Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

N. del-Toro, M. Duesbury, M. Koch, L. Perfetto, A. Shrivastava, D. Ochoa, O. Wagih, J. Piñero, M. Kotlyar, C. Pastrello, P. Beltrao, L. I. Furlong, I. Jurisica, H. Hermjakob, S. Orchard, P. Porras, J. Khadake, B. Meldal, S. Panni, D. Thorneycroft & 23 others K. van Roey, S. Abbani, L. Salwinski, M. Pellegrini, M. Iannuccelli, L. Licata, G. Cesareni, B. Roechert, A. Bridge, M. G. Ammari, F. McCarthy, F. Broackes-Carter, N. H. Campbell, A. N. Melidoni, M. Rodriguez-Lopez, R. C. Lovering, S. Jagannathan, C. Chen, D. J. Lynn, S. Ricard-Blum, U. Mahadevan, A. Raghunath, IMEx Consortium contributing authors

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.
LanguageEnglish
JournalNature Communications
Volume10
Issue number1
DOIs
Publication statusPublished - 2019

Cite this

del-Toro, N., Duesbury, M., Koch, M., Perfetto, L., Shrivastava, A., Ochoa, D., ... authors, IME. C. C. (2019). Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. Nature Communications, 10(1). https://doi.org/10.1038/s41467-018-07709-6
del-Toro, N. ; Duesbury, M. ; Koch, M. ; Perfetto, L. ; Shrivastava, A. ; Ochoa, D. ; Wagih, O. ; Piñero, J. ; Kotlyar, M. ; Pastrello, C. ; Beltrao, P. ; Furlong, L. I. ; Jurisica, I. ; Hermjakob, H. ; Orchard, S. ; Porras, P. ; Khadake, J. ; Meldal, B. ; Panni, S. ; Thorneycroft, D. ; van Roey, K. ; Abbani, S. ; Salwinski, L. ; Pellegrini, M. ; Iannuccelli, M. ; Licata, L. ; Cesareni, G. ; Roechert, B. ; Bridge, A. ; Ammari, M. G. ; McCarthy, F. ; Broackes-Carter, F. ; Campbell, N. H. ; Melidoni, A. N. ; Rodriguez-Lopez, M. ; Lovering, R. C. ; Jagannathan, S. ; Chen, C. ; Lynn, D. J. ; Ricard-Blum, S. ; Mahadevan, U. ; Raghunath, A. ; authors, IMEx Consortium contributing. / Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. In: Nature Communications. 2019 ; Vol. 10, No. 1.
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abstract = "The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.",
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del-Toro, N, Duesbury, M, Koch, M, Perfetto, L, Shrivastava, A, Ochoa, D, Wagih, O, Piñero, J, Kotlyar, M, Pastrello, C, Beltrao, P, Furlong, LI, Jurisica, I, Hermjakob, H, Orchard, S, Porras, P, Khadake, J, Meldal, B, Panni, S, Thorneycroft, D, van Roey, K, Abbani, S, Salwinski, L, Pellegrini, M, Iannuccelli, M, Licata, L, Cesareni, G, Roechert, B, Bridge, A, Ammari, MG, McCarthy, F, Broackes-Carter, F, Campbell, NH, Melidoni, AN, Rodriguez-Lopez, M, Lovering, RC, Jagannathan, S, Chen, C, Lynn, DJ, Ricard-Blum, S, Mahadevan, U, Raghunath, A & authors, IMECC 2019, 'Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set', Nature Communications, vol. 10, no. 1. https://doi.org/10.1038/s41467-018-07709-6

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set. / del-Toro, N.; Duesbury, M.; Koch, M.; Perfetto, L.; Shrivastava, A.; Ochoa, D.; Wagih, O.; Piñero, J.; Kotlyar, M.; Pastrello, C.; Beltrao, P.; Furlong, L. I.; Jurisica, I.; Hermjakob, H.; Orchard, S.; Porras, P.; Khadake, J.; Meldal, B.; Panni, S.; Thorneycroft, D.; van Roey, K.; Abbani, S.; Salwinski, L.; Pellegrini, M.; Iannuccelli, M.; Licata, L.; Cesareni, G.; Roechert, B.; Bridge, A.; Ammari, M. G.; McCarthy, F.; Broackes-Carter, F.; Campbell, N. H.; Melidoni, A. N.; Rodriguez-Lopez, M.; Lovering, R. C.; Jagannathan, S.; Chen, C.; Lynn, D. J.; Ricard-Blum, S.; Mahadevan, U.; Raghunath, A.; authors, IMEx Consortium contributing.

In: Nature Communications, Vol. 10, No. 1, 2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

AU - del-Toro, N.

AU - Duesbury, M.

AU - Koch, M.

AU - Perfetto, L.

AU - Shrivastava, A.

AU - Ochoa, D.

AU - Wagih, O.

AU - Piñero, J.

AU - Kotlyar, M.

AU - Pastrello, C.

AU - Beltrao, P.

AU - Furlong, L. I.

AU - Jurisica, I.

AU - Hermjakob, H.

AU - Orchard, S.

AU - Porras, P.

AU - Khadake, J.

AU - Meldal, B.

AU - Panni, S.

AU - Thorneycroft, D.

AU - van Roey, K.

AU - Abbani, S.

AU - Salwinski, L.

AU - Pellegrini, M.

AU - Iannuccelli, M.

AU - Licata, L.

AU - Cesareni, G.

AU - Roechert, B.

AU - Bridge, A.

AU - Ammari, M. G.

AU - McCarthy, F.

AU - Broackes-Carter, F.

AU - Campbell, N. H.

AU - Melidoni, A. N.

AU - Rodriguez-Lopez, M.

AU - Lovering, R. C.

AU - Jagannathan, S.

AU - Chen, C.

AU - Lynn, D. J.

AU - Ricard-Blum, S.

AU - Mahadevan, U.

AU - Raghunath, A.

AU - authors, IMEx Consortium contributing

PY - 2019

Y1 - 2019

N2 - The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

AB - The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

U2 - 10.1038/s41467-018-07709-6

DO - 10.1038/s41467-018-07709-6

M3 - Article

VL - 10

JO - Nature Communications

T2 - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

ER -