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

  • 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).
  • 892 personal GEMs (only T-GEMs) built with Recon 2.2
  • 1,784 personal GEMs (both P-GEMs and T-GEMs) built with Recon 2M.1
  • 892 personal GEMs (only T-GEMs) built with Recon 2M.2

 

Publication

Jae Yong Ryu1, Hyun Uk Kim1 & Sang Yup Lee*. Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism., Proc. Natl. Acad. Sci. U.S.A., 2017, http://www.pnas.org/content/early/2017/10/23/1713050114

 

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.
Files (1.6 GB)
Name Size
Personal_TCGA_GEMs_using_recon2.2.zip
md5:915b99a9c6812352f87524cbd574127d
250.3 MB Download
Personal_TCGA_GEMs_using_recon2M.1.zip
md5:dcf384e5d13728941b143457f3dced66
743.6 MB Download
Personal_TCGA_GEMs_using_recon2M.2.zip
md5:7e7cd7e2628e6c873434e71b2791ec4a
335.7 MB Download
Recon2M.1_BiGG_Ensembl_Transcript.xml
md5:18272acd032bb2532ac649e5f2e578e7
15.3 MB Download
Recon2M.1_BiGG_Entrez_Gene.xml
md5:ab8a10e818eb293180696986af1db6d7
13.8 MB Download
Recon2M.1_BiGG_RefSeq_Transcript.xml
md5:72dd2241dbfe39c15022cc281b33c812
14.0 MB Download
Recon2M.1_BiGG_UCSC_Transcript.xml
md5:0151caa6cba6a579af367ada967b6bef
14.6 MB Download
Recon2M.1_MNX_Ensembl_Transcript.xml
md5:98f42ce4a6697e608aa4f374af4d9c80
15.7 MB Download
Recon2M.1_MNX_Entrez_Gene.xml
md5:97f19e1fa0e632c0c44678d5612f3207
14.2 MB Download
Recon2M.1_MNX_RefSeq_Transcript.xml
md5:a622e73e6b7d09838b86fa4da8771208
14.4 MB Download
Recon2M.1_MNX_UCSC_Transcript.xml
md5:be3f46e3972b651bebe598c4f5bd1691
15.0 MB Download
Recon2M.2_BiGG_Ensembl_Transcript.xml
md5:0d469d8120c5709d5338d12c209b25e5
15.3 MB Download
Recon2M.2_BiGG_Entrez_Gene.xml
md5:b3fee3061d3e2b1863d8c42cdbd76bf8
13.8 MB Download
Recon2M.2_BiGG_RefSeq_Transcript.xml
md5:789cf1c939a6a1b9781b6df054793fb3
14.0 MB Download
Recon2M.2_BiGG_UCSC_Transcript.xml
md5:9cd1f31e563f804eb5b7b3b0b27d5c95
14.6 MB Download
Recon2M.2_MNX_Ensembl_Transcript.xml
md5:ecc62ca7f3d76d5fae42a33c91513a92
15.7 MB Download
Recon2M.2_MNX_Entrez_Gene.xml
md5:833b9c7a00283be6eaece5fc51934de2
14.2 MB Download
Recon2M.2_MNX_RefSeq_Transcript.xml
md5:a70987c1d695f98e2ceb7f1882e66803
14.5 MB Download
Recon2M.2_MNX_UCSC_Transcript.xml
md5:f7eef6ca6eee6ba429d4dcdc3d1a354f
15.1 MB Download
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