Dataset Open Access

Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism

Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Human genome-scale metabolic model</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Recon</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Gene-transcript-protein-reaction associations (GeTPRA)</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Protein isoform</subfield>
  </datafield>
  <controlfield tag="005">20190410033856.0</controlfield>
  <datafield tag="500" ind1=" " ind2=" ">
    <subfield code="a">This work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries (NRF-2012M1A2A2026556 and NRF-2012M1A2A2026557) from the Ministry of Science, ICT and Future Planning (MSIP) through the National Research Foundation (NRF) of Korea.</subfield>
  </datafield>
  <controlfield tag="001">583326</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea</subfield>
    <subfield code="a">Kim, Hyun Uk</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea</subfield>
    <subfield code="a">Lee, Sang Yup</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">250316652</subfield>
    <subfield code="z">md5:915b99a9c6812352f87524cbd574127d</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Personal_TCGA_GEMs_using_recon2.2.zip</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">743575596</subfield>
    <subfield code="z">md5:dcf384e5d13728941b143457f3dced66</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Personal_TCGA_GEMs_using_recon2M.1.zip</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">335675521</subfield>
    <subfield code="z">md5:7e7cd7e2628e6c873434e71b2791ec4a</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Personal_TCGA_GEMs_using_recon2M.2.zip</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15284294</subfield>
    <subfield code="z">md5:18272acd032bb2532ac649e5f2e578e7</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_BiGG_Ensembl_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">13779758</subfield>
    <subfield code="z">md5:ab8a10e818eb293180696986af1db6d7</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_BiGG_Entrez_Gene.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14018459</subfield>
    <subfield code="z">md5:72dd2241dbfe39c15022cc281b33c812</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_BiGG_RefSeq_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14626756</subfield>
    <subfield code="z">md5:0151caa6cba6a579af367ada967b6bef</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_BiGG_UCSC_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15690218</subfield>
    <subfield code="z">md5:98f42ce4a6697e608aa4f374af4d9c80</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_MNX_Ensembl_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14185682</subfield>
    <subfield code="z">md5:97f19e1fa0e632c0c44678d5612f3207</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_MNX_Entrez_Gene.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14424383</subfield>
    <subfield code="z">md5:a622e73e6b7d09838b86fa4da8771208</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_MNX_RefSeq_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15032680</subfield>
    <subfield code="z">md5:be3f46e3972b651bebe598c4f5bd1691</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.1_MNX_UCSC_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15301181</subfield>
    <subfield code="z">md5:0d469d8120c5709d5338d12c209b25e5</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_BiGG_Ensembl_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">13811186</subfield>
    <subfield code="z">md5:b3fee3061d3e2b1863d8c42cdbd76bf8</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_BiGG_Entrez_Gene.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14046554</subfield>
    <subfield code="z">md5:789cf1c939a6a1b9781b6df054793fb3</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_BiGG_RefSeq_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14649098</subfield>
    <subfield code="z">md5:9cd1f31e563f804eb5b7b3b0b27d5c95</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_BiGG_UCSC_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15707229</subfield>
    <subfield code="z">md5:ecc62ca7f3d76d5fae42a33c91513a92</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_MNX_Ensembl_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14217234</subfield>
    <subfield code="z">md5:833b9c7a00283be6eaece5fc51934de2</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_MNX_Entrez_Gene.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">14452602</subfield>
    <subfield code="z">md5:a70987c1d695f98e2ceb7f1882e66803</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_MNX_RefSeq_Transcript.xml</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">15055146</subfield>
    <subfield code="z">md5:f7eef6ca6eee6ba429d4dcdc3d1a354f</subfield>
    <subfield code="u">https://zenodo.org/record/583326/files/Recon2M.2_MNX_UCSC_Transcript.xml</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2017-05-28</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire_data</subfield>
    <subfield code="o">oai:zenodo.org:583326</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea</subfield>
    <subfield code="a">Ryu, Jae Yong</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">http://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;ul&gt;
	&lt;li&gt;Eight versions of COBRA-compliant SBML files are available for each Recon 2M.1 and Recon 2M.2 depending on the use of: MNXref versus BiGG IDs; Entrez gene IDs (GPR associations) versus Ensembl transcript IDs versus RefSeq transcript IDs versus UCSC transcript IDs (TPR associations for the last three database IDs).&lt;/li&gt;
	&lt;li&gt;892 personal GEMs (only T-GEMs) built with Recon 2.2&lt;/li&gt;
	&lt;li&gt;1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1&lt;/li&gt;
	&lt;li&gt;892 personal GEMs (only T-GEMs) built with Recon 2M.2&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt; &lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Publication&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Jae Yong Ryu&lt;sup&gt;1&lt;/sup&gt;, Hyun Uk Kim&lt;sup&gt;1&lt;/sup&gt; &amp;amp; Sang Yup Lee&lt;sup&gt;*&lt;/sup&gt;. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., &lt;em&gt;Proc. Natl. Acad. Sci. U.S.A.&lt;/em&gt;, 2017, http://www.pnas.org/content/early/2017/10/23/1713050114&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.599876</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.583326</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">dataset</subfield>
  </datafield>
</record>
1,215
225
views
downloads
All versions This version
Views 1,2151,215
Downloads 225225
Data volume 7.8 GB7.8 GB
Unique views 1,1761,176
Unique downloads 146146

Share

Cite as