Ontology type: schema:ScholarlyArticle Open Access: True
2016-12
AUTHORSJing Zhu, Natasha G Deane, Keeli B Lewis, Chandrasekhar Padmanabhan, M Kay Washington, Kristen K Ciombor, Cynthia Timmers, Richard M Goldberg, R Daniel Beauchamp, Xi Chen
ABSTRACTDefining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients. More... »
PAGES33273
http://scigraph.springernature.com/pub.10.1038/srep33273
DOIhttp://dx.doi.org/10.1038/srep33273
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1041622917
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/27623752
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/2008/1112",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Oncology and Carcinogenesis",
"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"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Colorectal Neoplasms",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Disease-Free Survival",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Female",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Formaldehyde",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Gene Expression Regulation, Neoplastic",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Male",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Neoplasm Recurrence, Local",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Oligonucleotide Array Sequence Analysis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Paraffin Embedding",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Prognosis",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Tissue Fixation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Transcriptome",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Department of Surgery, Nashville, 37232, USA.",
"Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Zhu",
"givenName": "Jing",
"id": "sg:person.010361370317.26",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010361370317.26"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Department of Surgery, Nashville, 37232, USA.",
"Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Deane",
"givenName": "Natasha G",
"id": "sg:person.013423171227.08",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013423171227.08"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Department of Surgery, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Lewis",
"givenName": "Keeli B",
"id": "sg:person.01007467513.09",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01007467513.09"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Department of Surgery, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Padmanabhan",
"givenName": "Chandrasekhar",
"id": "sg:person.015457512055.51",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015457512055.51"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.",
"Vanderbilt University, Department of Pathology, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Washington",
"givenName": "M Kay",
"id": "sg:person.014213320717.05",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014213320717.05"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "The Ohio State University",
"id": "https://www.grid.ac/institutes/grid.261331.4",
"name": [
"The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.",
"Ohio State University, Division of Medical Oncology, Department of Internal Medicine, Columbus, 43210, USA."
],
"type": "Organization"
},
"familyName": "Ciombor",
"givenName": "Kristen K",
"id": "sg:person.0616765656.87",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0616765656.87"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "The Ohio State University",
"id": "https://www.grid.ac/institutes/grid.261331.4",
"name": [
"The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA."
],
"type": "Organization"
},
"familyName": "Timmers",
"givenName": "Cynthia",
"id": "sg:person.01042136451.04",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042136451.04"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "The Ohio State University",
"id": "https://www.grid.ac/institutes/grid.261331.4",
"name": [
"The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.",
"Ohio State University, Division of Medical Oncology, Department of Internal Medicine, Columbus, 43210, USA."
],
"type": "Organization"
},
"familyName": "Goldberg",
"givenName": "Richard M",
"id": "sg:person.016472106717.33",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016472106717.33"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Vanderbilt University",
"id": "https://www.grid.ac/institutes/grid.152326.1",
"name": [
"Vanderbilt University, Department of Surgery, Nashville, 37232, USA.",
"Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.",
"Vanderbilt University, Department of Cell and Developmental Biology, Nashville, 37232, USA.",
"Vanderbilt University, Department of Cancer Biology, Nashville, 37232, USA."
],
"type": "Organization"
},
"familyName": "Beauchamp",
"givenName": "R Daniel",
"id": "sg:person.01355254152.34",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355254152.34"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Sylvester Comprehensive Cancer Center",
"id": "https://www.grid.ac/institutes/grid.419791.3",
"name": [
"University of Miami Miller School of Medicine, Division of Biostatistics, Department of Public Health Sciences, Miami, 33136, USA.",
"University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, 33136, USA."
],
"type": "Organization"
},
"familyName": "Chen",
"givenName": "Xi",
"id": "sg:person.0602643340.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602643340.16"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1186/1755-8794-4-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000096355",
"https://doi.org/10.1186/1755-8794-4-9"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2014.60.0213",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004354210"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1053/j.gastro.2009.03.041",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007709286"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0140-6736(10)60353-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1008954947"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/ijc.22975",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009260280"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1158/0008-5472.can-06-1514",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010157341"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/j.stem.2011.02.020",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010215023"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature11252",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010619765",
"https://doi.org/10.1038/nature11252"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3322/caac.21254",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011682275"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/sj.onc.1210060",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016096158",
"https://doi.org/10.1038/sj.onc.1210060"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/sj.onc.1210060",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016096158",
"https://doi.org/10.1038/sj.onc.1210060"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/biostatistics/kxj037",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016217055"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/annonc/mdu100",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1017253169"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0041292",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021741909"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2004.08.186",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023382518"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2010.28.9538",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024773369"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2005.00.695",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1027666537"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2407-11-529",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028267348",
"https://doi.org/10.1186/1471-2407-11-529"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-59745-551-0_18",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028408098",
"https://doi.org/10.1007/978-1-59745-551-0_18"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/978-1-59745-551-0_18",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028408098",
"https://doi.org/10.1007/978-1-59745-551-0_18"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2011.35.4498",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029028643"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2010.30.1077",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029360766"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/bts188",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030426505"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/14651858.cd005390.pub2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030841908"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3322/caac.21235",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033662969"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/biostatistics/4.2.249",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1037543114"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1158/0008-5472.can-14-1592",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038570075"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1158/1078-0432.ccr-05-2734",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038753948"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2005.05.0229",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039902598"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/jnci/dju247",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041742688"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0079282",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043238843"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1053/j.gastro.2009.11.005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043914495"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature14966",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044817288",
"https://doi.org/10.1038/nature14966"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nbt0308-293",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046235114",
"https://doi.org/10.1038/nbt0308-293"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0153784",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047572418"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0153784",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047572418"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1472-6750-11-46",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048969581",
"https://doi.org/10.1186/1472-6750-11-46"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2353/jmoldx.2008.080011",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049401881"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/gutjnl-2011-300812",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051730844"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1200/jco.2010.34.3426",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1053409060"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1080/02841860151116367",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058315961"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3892/or.17.5.1089",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1071530404"
],
"type": "CreativeWork"
}
],
"datePublished": "2016-12",
"datePublishedReg": "2016-12-01",
"description": "Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter\u00ae and Affymetrix GeneChip\u00ae Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR\u2009<\u20090.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P\u2009<\u20090.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P\u2009<\u20090.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.",
"genre": "research_article",
"id": "sg:pub.10.1038/srep33273",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2481416",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2440181",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1045337",
"issn": [
"2045-2322"
],
"name": "Scientific Reports",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "6"
}
],
"name": "Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples",
"pagination": "33273",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"c646afc285b931bb7fcde2f5ef55fb5973e7b12b75fbde842961403273b2cd67"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"27623752"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101563288"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/srep33273"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1041622917"
]
}
],
"sameAs": [
"https://doi.org/10.1038/srep33273",
"https://app.dimensions.ai/details/publication/pub.1041622917"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-10T21:44",
"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/v90/0000000001_0000000264/records_8687_00000551.jsonl",
"type": "ScholarlyArticle",
"url": "http://www.nature.com/srep/2016/160914/srep33273/full/srep33273.html"
}
]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/srep33273'
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/srep33273'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/srep33273'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/srep33273'
This table displays all metadata directly associated to this object as RDF triples.
324 TRIPLES
21 PREDICATES
81 URIs
34 LITERALS
22 BLANK NODES