) between 2 nodes may be noisy or incomplete, it can be desirable to consider alternative measures of pairwise interconnectedness. Here we study a class of measures that are proportional to the number of neighbors that a pair of nodes share in common. For example, the topological overlap measure by Ravasz <it>et al</it>. <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> can be interpreted as a measure of agreement between the <it>m </it>= 1 step neighborhoods of 2 nodes. Several studies have shown that two proteins having a higher topological overlap are more likely to belong to the same functional class than proteins having a lower topological overlap. Here we address the question whether a measure of topological overlap based on higher-order neighborhoods could give rise to a more robust and sensitive measure of interconnectedness.</p> <p>Results</p> <p>We generalize the topological overlap measure from <it>m </it>= 1 step neighborhoods to <it>m </it>≥ 2 step neighborhoods. This allows us to define the <it>m</it>-th order generalized topological overlap measure (GTOM) by (i) counting the number of <it>m</it>-step neighbors that a pair of nodes share and (ii) normalizing it to take a value between 0 and 1. Using theoretical arguments, a yeast co-expression network application, and a fly protein network application, we illustrate the usefulness of the proposed measure for module detection and gene neighborhood analysis.</p> <p>Conclusion</p> <p>Topological overlap can serve as an important filter to counter the effects of spurious or missing connections between network nodes. The <it>m</it>-th order topological overlap measure allows one to trade-off sensitivity versus specificity when it comes to defining pairwise interconnectedness and network modules.</p>http://www.biomedcentral.com/1471-2105/8/22 |
| spellingShingle | Horvath Steve Yip Andy M Gene network interconnectedness and the generalized topological overlap measure BMC Bioinformatics |
| title | Gene network interconnectedness and the generalized topological overlap measure |
| title_full | Gene network interconnectedness and the generalized topological overlap measure |
| title_fullStr | Gene network interconnectedness and the generalized topological overlap measure |
| title_full_unstemmed | Gene network interconnectedness and the generalized topological overlap measure |
| title_short | Gene network interconnectedness and the generalized topological overlap measure |
| title_sort | gene network interconnectedness and the generalized topological overlap measure |
| url | http://www.biomedcentral.com/1471-2105/8/22 |
| work_keys_str_mv | AT horvathsteve genenetworkinterconnectednessandthegeneralizedtopologicaloverlapmeasure AT yipandym genenetworkinterconnectednessandthegeneralizedtopologicaloverlapmeasure |