Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury. View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2002-10-25

AUTHORS

Michael Costigan, Katia Befort, Laurie Karchewski, Robert S Griffin, Donatella D'Urso, Andrew Allchorne, Joanne Sitarski, James W Mannion, Richard E Pratt, Clifford J Woolf

ABSTRACT

BACKGROUND: Rat oligonucleotide microarrays were used to detect changes in gene expression in the dorsal root ganglion (DRG) 3 days following sciatic nerve transection (axotomy). Two comparisons were made using two sets of triplicate microarrays, naïve versus naïve and naïve versus axotomy. RESULTS: Microarray variability was assessed using the naïve versus naïve comparison. These results support use of a P < 0.05 significance threshold for detecting regulated genes, despite the large number of hypothesis tests required. For the naïve versus axotomy comparison, a 2-fold cut off alone led to an estimated error rate of 16%; combining a >1.5-fold expression change and P < 0.05 significance reduced the estimated error to 5%. The 2-fold cut off identified 178 genes while the combined >1.5-fold and P < 0.05 criteria generated 240 putatively regulated genes, which we have listed. Many of these have not been described as regulated in the DRG by axotomy. Northern blot, quantitative slot blots and in situ hybridization verified the expression of 24 transcripts. These data showed an 83% concordance rate with the arrays; most mismatches represent genes with low expression levels reflecting limits of array sensitivity. A significant correlation was found between actual mRNA differences and relative changes between microarrays (r2 = 0.8567). Temporal patterns of individual genes regulation varied. CONCLUSIONS: We identify parameters for microarray analysis which reduce error while identifying many putatively regulated genes. Functional classification of these genes suggest reorganization of cell structural components, activation of genes expressed by immune and inflammatory cells and down-regulation of genes involved in neurotransmission. More... »

PAGES

16-16

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2202-3-16

DOI

http://dx.doi.org/10.1186/1471-2202-3-16

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007072033

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/12401135


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

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/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Apoptosis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Axotomy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Blotting, Northern", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cytoskeleton", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Disease Models, Animal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Ganglia, Spinal", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Profiling", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "In Situ Hybridization", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Male", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Neurons", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Oligonucleotide Array Sequence Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Peripheral Nerve Injuries", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Peripheral Nerves", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Rats", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Rats, Sprague-Dawley", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reproducibility of Results", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sciatic Neuropathy", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sensitivity and Specificity", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Costigan", 
        "givenName": "Michael", 
        "id": "sg:person.01041441555.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01041441555.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Befort", 
        "givenName": "Katia", 
        "id": "sg:person.0622412705.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622412705.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Karchewski", 
        "givenName": "Laurie", 
        "id": "sg:person.01366015505.08", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366015505.08"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Griffin", 
        "givenName": "Robert S", 
        "id": "sg:person.0721522537.86", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0721522537.86"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Bayer AG, Wuppertal, Germany", 
          "id": "http://www.grid.ac/institutes/grid.420044.6", 
          "name": [
            "Bayer AG, Wuppertal, Germany"
          ], 
          "type": "Organization"
        }, 
        "familyName": "D'Urso", 
        "givenName": "Donatella", 
        "id": "sg:person.01157425752.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157425752.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Allchorne", 
        "givenName": "Andrew", 
        "id": "sg:person.01225541152.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01225541152.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Sitarski", 
        "givenName": "Joanne", 
        "id": "sg:person.01034202555.95", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034202555.95"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mannion", 
        "givenName": "James W", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA 02115, USA", 
          "id": "http://www.grid.ac/institutes/grid.62560.37", 
          "name": [
            "Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA 02115, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pratt", 
        "givenName": "Richard E", 
        "id": "sg:person.01314531204.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01314531204.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA", 
          "id": "http://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Woolf", 
        "givenName": "Clifford J", 
        "id": "sg:person.0740501552.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0740501552.00"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/82881", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019587997", 
          "https://doi.org/10.1038/82881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-3-642-60777-6_11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007556147", 
          "https://doi.org/10.1007/978-3-642-60777-6_11"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/37615", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031769355", 
          "https://doi.org/10.1038/37615"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/sj.onc.1200997", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038115251", 
          "https://doi.org/10.1038/sj.onc.1200997"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf01195557", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022261990", 
          "https://doi.org/10.1007/bf01195557"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/377737a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029826955", 
          "https://doi.org/10.1038/377737a0"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2002-10-25", 
    "datePublishedReg": "2002-10-25", 
    "description": "BACKGROUND: Rat oligonucleotide microarrays were used to detect changes in gene expression in the dorsal root ganglion (DRG) 3 days following sciatic nerve transection (axotomy). Two comparisons were made using two sets of triplicate microarrays, na\u00efve versus na\u00efve and na\u00efve versus axotomy.\nRESULTS: Microarray variability was assessed using the na\u00efve versus na\u00efve comparison. These results support use of a P < 0.05 significance threshold for detecting regulated genes, despite the large number of hypothesis tests required. For the na\u00efve versus axotomy comparison, a 2-fold cut off alone led to an estimated error rate of 16%; combining a >1.5-fold expression change and P < 0.05 significance reduced the estimated error to 5%. The 2-fold cut off identified 178 genes while the combined >1.5-fold and P < 0.05 criteria generated 240 putatively regulated genes, which we have listed. Many of these have not been described as regulated in the DRG by axotomy. Northern blot, quantitative slot blots and in situ hybridization verified the expression of 24 transcripts. These data showed an 83% concordance rate with the arrays; most mismatches represent genes with low expression levels reflecting limits of array sensitivity. A significant correlation was found between actual mRNA differences and relative changes between microarrays (r2 = 0.8567). Temporal patterns of individual genes regulation varied.\nCONCLUSIONS: We identify parameters for microarray analysis which reduce error while identifying many putatively regulated genes. Functional classification of these genes suggest reorganization of cell structural components, activation of genes expressed by immune and inflammatory cells and down-regulation of genes involved in neurotransmission.", 
    "genre": "article", 
    "id": "sg:pub.10.1186/1471-2202-3-16", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2558976", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2526131", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1024257", 
        "issn": [
          "1471-2202"
        ], 
        "name": "BMC Neuroscience", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "3"
      }
    ], 
    "keywords": [
      "oligonucleotide microarrays", 
      "quantitative slot blots", 
      "individual gene regulation", 
      "cell structural components", 
      "regulation of genes", 
      "activation of genes", 
      "rat oligonucleotide microarray", 
      "gene regulation", 
      "regulated genes", 
      "low expression levels", 
      "gene expression", 
      "expression changes", 
      "microarray analysis", 
      "genes", 
      "Northern blot", 
      "functional classification", 
      "microarrays", 
      "situ hybridization", 
      "expression levels", 
      "significance threshold", 
      "slot blots", 
      "mRNA differences", 
      "regulation", 
      "structural components", 
      "expression", 
      "blot", 
      "temporal patterns", 
      "transcripts", 
      "hybridization", 
      "large number", 
      "cells", 
      "activation", 
      "reorganization", 
      "dorsal root ganglia", 
      "changes", 
      "na\u00efve", 
      "root ganglia", 
      "most mismatches", 
      "hundreds", 
      "neurotransmission", 
      "patterns", 
      "axotomy", 
      "variability", 
      "sciatic nerve transection", 
      "relative changes", 
      "components", 
      "levels", 
      "array sensitivity", 
      "comparison", 
      "significance", 
      "array", 
      "analysis", 
      "number", 
      "significant correlation", 
      "inflammatory cells", 
      "rate", 
      "na\u00efve comparison", 
      "concordance rate", 
      "differences", 
      "sensitivity", 
      "data", 
      "results", 
      "set", 
      "ganglia", 
      "correlation", 
      "DRG", 
      "days", 
      "mismatch", 
      "use", 
      "classification", 
      "nerve transection", 
      "injury", 
      "peripheral nerve injury", 
      "threshold", 
      "hypothesis test", 
      "test", 
      "cut", 
      "parameters", 
      "limit", 
      "error rate", 
      "nerve injury", 
      "criteria", 
      "transection", 
      "error", 
      "dorsal root ganglion (DRG) 3 days", 
      "root ganglion (DRG) 3 days", 
      "ganglion (DRG) 3 days", 
      "triplicate microarrays", 
      "Microarray variability", 
      "axotomy comparison", 
      "actual mRNA differences", 
      "high-density rat genome oligonucleotide microarrays", 
      "rat genome oligonucleotide microarrays", 
      "genome oligonucleotide microarrays"
    ], 
    "name": "Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury.", 
    "pagination": "16-16", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1007072033"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2202-3-16"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "12401135"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2202-3-16", 
      "https://app.dimensions.ai/details/publication/pub.1007072033"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-12-01T19:14", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/article/article_358.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1186/1471-2202-3-16"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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.10.1186/1471-2202-3-16'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2202-3-16'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2202-3-16'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2202-3-16'


 

This table displays all metadata directly associated to this object as RDF triples.

335 TRIPLES      22 PREDICATES      147 URIs      133 LITERALS      28 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2202-3-16 schema:about N052923e1bbd84d30847c590f05c602f0
2 N0af5c800cde04452a66b2bab89c6d1ed
3 N0f813a32e6364a409f4b5e4d7df5aa01
4 N128ca69e5a6747bb93de04977c60f024
5 N28672d57944d4c628a72b6f04eb7fb36
6 N2a841ea5193b44089a8bd2939403b659
7 N2e69bd8f9b78418785455ae7e4b86d3e
8 N372ccaac2efe4206a81755b9e65ddbdc
9 N45516b1836f54425983ed1b13118189d
10 N4c3d4bf00c2646d6ae30541993e51c9b
11 N5d07a282a98a4884849b767c5015b9ff
12 N6898a81e293240ce8d7c76de03819da9
13 N76b5b347f5964192b443086d3c910bb3
14 N786ce884ba8c4c4aa13cf0afc951151d
15 N80b3f41ffc184851a8df6b1e446ae570
16 N9fc93c347afd4e70a3eedc49e0f9345e
17 Nbad2f1a9c01e4c88addf1a258592dc81
18 Ncc7e0505dd92482f949663529d8ac170
19 Nda403e1455c943d4bcf91f594aa3c2d1
20 Ndc766c39ebf142ac8293c1a414819624
21 Ne53fd48a55344057a2a46a593980c668
22 anzsrc-for:06
23 anzsrc-for:0604
24 schema:author Nc9baec8eb8e140c0b8898990253b3af5
25 schema:citation sg:pub.10.1007/978-3-642-60777-6_11
26 sg:pub.10.1007/bf01195557
27 sg:pub.10.1038/37615
28 sg:pub.10.1038/377737a0
29 sg:pub.10.1038/82881
30 sg:pub.10.1038/sj.onc.1200997
31 schema:datePublished 2002-10-25
32 schema:datePublishedReg 2002-10-25
33 schema:description BACKGROUND: Rat oligonucleotide microarrays were used to detect changes in gene expression in the dorsal root ganglion (DRG) 3 days following sciatic nerve transection (axotomy). Two comparisons were made using two sets of triplicate microarrays, naïve versus naïve and naïve versus axotomy. RESULTS: Microarray variability was assessed using the naïve versus naïve comparison. These results support use of a P < 0.05 significance threshold for detecting regulated genes, despite the large number of hypothesis tests required. For the naïve versus axotomy comparison, a 2-fold cut off alone led to an estimated error rate of 16%; combining a >1.5-fold expression change and P < 0.05 significance reduced the estimated error to 5%. The 2-fold cut off identified 178 genes while the combined >1.5-fold and P < 0.05 criteria generated 240 putatively regulated genes, which we have listed. Many of these have not been described as regulated in the DRG by axotomy. Northern blot, quantitative slot blots and in situ hybridization verified the expression of 24 transcripts. These data showed an 83% concordance rate with the arrays; most mismatches represent genes with low expression levels reflecting limits of array sensitivity. A significant correlation was found between actual mRNA differences and relative changes between microarrays (r2 = 0.8567). Temporal patterns of individual genes regulation varied. CONCLUSIONS: We identify parameters for microarray analysis which reduce error while identifying many putatively regulated genes. Functional classification of these genes suggest reorganization of cell structural components, activation of genes expressed by immune and inflammatory cells and down-regulation of genes involved in neurotransmission.
34 schema:genre article
35 schema:inLanguage en
36 schema:isAccessibleForFree true
37 schema:isPartOf N351a429b7c494021b2f0ce73a3b9642e
38 Ne35ea45c21ab4988881ce9e661de2185
39 sg:journal.1024257
40 schema:keywords DRG
41 Microarray variability
42 Northern blot
43 activation
44 activation of genes
45 actual mRNA differences
46 analysis
47 array
48 array sensitivity
49 axotomy
50 axotomy comparison
51 blot
52 cell structural components
53 cells
54 changes
55 classification
56 comparison
57 components
58 concordance rate
59 correlation
60 criteria
61 cut
62 data
63 days
64 differences
65 dorsal root ganglia
66 dorsal root ganglion (DRG) 3 days
67 error
68 error rate
69 expression
70 expression changes
71 expression levels
72 functional classification
73 ganglia
74 ganglion (DRG) 3 days
75 gene expression
76 gene regulation
77 genes
78 genome oligonucleotide microarrays
79 high-density rat genome oligonucleotide microarrays
80 hundreds
81 hybridization
82 hypothesis test
83 individual gene regulation
84 inflammatory cells
85 injury
86 large number
87 levels
88 limit
89 low expression levels
90 mRNA differences
91 microarray analysis
92 microarrays
93 mismatch
94 most mismatches
95 naïve
96 naïve comparison
97 nerve injury
98 nerve transection
99 neurotransmission
100 number
101 oligonucleotide microarrays
102 parameters
103 patterns
104 peripheral nerve injury
105 quantitative slot blots
106 rat genome oligonucleotide microarrays
107 rat oligonucleotide microarray
108 rate
109 regulated genes
110 regulation
111 regulation of genes
112 relative changes
113 reorganization
114 results
115 root ganglia
116 root ganglion (DRG) 3 days
117 sciatic nerve transection
118 sensitivity
119 set
120 significance
121 significance threshold
122 significant correlation
123 situ hybridization
124 slot blots
125 structural components
126 temporal patterns
127 test
128 threshold
129 transcripts
130 transection
131 triplicate microarrays
132 use
133 variability
134 schema:name Replicate high-density rat genome oligonucleotide microarrays reveal hundreds of regulated genes in the dorsal root ganglion after peripheral nerve injury.
135 schema:pagination 16-16
136 schema:productId N01b30f5a2aff44cbbabd4da02aff7a42
137 N1f86eae49b374f06aba56e3944fb6dde
138 N313bff4bb4e44738b3f5b89df0ae208a
139 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007072033
140 https://doi.org/10.1186/1471-2202-3-16
141 schema:sdDatePublished 2021-12-01T19:14
142 schema:sdLicense https://scigraph.springernature.com/explorer/license/
143 schema:sdPublisher N7914a3df7b094e7391336d61c3c8ccb0
144 schema:url https://doi.org/10.1186/1471-2202-3-16
145 sgo:license sg:explorer/license/
146 sgo:sdDataset articles
147 rdf:type schema:ScholarlyArticle
148 N01b30f5a2aff44cbbabd4da02aff7a42 schema:name dimensions_id
149 schema:value pub.1007072033
150 rdf:type schema:PropertyValue
151 N052923e1bbd84d30847c590f05c602f0 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name Apoptosis
153 rdf:type schema:DefinedTerm
154 N0af5c800cde04452a66b2bab89c6d1ed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
155 schema:name Peripheral Nerve Injuries
156 rdf:type schema:DefinedTerm
157 N0f813a32e6364a409f4b5e4d7df5aa01 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Oligonucleotide Array Sequence Analysis
159 rdf:type schema:DefinedTerm
160 N128ca69e5a6747bb93de04977c60f024 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
161 schema:name Sensitivity and Specificity
162 rdf:type schema:DefinedTerm
163 N1f86eae49b374f06aba56e3944fb6dde schema:name doi
164 schema:value 10.1186/1471-2202-3-16
165 rdf:type schema:PropertyValue
166 N24d16e3194db41cb93914e3a39287fa1 rdf:first Nf6839a74b9074a15bc71d5b3f9748047
167 rdf:rest N65ed5405ea7e4b2096419312c99d4f90
168 N28672d57944d4c628a72b6f04eb7fb36 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
169 schema:name Sciatic Neuropathy
170 rdf:type schema:DefinedTerm
171 N2a841ea5193b44089a8bd2939403b659 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
172 schema:name Genome
173 rdf:type schema:DefinedTerm
174 N2e69bd8f9b78418785455ae7e4b86d3e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
175 schema:name Rats, Sprague-Dawley
176 rdf:type schema:DefinedTerm
177 N2f349926f11b435e953eea1edfb05ede rdf:first sg:person.01225541152.46
178 rdf:rest N74a222fb9c5342728958e053588734ae
179 N313bff4bb4e44738b3f5b89df0ae208a schema:name pubmed_id
180 schema:value 12401135
181 rdf:type schema:PropertyValue
182 N351a429b7c494021b2f0ce73a3b9642e schema:volumeNumber 3
183 rdf:type schema:PublicationVolume
184 N372ccaac2efe4206a81755b9e65ddbdc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
185 schema:name Neurons
186 rdf:type schema:DefinedTerm
187 N45516b1836f54425983ed1b13118189d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
188 schema:name Peripheral Nerves
189 rdf:type schema:DefinedTerm
190 N4c3d4bf00c2646d6ae30541993e51c9b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
191 schema:name Cytoskeleton
192 rdf:type schema:DefinedTerm
193 N5b15fb671680480eb0e575c59b2022dd rdf:first sg:person.01366015505.08
194 rdf:rest Ned2b80b7bb73472996f9bf7764c1fb9e
195 N5d07a282a98a4884849b767c5015b9ff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
196 schema:name Disease Models, Animal
197 rdf:type schema:DefinedTerm
198 N65ed5405ea7e4b2096419312c99d4f90 rdf:first sg:person.01314531204.37
199 rdf:rest Ndb8ceab3d0074f94bddde71ae9f0655b
200 N6898a81e293240ce8d7c76de03819da9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
201 schema:name Gene Expression Profiling
202 rdf:type schema:DefinedTerm
203 N74a222fb9c5342728958e053588734ae rdf:first sg:person.01034202555.95
204 rdf:rest N24d16e3194db41cb93914e3a39287fa1
205 N76b5b347f5964192b443086d3c910bb3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
206 schema:name Reproducibility of Results
207 rdf:type schema:DefinedTerm
208 N786ce884ba8c4c4aa13cf0afc951151d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
209 schema:name Animals
210 rdf:type schema:DefinedTerm
211 N7914a3df7b094e7391336d61c3c8ccb0 schema:name Springer Nature - SN SciGraph project
212 rdf:type schema:Organization
213 N80b3f41ffc184851a8df6b1e446ae570 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
214 schema:name Gene Expression Regulation
215 rdf:type schema:DefinedTerm
216 N84043e148aeb4195a55de69f20ce135a rdf:first sg:person.0622412705.06
217 rdf:rest N5b15fb671680480eb0e575c59b2022dd
218 N8b46fe26d7f249fd94ebd83470da5b05 rdf:first sg:person.01157425752.12
219 rdf:rest N2f349926f11b435e953eea1edfb05ede
220 N9fc93c347afd4e70a3eedc49e0f9345e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
221 schema:name Ganglia, Spinal
222 rdf:type schema:DefinedTerm
223 Nbad2f1a9c01e4c88addf1a258592dc81 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
224 schema:name Blotting, Northern
225 rdf:type schema:DefinedTerm
226 Nc9baec8eb8e140c0b8898990253b3af5 rdf:first sg:person.01041441555.34
227 rdf:rest N84043e148aeb4195a55de69f20ce135a
228 Ncc7e0505dd92482f949663529d8ac170 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
229 schema:name Rats
230 rdf:type schema:DefinedTerm
231 Nda403e1455c943d4bcf91f594aa3c2d1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
232 schema:name In Situ Hybridization
233 rdf:type schema:DefinedTerm
234 Ndb8ceab3d0074f94bddde71ae9f0655b rdf:first sg:person.0740501552.00
235 rdf:rest rdf:nil
236 Ndc766c39ebf142ac8293c1a414819624 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
237 schema:name Axotomy
238 rdf:type schema:DefinedTerm
239 Ne35ea45c21ab4988881ce9e661de2185 schema:issueNumber 1
240 rdf:type schema:PublicationIssue
241 Ne53fd48a55344057a2a46a593980c668 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
242 schema:name Male
243 rdf:type schema:DefinedTerm
244 Ned2b80b7bb73472996f9bf7764c1fb9e rdf:first sg:person.0721522537.86
245 rdf:rest N8b46fe26d7f249fd94ebd83470da5b05
246 Nf6839a74b9074a15bc71d5b3f9748047 schema:affiliation grid-institutes:grid.38142.3c
247 schema:familyName Mannion
248 schema:givenName James W
249 rdf:type schema:Person
250 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
251 schema:name Biological Sciences
252 rdf:type schema:DefinedTerm
253 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
254 schema:name Genetics
255 rdf:type schema:DefinedTerm
256 sg:grant.2526131 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2202-3-16
257 rdf:type schema:MonetaryGrant
258 sg:grant.2558976 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2202-3-16
259 rdf:type schema:MonetaryGrant
260 sg:journal.1024257 schema:issn 1471-2202
261 schema:name BMC Neuroscience
262 schema:publisher Springer Nature
263 rdf:type schema:Periodical
264 sg:person.01034202555.95 schema:affiliation grid-institutes:grid.38142.3c
265 schema:familyName Sitarski
266 schema:givenName Joanne
267 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01034202555.95
268 rdf:type schema:Person
269 sg:person.01041441555.34 schema:affiliation grid-institutes:grid.38142.3c
270 schema:familyName Costigan
271 schema:givenName Michael
272 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01041441555.34
273 rdf:type schema:Person
274 sg:person.01157425752.12 schema:affiliation grid-institutes:grid.420044.6
275 schema:familyName D'Urso
276 schema:givenName Donatella
277 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157425752.12
278 rdf:type schema:Person
279 sg:person.01225541152.46 schema:affiliation grid-institutes:grid.38142.3c
280 schema:familyName Allchorne
281 schema:givenName Andrew
282 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01225541152.46
283 rdf:type schema:Person
284 sg:person.01314531204.37 schema:affiliation grid-institutes:grid.62560.37
285 schema:familyName Pratt
286 schema:givenName Richard E
287 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01314531204.37
288 rdf:type schema:Person
289 sg:person.01366015505.08 schema:affiliation grid-institutes:grid.38142.3c
290 schema:familyName Karchewski
291 schema:givenName Laurie
292 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366015505.08
293 rdf:type schema:Person
294 sg:person.0622412705.06 schema:affiliation grid-institutes:grid.38142.3c
295 schema:familyName Befort
296 schema:givenName Katia
297 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622412705.06
298 rdf:type schema:Person
299 sg:person.0721522537.86 schema:affiliation grid-institutes:grid.38142.3c
300 schema:familyName Griffin
301 schema:givenName Robert S
302 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0721522537.86
303 rdf:type schema:Person
304 sg:person.0740501552.00 schema:affiliation grid-institutes:grid.38142.3c
305 schema:familyName Woolf
306 schema:givenName Clifford J
307 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0740501552.00
308 rdf:type schema:Person
309 sg:pub.10.1007/978-3-642-60777-6_11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007556147
310 https://doi.org/10.1007/978-3-642-60777-6_11
311 rdf:type schema:CreativeWork
312 sg:pub.10.1007/bf01195557 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022261990
313 https://doi.org/10.1007/bf01195557
314 rdf:type schema:CreativeWork
315 sg:pub.10.1038/37615 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031769355
316 https://doi.org/10.1038/37615
317 rdf:type schema:CreativeWork
318 sg:pub.10.1038/377737a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029826955
319 https://doi.org/10.1038/377737a0
320 rdf:type schema:CreativeWork
321 sg:pub.10.1038/82881 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019587997
322 https://doi.org/10.1038/82881
323 rdf:type schema:CreativeWork
324 sg:pub.10.1038/sj.onc.1200997 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038115251
325 https://doi.org/10.1038/sj.onc.1200997
326 rdf:type schema:CreativeWork
327 grid-institutes:grid.38142.3c schema:alternateName Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
328 schema:name Neural Plasticity Research Group, Department of Anesthesia and Critical Care, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
329 rdf:type schema:Organization
330 grid-institutes:grid.420044.6 schema:alternateName Bayer AG, Wuppertal, Germany
331 schema:name Bayer AG, Wuppertal, Germany
332 rdf:type schema:Organization
333 grid-institutes:grid.62560.37 schema:alternateName Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA 02115, USA
334 schema:name Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, MA 02115, USA
335 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...