Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSJisoo Park, Benjamin J Hescott, Donna K Slonim
ABSTRACTIdentification of functional pathways mediating molecular responses may lead to better understanding of disease processes and suggest new therapeutic approaches. We introduce a method to detect such mediating functions using topological properties of protein-protein interaction networks. We define the concept of pathway centrality, a measure of communication between disease genes and differentially expressed genes. Using pathway centrality, we identify mediating pathways in three pulmonary diseases (asthma; bronchopulmonary dysplasia (BPD); and chronic obstructive pulmonary disease (COPD)). We systematically evaluate the significance of all identified central pathways using genetic interactions. Mediating pathways shared by all three pulmonary disorders favor innate immune and inflammation-related processes, including toll-like receptor (TLR) signaling, PDGF- and angiotensin-regulated airway remodeling, the JAK-STAT signaling pathway, and interferon gamma. Disease-specific mediators, such as neurodevelopmental processes in BPD or adhesion molecules in COPD, are also highlighted. Some of our findings implicate pathways already in development as drug targets, while others may suggest new therapeutic approaches. More... »
PAGES5863
http://scigraph.springernature.com/pub.10.1038/s41598-019-42299-3
DOIhttp://dx.doi.org/10.1038/s41598-019-42299-3
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1113355958
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30971743
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1102",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Cardiorespiratory Medicine and Haematology",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/11",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Medical and Health Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "University of California, San Diego",
"id": "https://www.grid.ac/institutes/grid.266100.3",
"name": [
"School of Medicine, University of California, San Diego, CA, 92093, USA. jisoopark@ucsd.edu."
],
"type": "Organization"
},
"familyName": "Park",
"givenName": "Jisoo",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Northeastern University",
"id": "https://www.grid.ac/institutes/grid.261112.7",
"name": [
"College of Computer and Information Science, Northeastern University, Boston, MA, 02115, USA."
],
"type": "Organization"
},
"familyName": "Hescott",
"givenName": "Benjamin J",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Tufts University",
"id": "https://www.grid.ac/institutes/grid.429997.8",
"name": [
"Department of Computer Science, Tufts University, Medford, MA, 02155, USA. slonim@cs.tufts.edu.",
"Department of Immunology, Tufts University School of Medicine, Boston, MA, 02111, USA. slonim@cs.tufts.edu."
],
"type": "Organization"
},
"familyName": "Slonim",
"givenName": "Donna K",
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1371/journal.pone.0078585",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001186883"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0078585",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001186883"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0078585",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001186883"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/0022250x.1999.9990219",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001455021"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/b978-0-12-374001-4.00079-1",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002071080"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev-med-051113-024537",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002179265"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s1569-9048(03)00154-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002979713"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s1569-9048(03)00154-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002979713"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.gene.2016.07.049",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003247594"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.2165/00063030-200822020-00002",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003512128",
"https://doi.org/10.2165/00063030-200822020-00002"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1159/000354173",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004022057"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2164-13-356",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005720233",
"https://doi.org/10.1186/1471-2164-13-356"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1513/annalsats.201403-118aw",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1006519270"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1038/msb.2008.4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007650467"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1038/msb.2008.4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007650467"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/acs.jmedchem.5b01647",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007822867"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkv1046",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009932957"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp618",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016138230"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.0707413104",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016706328"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pcbi.1001095",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019068006"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.4155/fmc.16.4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020028855"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1172/jci88555",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021780136"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1103/physreve.67.017101",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022782935"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1103/physreve.67.017101",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022782935"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkw985",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023958838"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2147/copd.s35294",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023959808"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2334/josnusd.16-0187",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029397588"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/527s14a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033566282",
"https://doi.org/10.1038/527s14a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1203/00006450-201011001-00656",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034114799",
"https://doi.org/10.1203/00006450-201011001-00656"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1053/j.semperi.2006.05.010",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035387272"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0163967",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036472730"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkv1290",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037647823"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1164/rccm.200606-777pp",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038227135"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btr260",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039284123"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.337",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039470729",
"https://doi.org/10.1038/ng.337"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1124/pr.116.012518",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039837718"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pcbi.0030059",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041455110"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btl234",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043247612"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00059-016-4510-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047783824",
"https://doi.org/10.1007/s00059-016-4510-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00059-016-4510-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047783824",
"https://doi.org/10.1007/s00059-016-4510-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00059-016-4510-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047783824",
"https://doi.org/10.1007/s00059-016-4510-9"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pcbi.1003578",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047940975"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/gkn665",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047944503"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1155/2015/206937",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048060261"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.1239303",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052744398"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1152/ajplung.00315.2001",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1063195536"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1542/peds.102.4.927",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1067819677"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1078447680",
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2017.05.038",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1086036175"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.cell.2017.05.038",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1086036175"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/mcp.0000000000000436",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092218317"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1097/mcp.0000000000000436",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092218317"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1001/jamapediatrics.2017.5323",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101110234"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2307/3033543",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1102895783"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "Identification of functional pathways mediating molecular responses may lead to better understanding of disease processes and suggest new therapeutic approaches. We introduce a method to detect such mediating functions using topological properties of protein-protein interaction networks. We define the concept of pathway centrality, a measure of communication between disease genes and differentially expressed genes. Using pathway centrality, we identify mediating pathways in three pulmonary diseases (asthma; bronchopulmonary dysplasia (BPD); and chronic obstructive pulmonary disease (COPD)). We systematically evaluate the significance of all identified central pathways using genetic interactions. Mediating pathways shared by all three pulmonary disorders favor innate immune and inflammation-related processes, including toll-like receptor (TLR) signaling, PDGF- and angiotensin-regulated airway remodeling, the JAK-STAT signaling pathway, and interferon gamma. Disease-specific mediators, such as neurodevelopmental processes in BPD or adhesion molecules in COPD, are also highlighted. Some of our findings implicate pathways already in development as drug targets, while others may suggest new therapeutic approaches.",
"genre": "research_article",
"id": "sg:pub.10.1038/s41598-019-42299-3",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2528667",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1045337",
"issn": [
"2045-2322"
],
"name": "Scientific Reports",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "9"
}
],
"name": "Pathway centrality in protein interaction networks identifies putative functional mediating pathways in pulmonary disease.",
"pagination": "5863",
"productId": [
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41598-019-42299-3"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1113355958"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101563288"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30971743"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41598-019-42299-3",
"https://app.dimensions.ai/details/publication/pub.1113355958"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-15T09:13",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000376_0000000376/records_56159_00000006.jsonl",
"type": "ScholarlyArticle",
"url": "http://www.nature.com/articles/s41598-019-42299-3"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41598-019-42299-3'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41598-019-42299-3'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41598-019-42299-3'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41598-019-42299-3'
This table displays all metadata directly associated to this object as RDF triples.
224 TRIPLES
21 PREDICATES
73 URIs
20 LITERALS
8 BLANK NODES