Dataset Information

LinkinPath: from sequence to interconnected pathway.

ABSTRACT:

Summary

LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein sequences to LinkinPath to (i) determine the co-occurrence and co-absence of genes/proteins on animated KEGG pathway maps; (ii) compare functional compositions within and among the datasets using TreeMaps; (iii) analyze the statistically enriched pathways across the datasets; (iv) build the pathway-to-pathway networks for each dataset; (v) explore potential interaction/reaction paths between pathways; and (vi) identify common pathway-to-pathway networks across the datasets.

Availability

LinkinPath is freely available to all interested users at http://www.biotec.or.th/isl/linkinpath/.

SUBMITTER: Ingsriswang S

PROVIDER: S-EPMC3129532 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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Publications

LinkinPath: from sequence to interconnected pathway.

Ingsriswang Supawadee S Yokwai Sunai S Wichadakul Duangdao D

Bioinformatics (Oxford, England) 20110602 14

<h4>Summary</h4>LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein sequences to LinkinPath to (i) determine the co-occurrence and co-absence of genes/proteins on a ...[more]

PMID: 21636594

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Project description:Background: The clearance of medical devices by the US Food and Drug Administration (FDA) has remained largely unchanged since 1976, when the Medical Device Amendments Act established a system classifying devices into 3 categories based on safety risk to the consumer. The system allows for the clearance of many orthopedics devices through the 510(k) premarket pathway, which is based on “predicate ancestors,” previously cleared devices that are “substantially equivalent.” Purpose: We sought to trace the predicate ancestors of modern total knee arthroplasty (TKA) devices, specifically those recently cleared for marketing by the 510(k) pathway that claim substantial equivalence to prior devices, despite potential differences in material science and design. In addition, we aimed to document which TKA devices cleared by the 510(k) pathway have substantial equivalence to devices that have since been recalled by the FDA. Methods: To create a comprehensive list of TKA devices, we used FDA Classification Process Codes corresponding to knee arthroplasty to search the FDA’s databases from May 28, 1976, the start of the 510(k) process, to May 1, 2021. Of 1309 resulting devices, 89 were excluded as not related to arthroplasty. For each of the remaining devices, we analyzed the descendant devices that claimed substantial equivalence, either directly or indirectly. We used data of recalled designs to determine both the absolute number of recalled devices and the number of currently cleared devices that presented substantial equivalence claims upon predicates that have since been recalled. Results: Of 1220 knee devices cleared or approved, 6 (0.5%) were approved through the premarket approval application (PMA) process, and 1214 (99.5%) were cleared through the 510(k) pathway. Of the 1214 cleared devices, 217 (17.9%) have been recalled and 204 (16.8%) have ties to at least 1 recalled predicate device linked through generational claims of substantial equivalence. We found 90 devices (7.4%) linked directly to a recalled predicate device. Conclusions: Most knee arthroplasty devices are cleared for marketing through reliance on a complex web of equivalency to previously cleared predicates. We found that many TKA devices thus connected were cleared decades apart, with multiple iterations of design and material modifications. Many currently marketed TKA devices have claimed equivalency to predicates that have been recalled. Our findings suggest the need for novel regulatory strategies that might further patient safety while balancing the unwanted effects of regulatory burden.

Dataset Information

LinkinPath: from sequence to interconnected pathway.

Summary

Availability

Publications

LinkinPath: from sequence to interconnected pathway.

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