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Table 1 Illustration of data preparation

From: Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT

IntAct

Pubmed Id: 24291004 , Uniprot protein pair: P04150, P31749, Interaction type: Phosphorylation

Corresponding abstract

Glucocorticoid resistance ..[truncated display].... we identify the AKT1 kinase as a major negative regulator of the NR3C1 glucocorticoid receptor protein activity driving glucocorticoid resistance in T-ALL. Mechanistically, AKT1 impairs glucocorticoid-induced gene expression by direct phosphorylation of NR3C1 at position S134 and blocking glucocorticoid-induced NR3C1 translocation to the nucleus. Moreover, we demonstrate that loss of PTEN and consequent AKT1 activation can effectively block glucocorticoid-induced apoptosis and induce resistance to glucocorticoid therapy. Conversely, pharmacologic inhibition of AKT with MK2206 effectively restores glucocorticoid-induced NR3C1 translocation .... in vitro and in vivo.

Genes and normalised NCBI ids

\(\bullet\) Start-End, Gene Mention, NCBI gene Id

\(\bullet\) 137 - 141, AKT1, 207

\(\bullet\) 186 - 191, NR3C1, 2908

\(\bullet\) 294 - 298, AKT1, 207

\(\bullet\) 375 - 380, NR3C1, 2908

\(\bullet\) 434 - 439, NR3C1, 2908

\(\bullet\) 508 - 512, PTEN, 5728

\(\bullet\) 528 - 532, AKT1, 207

\(\bullet\) 748 - 753, NR3C1, 2908

NCBI to Uniprot map

\(\bullet\) NCBI gene: Uniprot identifiers

\(\bullet\) 2908: E5KQF5, E5KQF6, F1D8N4, P04150, B7Z7I2

\(\bullet\) 207: B0LPE5, P31749, B3KVH4

\(\bullet\) 5728: P60484, F6KD01

Normalised abstract for pair P04150, P31749

Glucocorticoid resistance ....[truncated display].... we identify the P31749 kinase as a major negative regulator of the P04150 glucocorticoid receptor protein activity driving glucocorticoid resistance in T-ALL. Mechanistically, P31749 impairs glucocorticoid-induced gene expression by direct phosphorylation of P04150 at position S134 and blocking glucocorticoid-induced P04150 translocation to the nucleus. Moreover, we demonstrate that loss of P60484 and consequent P31749 activation can effectively block glucocorticoid-induced apoptosis and induce resistance to glucocorticoid therapy. Conversely, pharmacologic inhibition of AKT with MK2206 effectively restores glucocorticoid-induced P04150 translocation ..... in vitro and in vivo.

Negative sample pairs

\(\bullet\) P04150, P60484

\(\bullet\) P31749, P60484

  1. The bold highlights where the relationship is specified within the abstract
  2. The IntAct database has the PubMedId, the Uniprot identifiers of the participating proteins and the interaction type. More than 1 pair of interacting proteins can be annotated against a given PubMed Id and not all of these interactions are described in the abstract. This forms the noisily labelled training data
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BMC Bioinformatics

ISSN: 1471-2105

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