{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,11]],"date-time":"2025-06-11T07:30:48Z","timestamp":1749627048285,"version":"3.37.3"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,7,7]],"date-time":"2017-07-07T00:00:00Z","timestamp":1499385600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["EP\/K032402\/1"],"award-info":[{"award-number":["EP\/K032402\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Our work is motivated by an interest in constructing a protein\u2013protein interaction network that captures key features associated with Parkinson\u2019s disease. While there is an abundance of subnetwork construction methods available, it is often far from obvious which subnetwork is the most suitable starting point for further investigation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We provide a method to assess whether a subnetwork constructed from a seed list (a list of nodes known to be important in the area of interest) differs significantly from a randomly generated subnetwork. The proposed method uses a Monte Carlo approach. As different seed lists can give rise to the same subnetwork, we control for redundancy by constructing a minimal seed list as the starting point for the significance test. The null model is based on random seed lists of the same length as a minimum seed list that generates the subnetwork; in this random seed list the nodes have (approximately) the same degree distribution as the nodes in the minimum seed list. We use this null model to select subnetworks which deviate significantly from random on an appropriate set of statistics and might capture useful information for a real world protein\u2013protein interaction network.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software used in this paper are available for download at https:\/\/sites.google.com\/site\/elliottande\/. The software is written in Python and uses the NetworkX library.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx419","type":"journal-article","created":{"date-parts":[[2017,6,30]],"date-time":"2017-06-30T19:13:46Z","timestamp":1498850026000},"page":"64-71","source":"Crossref","is-referenced-by-count":6,"title":["A nonparametric significance test for sampled networks"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4536-5244","authenticated-orcid":false,"given":"Andrew","family":"Elliott","sequence":"first","affiliation":[{"name":"CABDyN Complexity Centre, Sa\u00efd Business School, University of Oxford, Oxford OX1\u20091HP, UK"}]},{"given":"Elizabeth","family":"Leicht","sequence":"additional","affiliation":[{"name":"CABDyN Complexity Centre, Sa\u00efd Business School, University of Oxford, Oxford OX1\u20091HP, UK"}]},{"given":"Alan","family":"Whitmore","sequence":"additional","affiliation":[{"name":"e-Therapeutics plc, Long Hanborough, OX29\u20098LN, UK"}]},{"given":"Gesine","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"}]},{"given":"Felix","family":"Reed-Tsochas","sequence":"additional","affiliation":[{"name":"CABDyN Complexity Centre, Sa\u00efd Business School, University of Oxford, Oxford OX1\u20091HP, UK"},{"name":"Oxford Martin School, University of Oxford, Oxford, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,7,7]]},"reference":[{"volume-title":"Handbook of Statistical Systems Biology","year":"2011","author":"Ali","key":"2023020208402204200_btx419-B1"},{"key":"2023020208402204200_btx419-B2","doi-asserted-by":"crossref","first-page":"372.","DOI":"10.1186\/1471-2105-8-372","article-title":"Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases","volume":"8","author":"Berger","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023020208402204200_btx419-B3","doi-asserted-by":"crossref","first-page":"ii11","DOI":"10.1136\/sti.2010.044446","article-title":"Counting hard-to-count populations: the network scale-up method for public health","volume":"86","author":"Bernard","year":"2010","journal-title":"Sex Transm. 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