NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle Research
Identifieur interne : 000215 ( Main/Exploration ); précédent : 000214; suivant : 000216NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle Research
Auteurs : Lingjia Kong [Finlande] ; Soile Tuomela [Finlande] ; Lauri Hahne [Finlande] ; Helena Ahlfors [Finlande] ; Olli Yli-Harja [Finlande] ; Bengt Fadeel [Suède] ; Riitta Lahesmaa [Finlande] ; Reija Autio [Finlande]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
The potential impact of nanoparticles on the environment and on human health has attracted considerable interest worldwide. The amount of transcriptomics data, in which tissues and cell lines are exposed to nanoparticles, increases year by year. In addition to the importance of the original findings, this data can have value in broader context when combined with other previously acquired and published results. In order to facilitate the efficient usage of the data, we have developed the NanoMiner web resource (
Url:
DOI: 10.1371/journal.pone.0068414
PubMed: 23874618
PubMed Central: 3709991
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000451
- to stream Pmc, to step Curation: 000450
- to stream Pmc, to step Checkpoint: 000183
- to stream Ncbi, to step Merge: 000258
- to stream Ncbi, to step Curation: 000258
- to stream Ncbi, to step Checkpoint: 000258
- to stream Main, to step Merge: 000216
- to stream Main, to step Curation: 000215
Le document en format XML
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wicri:level="3"><nlm:aff id="aff2"><addr-line>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Yli Harja, Olli" sort="Yli Harja, Olli" uniqKey="Yli Harja O" first="Olli" last="Yli-Harja">Olli Yli-Harja</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Signal Processing, Tampere University of Technology, Tampere, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Signal Processing, Tampere University of Technology, Tampere</wicri:regionArea><wicri:noRegion>Tampere</wicri:noRegion></affiliation></author><author><name sortKey="Fadeel, Bengt" sort="Fadeel, Bengt" uniqKey="Fadeel B" first="Bengt" last="Fadeel">Bengt Fadeel</name><affiliation wicri:level="3"><nlm:aff id="aff4"><addr-line>Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden</addr-line></nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm</wicri:regionArea><placeName><settlement type="city">Stockholm</settlement><region nuts="2">Svealand</region></placeName></affiliation></author><author><name sortKey="Lahesmaa, Riitta" sort="Lahesmaa, Riitta" uniqKey="Lahesmaa R" first="Riitta" last="Lahesmaa">Riitta Lahesmaa</name><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author><author><name sortKey="Autio, Reija" sort="Autio, Reija" uniqKey="Autio R" first="Reija" last="Autio">Reija Autio</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Signal Processing, Tampere University of Technology, Tampere, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Department of Signal Processing, Tampere University of Technology, Tampere</wicri:regionArea><wicri:noRegion>Tampere</wicri:noRegion></affiliation><affiliation wicri:level="3"><nlm:aff id="aff2"><addr-line>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland</addr-line></nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku</wicri:regionArea><placeName><settlement type="city">Turku</settlement><region type="région" nuts="2">Finlande occidentale</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The potential impact of nanoparticles on the environment and on human health has attracted considerable interest worldwide. The amount of transcriptomics data, in which tissues and cell lines are exposed to nanoparticles, increases year by year. In addition to the importance of the original findings, this data can have value in broader context when combined with other previously acquired and published results. In order to facilitate the efficient usage of the data, we have developed the NanoMiner web resource (<ext-link ext-link-type="uri" xlink:href="http://nanominer.cs.tut.fi/">http://nanominer.cs.tut.fi/</ext-link>), which contains 404 human transcriptome samples exposed to various types of nanoparticles. All the samples in NanoMiner have been annotated, preprocessed and normalized using standard methods that ensure the quality of the data analyses and enable the users to utilize the database systematically across the different experimental setups and platforms. With NanoMiner it is possible to 1) search and plot the expression profiles of one or several genes of interest, 2) cluster the samples within the datasets, 3) find differentially expressed genes in various nanoparticle studies, 4) detect the nanoparticles causing differential expression of selected genes, 5) analyze enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) terms for the detected genes and 6) search the expression values and differential expressions of the genes belonging to a specific KEGG pathway or Gene Ontology. In sum, NanoMiner database is a valuable collection of microarray data which can be also used as a data repository for future analyses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Krug, Hf" uniqKey="Krug H">HF Krug</name></author><author><name sortKey="Wick, P" uniqKey="Wick P">P Wick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shvedova, Aa" uniqKey="Shvedova A">AA Shvedova</name></author><author><name sortKey="Kagan, Ve" uniqKey="Kagan V">VE Kagan</name></author><author><name sortKey="Fadeel, B" uniqKey="Fadeel B">B Fadeel</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Busch, W" uniqKey="Busch W">W Busch</name></author><author><name sortKey="Kuhnel, D" uniqKey="Kuhnel D">D Kuhnel</name></author><author><name sortKey="Schirmer, K" uniqKey="Schirmer K">K Schirmer</name></author><author><name sortKey="Scholz, S" uniqKey="Scholz 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Gentleman</name></author><author><name sortKey="Carey, Vj" uniqKey="Carey V">VJ Carey</name></author><author><name sortKey="Bates, Dm" uniqKey="Bates D">DM Bates</name></author><author><name sortKey="Bolstad, B" uniqKey="Bolstad B">B Bolstad</name></author><author><name sortKey="Dettling, M" uniqKey="Dettling M">M Dettling</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bolstad, Bm" uniqKey="Bolstad B">BM Bolstad</name></author><author><name sortKey="Irizarry, Ra" uniqKey="Irizarry R">RA Irizarry</name></author><author><name sortKey="Astrand, M" uniqKey="Astrand M">M Astrand</name></author><author><name sortKey="Speed, Tp" uniqKey="Speed T">TP Speed</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gautier, L" uniqKey="Gautier L">L Gautier</name></author><author><name sortKey="Cope, L" uniqKey="Cope L">L Cope</name></author><author><name sortKey="Bolstad, Bm" uniqKey="Bolstad B">BM Bolstad</name></author><author><name sortKey="Irizarry, Ra" uniqKey="Irizarry R">RA Irizarry</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dai, M" uniqKey="Dai M">M Dai</name></author><author><name sortKey="Wang, P" uniqKey="Wang P">P Wang</name></author><author><name sortKey="Boyd, Ad" uniqKey="Boyd A">AD Boyd</name></author><author><name sortKey="Kostov, G" uniqKey="Kostov G">G Kostov</name></author><author><name sortKey="Athey, B" uniqKey="Athey B">B Athey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Flicek, P" uniqKey="Flicek P">P Flicek</name></author><author><name sortKey="Amode, Mr" uniqKey="Amode M">MR Amode</name></author><author><name sortKey="Barrell, D" uniqKey="Barrell D">D Barrell</name></author><author><name sortKey="Beal, K" uniqKey="Beal K">K Beal</name></author><author><name sortKey="Brent, S" uniqKey="Brent S">S Brent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Du, P" uniqKey="Du P">P Du</name></author><author><name sortKey="Kibbe, Wa" uniqKey="Kibbe W">WA Kibbe</name></author><author><name sortKey="Lin, Sm" uniqKey="Lin S">SM Lin</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ritchie, Me" uniqKey="Ritchie M">ME Ritchie</name></author><author><name sortKey="Silver, J" uniqKey="Silver J">J Silver</name></author><author><name sortKey="Oshlack, A" uniqKey="Oshlack A">A Oshlack</name></author><author><name sortKey="Holmes, M" uniqKey="Holmes M">M Holmes</name></author><author><name sortKey="Diyagama, D" uniqKey="Diyagama D">D Diyagama</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Durinck, S" uniqKey="Durinck S">S Durinck</name></author><author><name sortKey="Moreau, Y" uniqKey="Moreau Y">Y Moreau</name></author><author><name sortKey="Kasprzyk, A" uniqKey="Kasprzyk A">A Kasprzyk</name></author><author><name sortKey="Davis, S" uniqKey="Davis S">S Davis</name></author><author><name sortKey="De Moor, B" uniqKey="De Moor B">B De Moor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lucas, A" uniqKey="Lucas A">A Lucas</name></author><author><name sortKey="Jasson, S" uniqKey="Jasson S">S Jasson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smyth, Gk" uniqKey="Smyth G">GK Smyth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benjamini, Y" uniqKey="Benjamini Y">Y Benjamini</name></author><author><name sortKey="Yekutieli, D" uniqKey="Yekutieli D">D Yekutieli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Falcon, S" uniqKey="Falcon S">S Falcon</name></author><author><name sortKey="Gentleman, R" uniqKey="Gentleman R">R Gentleman</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Finlande</li><li>Suède</li></country><region><li>Finlande occidentale</li><li>Svealand</li></region><settlement><li>Stockholm</li><li>Turku</li></settlement></list><tree><country name="Finlande"><noRegion><name sortKey="Kong, Lingjia" sort="Kong, Lingjia" uniqKey="Kong L" first="Lingjia" last="Kong">Lingjia Kong</name></noRegion><name sortKey="Ahlfors, Helena" sort="Ahlfors, Helena" uniqKey="Ahlfors H" first="Helena" last="Ahlfors">Helena Ahlfors</name><name sortKey="Autio, Reija" sort="Autio, Reija" uniqKey="Autio R" first="Reija" last="Autio">Reija Autio</name><name sortKey="Autio, Reija" sort="Autio, Reija" uniqKey="Autio R" first="Reija" last="Autio">Reija Autio</name><name sortKey="Hahne, Lauri" sort="Hahne, Lauri" uniqKey="Hahne L" first="Lauri" last="Hahne">Lauri Hahne</name><name sortKey="Hahne, Lauri" sort="Hahne, Lauri" uniqKey="Hahne L" first="Lauri" last="Hahne">Lauri Hahne</name><name sortKey="Kong, Lingjia" sort="Kong, Lingjia" uniqKey="Kong L" first="Lingjia" last="Kong">Lingjia Kong</name><name sortKey="Lahesmaa, Riitta" sort="Lahesmaa, Riitta" uniqKey="Lahesmaa R" first="Riitta" last="Lahesmaa">Riitta Lahesmaa</name><name sortKey="Tuomela, Soile" sort="Tuomela, Soile" uniqKey="Tuomela S" first="Soile" last="Tuomela">Soile Tuomela</name><name sortKey="Tuomela, Soile" sort="Tuomela, Soile" uniqKey="Tuomela S" first="Soile" last="Tuomela">Soile Tuomela</name><name sortKey="Yli Harja, Olli" sort="Yli Harja, Olli" uniqKey="Yli Harja O" first="Olli" last="Yli-Harja">Olli Yli-Harja</name></country><country name="Suède"><region name="Svealand"><name sortKey="Fadeel, Bengt" sort="Fadeel, Bengt" uniqKey="Fadeel B" first="Bengt" last="Fadeel">Bengt Fadeel</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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