Literature DB >> 25609363

Proteogenomics: emergence and promise.

Sam Faulkner1, Matthew D Dun, Hubert Hondermarck.   

Abstract

Proteogenomics, or the integration of proteomics with genomics and transcriptomics, is emerging as the next step towards a unified understanding of cellular functions. Looking globally and simultaneously at gene structure, RNA expression, protein synthesis and post-translational modifications have become technically feasible and offer a new perspective to molecular processes. Recent publications have highlighted the value of proteogenomics in oncology for defining the molecular signature of human tumors, and translation to other areas of biomedicine and life sciences is anticipated. This mini-review will discuss recent developments, challenges and perspectives in proteogenomics.

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Year:  2015        PMID: 25609363     DOI: 10.1007/s00018-015-1837-y

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  24 in total

Review 1.  Trends in ultrasensitive proteomics.

Authors:  A F Maarten Altelaar; Albert J R Heck
Journal:  Curr Opin Chem Biol       Date:  2012-01-07       Impact factor: 8.822

2.  An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.

Authors:  Natalie E Castellana; Zhouxin Shen; Yupeng He; Justin W Walley; California Jack Cassidy; Steven P Briggs; Vineet Bafna
Journal:  Mol Cell Proteomics       Date:  2013-10-18       Impact factor: 5.911

Review 3.  Omics technologies, data and bioinformatics principles.

Authors:  Maria V Schneider; Sandra Orchard
Journal:  Methods Mol Biol       Date:  2011

Review 4.  Proteogenomics for environmental microbiology.

Authors:  Jean Armengaud; Erica Marie Hartmann; Céline Bland
Journal:  Proteomics       Date:  2013-06-18       Impact factor: 3.984

5.  Plant proteogenomics: from protein extraction to improved gene predictions.

Authors:  Brett Chapman; Natalie Castellana; Alex Apffel; Ryan Ghan; Grant R Cramer; Matthew Bellgard; Paul A Haynes; Steven C Van Sluyter
Journal:  Methods Mol Biol       Date:  2013

6.  Linking cancer genome to proteome: NCI's investment into proteogenomics.

Authors:  Robert C Rivers; Christopher Kinsinger; Emily S Boja; Tara Hiltke; Mehdi Mesri; Henry Rodriguez
Journal:  Proteomics       Date:  2014-10-18       Impact factor: 3.984

Review 7.  Insights into the regulation of protein abundance from proteomic and transcriptomic analyses.

Authors:  Christine Vogel; Edward M Marcotte
Journal:  Nat Rev Genet       Date:  2012-03-13       Impact factor: 53.242

Review 8.  Proteogenomics: concepts, applications and computational strategies.

Authors:  Alexey I Nesvizhskii
Journal:  Nat Methods       Date:  2014-11       Impact factor: 28.547

9.  Onco-proteogenomics: cancer proteomics joins forces with genomics.

Authors:  Javier A Alfaro; Ankit Sinha; Thomas Kislinger; Paul C Boutros
Journal:  Nat Methods       Date:  2014-11       Impact factor: 28.547

Review 10.  Hallmarks of cancer: the next generation.

Authors:  Douglas Hanahan; Robert A Weinberg
Journal:  Cell       Date:  2011-03-04       Impact factor: 41.582

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  11 in total

1.  GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

Authors:  Jia Zhang; Ming-Kun Yang; Honghui Zeng; Feng Ge
Journal:  Mol Cell Proteomics       Date:  2016-09-14       Impact factor: 5.911

2.  Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline.

Authors:  Xun Zhu; Shangbo Xie; Jean Armengaud; Wen Xie; Zhaojiang Guo; Shi Kang; Qingjun Wu; Shaoli Wang; Jixing Xia; Rongjun He; Youjun Zhang
Journal:  Mol Cell Proteomics       Date:  2016-02-22       Impact factor: 5.911

3.  Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis.

Authors:  Matthew D Dun; Robert J Chalkley; Sam Faulkner; Sheridan Keene; Kelly A Avery-Kiejda; Rodney J Scott; Lasse G Falkenby; Murray J Cairns; Martin R Larsen; Ralph A Bradshaw; Hubert Hondermarck
Journal:  Mol Cell Proteomics       Date:  2015-06-03       Impact factor: 5.911

4.  A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells.

Authors:  Anna Ressa; Evert Bosdriesz; Joep de Ligt; Sara Mainardi; Gianluca Maddalo; Anirudh Prahallad; Myrthe Jager; Lisanne de la Fonteijne; Martin Fitzpatrick; Stijn Groten; A F Maarten Altelaar; René Bernards; Edwin Cuppen; Lodewyk Wessels; Albert J R Heck
Journal:  Mol Cell Proteomics       Date:  2018-07-03       Impact factor: 5.911

5.  Creating reference gene annotation for the mouse C57BL6/J genome assembly.

Authors:  Jonathan M Mudge; Jennifer Harrow
Journal:  Mamm Genome       Date:  2015-07-18       Impact factor: 2.957

Review 6.  Proteomics in India: the clinical aspect.

Authors:  Somaditya Mukherjee; Arun Bandyopadhyay
Journal:  Clin Proteomics       Date:  2016-11-05       Impact factor: 3.988

Review 7.  Can Hemp Help? Low-THC Cannabis and Non-THC Cannabinoids for the Treatment of Cancer.

Authors:  Farjana Afrin; Mengna Chi; Andrew L Eamens; Ryan J Duchatel; Alicia M Douglas; Jennifer Schneider; Craig Gedye; Ameha S Woldu; Matthew D Dun
Journal:  Cancers (Basel)       Date:  2020-04-23       Impact factor: 6.639

8.  Could Causal Discovery in Proteogenomics Assist in Understanding Gene-Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model.

Authors:  Maria Ganopoulou; Michail Michailidis; Lefteris Angelis; Ioannis Ganopoulos; Athanassios Molassiotis; Aliki Xanthopoulou; Theodoros Moysiadis
Journal:  Cells       Date:  2021-12-29       Impact factor: 6.600

9.  Cell-Free DNA Blood Collection Tubes Are Appropriate for Clinical Proteomics: A Demonstration in Colorectal Cancer.

Authors:  Juhura G Almazi; Peter Pockney; Craig Gedye; Nathan D Smith; Hubert Hondermarck; Nicole M Verrills; Matthew D Dun
Journal:  Proteomics Clin Appl       Date:  2018-03-30       Impact factor: 3.494

Review 10.  Targeting Oncogenic Signaling in Mutant FLT3 Acute Myeloid Leukemia: The Path to Least Resistance.

Authors:  Dilana Staudt; Heather C Murray; Tabitha McLachlan; Frank Alvaro; Anoop K Enjeti; Nicole M Verrills; Matthew D Dun
Journal:  Int J Mol Sci       Date:  2018-10-16       Impact factor: 5.923

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