The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model
The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potent...
Saved in:
Published in | Biochimica et biophysica acta. General subjects Vol. 1864; no. 12; p. 129722 |
---|---|
Main Authors | , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
Netherlands
Elsevier B.V
01.12.2020
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape.
An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database.
Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes.
Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells.
This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems.
•The study of mutated proteomes in cancer cells is at its infancy.•A proteogenomics platform is developed that exploits DNA and RNA variant identification.•Mass spectrometry was used to identify and validate mutant protein expression.•P53-dependent mutant proteome networks were identified.•Proteogenomics pipelines form a blueprint for identifying mutated proteins in diseased systems. |
---|---|
AbstractList | The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape.
An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database.
Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes.
Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells.
This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems.
•The study of mutated proteomes in cancer cells is at its infancy.•A proteogenomics platform is developed that exploits DNA and RNA variant identification.•Mass spectrometry was used to identify and validate mutant protein expression.•P53-dependent mutant proteome networks were identified.•Proteogenomics pipelines form a blueprint for identifying mutated proteins in diseased systems. The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape. An isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database. Approximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes. Our study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells. This pipeline forms a blueprint for identifying mutated proteins in diseased cell systems. BACKGROUNDThe identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies including DNA variant identification, RNA sequencing, and mass spectrometry. Any one of these methodologies are not optimized for identifying potential mutated proteins and any one output fails to cover completely a specific landscape. METHODSAn isogenic melanoma cell with a p53-null genotype was created by CRISPR/CAS9 system to determine how p53 gene inactivation affects mutant proteome expression. A mutant peptide reference database was developed by comparing two distinct DNA and RNA variant detection platforms using these isogenic cells. Chemically fractionated tryptic peptides from lysates were processed using a TripleTOF 5600+ mass spectrometer and their spectra were identified against this mutant reference database. RESULTSApproximately 190 mutated peptides were enriched in wt-p53 cells, 187 mutant peptides were enriched in p53-null cells, with an overlap of 147 mutated peptides. STRING analysis highlighted that the wt-p53 cell line was enriched for mutant protein pathways such as CDC5L and POLR1B, whilst the p53-null cell line was enriched for mutated proteins comprising EGF/YES, Ubiquitination, and RPL26/5 nodes. CONCLUSIONOur study produces a well annotated p53-dependent and p53-independent mutant proteome of a common melanoma cell line model. Coupled to the application of an integrated DNA and RNA variant detection platform (CLCbio) and software for identification of proteins (ProteinPilot), this pipeline can be used to detect high confident mutant proteins in cells. GENERAL SIGNIFICANCEThis pipeline forms a blueprint for identifying mutated proteins in diseased cell systems. |
ArticleNumber | 129722 |
Author | O'Neill, J. Robert Kurkowiak, Małgorzata Faktor, Jakub Grasso, Giuseppa Singh, Ashita Hupp, Ted Muller, Petr Goodlett, David Vojtesek, Borek Ruidong, Li Mayordomo, Marcos Yébenes Zavadil Kokas, Filip Kote, Sachin |
Author_xml | – sequence: 1 givenname: Jakub surname: Faktor fullname: Faktor, Jakub organization: Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic – sequence: 2 givenname: Giuseppa surname: Grasso fullname: Grasso, Giuseppa organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK – sequence: 3 givenname: Filip surname: Zavadil Kokas fullname: Zavadil Kokas, Filip organization: Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic – sequence: 4 givenname: Małgorzata surname: Kurkowiak fullname: Kurkowiak, Małgorzata organization: University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland – sequence: 5 givenname: Marcos Yébenes surname: Mayordomo fullname: Mayordomo, Marcos Yébenes organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK – sequence: 6 givenname: Sachin surname: Kote fullname: Kote, Sachin organization: University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland – sequence: 7 givenname: Ashita surname: Singh fullname: Singh, Ashita organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK – sequence: 8 givenname: Li surname: Ruidong fullname: Ruidong, Li organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK – sequence: 9 givenname: J. Robert surname: O'Neill fullname: O'Neill, J. Robert organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK – sequence: 10 givenname: Petr surname: Muller fullname: Muller, Petr organization: Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic – sequence: 11 givenname: David surname: Goodlett fullname: Goodlett, David organization: University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland – sequence: 12 givenname: Borek surname: Vojtesek fullname: Vojtesek, Borek email: vojtesek@mou.cz organization: Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic – sequence: 13 givenname: Ted surname: Hupp fullname: Hupp, Ted email: ted.hupp@ed.ac.uk organization: University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, UK |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32866596$$D View this record in MEDLINE/PubMed |
BookMark | eNp9kE9r3DAQxUVIaDZJv0EpOvbirf7YWutSKKFNCgu9bM5iLI0SLba0tezQfvvIOMmxQiCYee_N6HdFzmOKSMgnzraccfX1uO06eMS4FUyUktA7Ic7Ihrc7UbWMqXOyYZLVVc1Vc0mucj6ychrdfCCXUrRKNVptCByekKL3aKdMk6enRtISijREsFN4himkSMsd5gniRE9jmjANxfP3NGLOSzdECvRpHqCosIeYBqAW-54OyWF_Qy489Bk_vr7X5OHnj8PtfbX_fffr9vu-sjVrp4p3XogOrK25R41MOKixA8ldrZWQXnslSqeVnZLOaaetFeB2zsmuBce1vCZf1tyy4p8Z82SGkJc1IGKasxG1LEGCy12R1qvUjinnEb05jWGA8Z_hzCxwzdGscM0C16xwi-3z64S5G9C9m95oFsG3VYDln88BR5NtwGjRhbEANi6F_094AWTpj5c |
CitedBy_id | crossref_primary_10_1016_j_csbj_2021_09_006 crossref_primary_10_1016_j_ad_2023_01_010 crossref_primary_10_1016_j_ad_2023_01_001 crossref_primary_10_1080_15476286_2021_1932345 crossref_primary_10_1016_j_talanta_2024_126460 |
Cites_doi | 10.1074/mcp.MR117.000024 10.1073/pnas.1200019109 10.1016/j.cell.2015.08.047 10.1371/journal.pone.0111153 10.1038/nature12213 10.1074/jbc.M003485200 10.1038/srep32417 10.1126/scitranslmed.3002925 10.1038/nature13438 10.4161/rna.22269 10.1038/nature10933 10.1021/acs.analchem.5b01166 10.1002/pmic.201200352 10.1093/bioinformatics/btu397 10.1038/nprot.2013.143 10.1186/s12859-016-1190-7 10.1093/nar/gky1131 10.1038/ng.3013 10.1038/nmeth.1322 10.1038/nrd3681 10.1002/pmic.201500501 10.1038/nature22991 10.1021/pr500893m 10.1093/bioinformatics/btv236 10.1101/gr.129684.111 10.1021/acs.jproteome.5b00490 10.1074/mcp.O111.016717 10.1016/j.molimm.2015.04.019 10.1038/s41467-017-00249-5 10.1093/bioinformatics/bty004 10.1038/sj.onc.1202014 10.1038/nature08768 10.1093/bioinformatics/btv639 10.18632/oncotarget.17300 10.1093/nar/gku1283 10.1371/journal.pone.0098187 10.1002/emmm.201202388 10.1038/nrc2273 10.1186/gb-2013-14-4-r36 10.1038/nature10351 10.1038/ng.3441 10.1073/pnas.1934852100 10.1126/science.aaa3828 10.1038/nature13387 10.1038/358015a0 10.1016/j.ejmech.2019.111709 |
ContentType | Journal Article |
Copyright | 2020 Copyright © 2020. Published by Elsevier B.V. |
Copyright_xml | – notice: 2020 – notice: Copyright © 2020. Published by Elsevier B.V. |
DBID | CGR CUY CVF ECM EIF NPM AAYXX CITATION 7X8 |
DOI | 10.1016/j.bbagen.2020.129722 |
DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef MEDLINE - Academic |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef MEDLINE - Academic |
DatabaseTitleList | MEDLINE MEDLINE - Academic |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Chemistry Biology |
EISSN | 1872-8006 |
EndPage | 129722 |
ExternalDocumentID | 10_1016_j_bbagen_2020_129722 32866596 S0304416520302348 |
Genre | Research Support, Non-U.S. Gov't Journal Article |
GrantInformation_xml | – fundername: Biotechnology and Biological Sciences Research Council grantid: BB/C511599/1 – fundername: Wellcome Trust grantid: 094417/Z/10/Z |
GroupedDBID | --- --K --M .~1 0R~ 1B1 1RT 1~. 1~5 23N 3O- 4.4 457 4G. 53G 5GY 5RE 5VS 7-5 71M 8P~ 9JM AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AAQXK AAXUO ABEFU ABFNM ABGSF ABMAC ABUDA ABXDB ABYKQ ACDAQ ACIUM ACRLP ADBBV ADEZE ADMUD ADUVX AEBSH AEHWI AEKER AFKWA AFTJW AFXIZ AGHFR AGRDE AGUBO AGYEJ AHHHB AIEXJ AIKHN AITUG AJBFU AJOXV ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ ASPBG AVWKF AXJTR AZFZN BKOJK BLXMC CS3 DOVZS EBS EFJIC EFLBG EJD EO8 EO9 EP2 EP3 FDB FEDTE FGOYB FIRID FNPLU FYGXN G-2 G-Q GBLVA HLW HVGLF HZ~ IHE J1W KOM LX3 M41 MO0 N9A O-L O9- OAUVE OHT OZT P-8 P-9 PC. Q38 R2- ROL RPZ SBG SCC SDF SDG SDP SES SEW SPCBC SSU SSZ T5K UQL WH7 WUQ XJT XPP ~G- AAHBH AAXKI AFJKZ AKRWK CGR CUY CVF ECM EIF NPM AAYXX ACRPL ADNMO CITATION 7X8 |
ID | FETCH-LOGICAL-c408t-1bf22bacc41fe9e02da4eba31d49623f9f621fe83b63dd9d9cc2ad7dd3b8ad193 |
IEDL.DBID | AIKHN |
ISSN | 0304-4165 |
IngestDate | Fri Oct 25 07:37:42 EDT 2024 Fri Dec 06 03:34:49 EST 2024 Sat Sep 28 08:27:45 EDT 2024 Fri Feb 23 02:47:57 EST 2024 |
IsDoiOpenAccess | false |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 12 |
Keywords | Protein mass spectrometry Proteogenomics Proteomics Cancer p53 |
Language | English |
License | Copyright © 2020. Published by Elsevier B.V. |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c408t-1bf22bacc41fe9e02da4eba31d49623f9f621fe83b63dd9d9cc2ad7dd3b8ad193 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
OpenAccessLink | https://www.pure.ed.ac.uk/ws/files/161937926/The_effects_of_p53_gene_inactivation_on_mutual_proteome_expression_in_a_human_melanoma_cell_model_AAM.pdf |
PMID | 32866596 |
PQID | 2439622137 |
PQPubID | 23479 |
PageCount | 1 |
ParticipantIDs | proquest_miscellaneous_2439622137 crossref_primary_10_1016_j_bbagen_2020_129722 pubmed_primary_32866596 elsevier_sciencedirect_doi_10_1016_j_bbagen_2020_129722 |
PublicationCentury | 2000 |
PublicationDate | December 2020 2020-12-00 20201201 |
PublicationDateYYYYMMDD | 2020-12-01 |
PublicationDate_xml | – month: 12 year: 2020 text: December 2020 |
PublicationDecade | 2020 |
PublicationPlace | Netherlands |
PublicationPlace_xml | – name: Netherlands |
PublicationTitle | Biochimica et biophysica acta. General subjects |
PublicationTitleAlternate | Biochim Biophys Acta Gen Subj |
PublicationYear | 2020 |
Publisher | Elsevier B.V |
Publisher_xml | – name: Elsevier B.V |
References | Blaydes, Luciani, Pospisilova, Ball, Vojtesek, Hupp (bb0130) 2001; 276 Carreno, Magrini, Becker-Hapak, Kaabinejadian, Hundal, Petti, Ly, Lie, Hildebrand, Mardis, Linette (bb0050) 2015; 348 Hedegaard, Thorsen, Lund, Hein, Hamilton-Dutoit, Vang, Nordentoft, Birkenkamp-Demtroder, Kruhoffer, Hager, Knudsen, Andersen, Sorensen, Pedersen, Orntoft, Dyrskjot (bb0110) 2014; 9 Blaydes, Hupp (bb0135) 1998; 17 Lane (bb0170) 1992; 358 Edlund, Larsson, Ameur, Bunikis, Gyllensten, Leroy, Sundstrom, Micke, Botling, Soussi (bb0175) 2012; 109 Kim, Pertea, Trapnell, Pimentel, Kelley, Salzberg (bb0210) 2013; 14 Wen, Xu, Sheynkman, Feng, Lin, Wang, Xu, Wang, Liu (bb0100) 2014; 30 Krasnov, Dmitriev, Kudryavtseva, Shargunov, Karpov, Uroshlev, Melnikova, Blinov, Poverennaya, Archakov, Lisitsa, Ponomarenko (bb0085) 2015; 14 Gillet, Navarro, Tate, Rost, Selevsek, Reiter, Bonner, Aebersold (bb0225) 2012; 11 Scannell, Blanckley, Boldon, Warrington (bb0015) 2012; 11 An, Pan, Hu, Pang, Huang, Chan, Li, Yan (bb0035) 2019; 183 Schumacher, Bunse, Pusch, Sahm, Wiestler, Quandt, Menn, Osswald, Oezen, Ott, Keil, Balss, Rauschenbach, Grabowska, Vogler, Diekmann, Trautwein, Eichmuller, Okun, Stevanovic, Riemer, Sahin, Friese, Beckhove, von Deimling, Wick, Platten (bb0045) 2014; 512 Ding, Kim, Kanchi, Dees, Lu, Griffith, Fenstermacher, Sung, Miller, Goetz, Wendl, Griffith, Cornelius, Linette, McMichael, Sondak, Fields, Ley, Mule, Wilson, Weber (bb0160) 2014; 9 Schlake, Thess, Fotin-Mleczek, Kallen (bb0055) 2012; 9 Way, Faktor, Dvorakova, Nicholson, Vojtesek, Graham, Ball, Hupp (bb0230) 2016; 16 Jagtap, Goslinga, Kooren, McGowan, Wroblewski, Seymour, Griffin (bb0090) 2013; 13 Bignell, Greenman, Davies, Butler, Edkins, Andrews, Buck, Chen, Beare, Latimer, Widaa, Hinton, Fahey, Fu, Swamy, Dalgliesh, Teh, Deloukas, Yang, Campbell, Futreal, Stratton (bb0005) 2010; 463 Tiedje, Ting, Herold, Synoracki, Latteyer, Moeller, Zwanziger, Stuschke, Fuehrer, Schmid (bb0115) 2017; 8 Collins, Hunter, Liu, Schilling, Rosenberger, Bader, Chan, Gibson, Gingras, Held, Hirayama-Kurogi, Hou, Krisp, Larsen, Lin, Liu, Molloy, Moritz, Ohtsuki, Schlapbach, Selevsek, Thomas, Tzeng, Zhang, Aebersold (bb0155) 2017; 8 Ott, Hu, Keskin, Shukla, Sun, Bozym, Zhang, Luoma, Giobbie-Hurder, Peter, Chen, Olive, Carter, Li, Lieb, Eisenhaure, Gjini, Stevens, Lane, Javeri, Nellaiappan, Salazar, Daley, Seaman, Buchbinder, Yoon, Harden, Lennon, Gabriel, Rodig, Barouch, Aster, Getz, Wucherpfennig, Neuberg, Ritz, Lander, Fritsch, Hacohen, Wu (bb0165) 2017; 547 Zhang, Wang, Wang, Zhu, Liu, Shi, Chambers, Zimmerman, Shaddox, Kim, Davies, Wang, Wang, Kinsinger, Rivers, Rodriguez, Townsend, Ellis, Carr, Tabb, Coffey, Slebos, Liebler, Nci (bb0065) 2014; 513 Paoloni, Khanna (bb0020) 2008; 8 Andreatta, Nielsen (bb0200) 2016; 32 Szklarczyk, Gable, Lyon, Junge, Wyder, Huerta-Cepas, Simonovic, Doncheva, Morris, Bork, Jensen, Mering (bb0240) 2019; 47 Ruggles, Krug, Wang, Clauser, Wang, Payne, Fenyo, Zhang, Mani (bb0070) 2017; 16 Zavadil Kokas, Faktor, Vojtesek (bb0235) 2019; 32 Wisniewski, Zougman, Nagaraj, Mann (bb0150) 2009; 6 Batth, Francavilla, Olsen (bb0220) 2014; 13 Weaver, Ross-Innes, Shannon, Lynch, Forshew, Barbera, Murtaza, Ong, Lao-Sirieix, Dunning, Smith, Smith, Anderson, Carvalho, O'Donovan, Underwood, May, Grehan, Hardwick, Davies, Oloumi, Aparicio, Caldas, Eldridge, Edwards, Rosenfeld, Tavare, Fitzgerald (bb0190) 2014; 46 Apcher, Daskalogianni, Fahraeus (bb0075) 2015; 68 Ran, Hsu, Wright, Agarwala, Scott, Zhang (bb0205) 2013; 8 Allison (bb0040) 2015; 162 Crappe, Ndah, Koch, Steyaert, Gawron, De Keulenaer, De Meester, De Meyer, Van Criekinge, Van Damme, Menschaert (bb0080) 2015; 43 Koboldt, Zhang, Larson, Shen, McLellan, Lin, Miller, Mardis, Ding, Wilson (bb0215) 2012; 22 Stratton (bb0010) 2013; 5 Zickmann, Renard (bb0105) 2015; 31 Nik-Zainal, Kucab, Morganella, Glodzik, Alexandrov, Arlt, Weninger, Hollstein, Stratton, Phillips (bb0030) 2015; 30 Lawrence, Stojanov, Polak, Kryukov, Cibulskis, Sivachenko, Carter, Stewart, Mermel, Roberts, Kiezun, Hammerman, McKenna, Drier, Zou, Ramos, Pugh, Stransky, Helman, Kim, Sougnez, Ambrogio, Nickerson, Shefler, Cortes, Auclair, Saksena, Voet, Noble, DiCara, Lin, Lichtenstein, Heiman, Fennell, Imielinski, Hernandez, Hodis, Baca, Dulak, Lohr, Landau, Wu, Melendez-Zajgla, Hidalgo-Miranda, Koren, McCarroll, Mora, Crompton, Onofrio, Parkin, Winckler, Ardlie, Gabriel, Roberts, Biegel, Stegmaier, Bass, Garraway, Meyerson, Golub, Gordenin, Sunyaev, Lander, Getz (bb0185) 2013; 499 Afsari, Guo, Considine, Florea, Kagohara, Stein-O’Brien, Kelley, Flam, Zambo, Ha, Geman, Ochs, Califano, Gaykalova, Favorov, Fertig (bb0095) 2018; 34 Gorshkov, Verano-Braga, Kjeldsen (bb0120) 2015; 87 do Valle, Giampieri, Simonetti, Padella, Manfrini, Ferrari, Papayannidis, Zironi, Garonzi, Bernardi, Delledonne, Martinelli, Remondini, Castellani (bb0125) 2016; 17 Shah, Roth, Goya, Oloumi, Ha, Zhao, Turashvili, Ding, Tse, Haffari, Bashashati, Prentice, Khattra, Burleigh, Yap, Bernard, McPherson, Shumansky, Crisan, Giuliany, Heravi-Moussavi, Rosner, Lai, Birol, Varhol, Tam, Dhalla, Zeng, Ma, Chan, Griffith, Moradian, Cheng, Morin, Watson, Gelmon, Chia, Chin, Curtis, Rueda, Pharoah, Damaraju, Mackey, Hoon, Harkins, Tadigotla, Sigaroudinia, Gascard, Tlsty, Costello, Meyer, Eaves, Wasserman, Jones, Huntsman, Hirst, Caldas, Marra, Aparicio (bb0140) 2012; 486 Garcia, Hayden, Birts, Britton, Cowie, Pickard, Mellone, Choh, Derouet, Duriez, Noble, White, Primrose, Strefford, Rose-Zerilli, Thomas, Ang, Sharrocks, Fitzgerald, Underwood (bb0195) 2016; 6 Alexandrov, Jones, Wedge, Sale, Campbell, Nik-Zainal, Stratton (bb0025) 2015; 47 Colloca, Barnes, Folgori, Ammendola, Capone, Cirillo, Siani, Naddeo, Grazioli, Esposito, Ambrosio, Sparacino, Bartiromo, Meola, Smith, Kurioka, O'Hara, Ewer, Anagnostou, Bliss, Hill, Traboni, Klenerman, Cortese, Nicosia (bb0060) 2012; 4 Morin, Mendez-Lago, Mungall, Goya, Mungall, Corbett, Johnson, Severson, Chiu, Field, Jackman, Krzywinski, Scott, Trinh, Tamura-Wells, Li, Firme, Rogic, Griffith, Chan, Yakovenko, Meyer, Zhao, Smailus, Moksa, Chittaranjan, Rimsza, Brooks-Wilson, Spinelli, Ben-Neriah, Meissner, Woolcock, Boyle, McDonald, Tam, Zhao, Delaney, Zeng, Tse, Butterfield, Birol, Holt, Schein, Horsman, Moore, Jones, Connors, Hirst, Gascoyne, Marra (bb0145) 2011; 476 Overholtzer, Rao, Favis, Lu, Elowitz, Barany, Ladanyi, Gorlick, Levine (bb0180) 2003; 100 Blaydes (10.1016/j.bbagen.2020.129722_bb0130) 2001; 276 Gorshkov (10.1016/j.bbagen.2020.129722_bb0120) 2015; 87 Stratton (10.1016/j.bbagen.2020.129722_bb0010) 2013; 5 Szklarczyk (10.1016/j.bbagen.2020.129722_bb0240) 2019; 47 Ran (10.1016/j.bbagen.2020.129722_bb0205) 2013; 8 Koboldt (10.1016/j.bbagen.2020.129722_bb0215) 2012; 22 Colloca (10.1016/j.bbagen.2020.129722_bb0060) 2012; 4 Nik-Zainal (10.1016/j.bbagen.2020.129722_bb0030) 2015; 30 Ruggles (10.1016/j.bbagen.2020.129722_bb0070) 2017; 16 Lane (10.1016/j.bbagen.2020.129722_bb0170) 1992; 358 Tiedje (10.1016/j.bbagen.2020.129722_bb0115) 2017; 8 Morin (10.1016/j.bbagen.2020.129722_bb0145) 2011; 476 Bignell (10.1016/j.bbagen.2020.129722_bb0005) 2010; 463 Schumacher (10.1016/j.bbagen.2020.129722_bb0045) 2014; 512 Crappe (10.1016/j.bbagen.2020.129722_bb0080) 2015; 43 Zickmann (10.1016/j.bbagen.2020.129722_bb0105) 2015; 31 Weaver (10.1016/j.bbagen.2020.129722_bb0190) 2014; 46 Batth (10.1016/j.bbagen.2020.129722_bb0220) 2014; 13 do Valle (10.1016/j.bbagen.2020.129722_bb0125) 2016; 17 Way (10.1016/j.bbagen.2020.129722_bb0230) 2016; 16 Lawrence (10.1016/j.bbagen.2020.129722_bb0185) 2013; 499 Carreno (10.1016/j.bbagen.2020.129722_bb0050) 2015; 348 Ott (10.1016/j.bbagen.2020.129722_bb0165) 2017; 547 An (10.1016/j.bbagen.2020.129722_bb0035) 2019; 183 Garcia (10.1016/j.bbagen.2020.129722_bb0195) 2016; 6 Scannell (10.1016/j.bbagen.2020.129722_bb0015) 2012; 11 Wen (10.1016/j.bbagen.2020.129722_bb0100) 2014; 30 Kim (10.1016/j.bbagen.2020.129722_bb0210) 2013; 14 Blaydes (10.1016/j.bbagen.2020.129722_bb0135) 1998; 17 Apcher (10.1016/j.bbagen.2020.129722_bb0075) 2015; 68 Schlake (10.1016/j.bbagen.2020.129722_bb0055) 2012; 9 Gillet (10.1016/j.bbagen.2020.129722_bb0225) 2012; 11 Hedegaard (10.1016/j.bbagen.2020.129722_bb0110) 2014; 9 Krasnov (10.1016/j.bbagen.2020.129722_bb0085) 2015; 14 Andreatta (10.1016/j.bbagen.2020.129722_bb0200) 2016; 32 Edlund (10.1016/j.bbagen.2020.129722_bb0175) 2012; 109 Paoloni (10.1016/j.bbagen.2020.129722_bb0020) 2008; 8 Afsari (10.1016/j.bbagen.2020.129722_bb0095) 2018; 34 Shah (10.1016/j.bbagen.2020.129722_bb0140) 2012; 486 Zavadil Kokas (10.1016/j.bbagen.2020.129722_bb0235) 2019; 32 Collins (10.1016/j.bbagen.2020.129722_bb0155) 2017; 8 Allison (10.1016/j.bbagen.2020.129722_bb0040) 2015; 162 Ding (10.1016/j.bbagen.2020.129722_bb0160) 2014; 9 Wisniewski (10.1016/j.bbagen.2020.129722_bb0150) 2009; 6 Zhang (10.1016/j.bbagen.2020.129722_bb0065) 2014; 513 Alexandrov (10.1016/j.bbagen.2020.129722_bb0025) 2015; 47 Jagtap (10.1016/j.bbagen.2020.129722_bb0090) 2013; 13 Overholtzer (10.1016/j.bbagen.2020.129722_bb0180) 2003; 100 |
References_xml | – volume: 100 start-page: 11547 year: 2003 end-page: 11552 ident: bb0180 article-title: The presence of p53 mutations in human osteosarcomas correlates with high levels of genomic instability publication-title: Proc. Natl. Acad. Sci. U. S. A. contributor: fullname: Levine – volume: 11 start-page: 191 year: 2012 end-page: 200 ident: bb0015 article-title: Diagnosing the decline in pharmaceutical R&D efficiency publication-title: Nat. Rev. Drug Discov. contributor: fullname: Warrington – volume: 512 start-page: 324 year: 2014 end-page: 327 ident: bb0045 article-title: A vaccine targeting mutant IDH1 induces antitumour immunity publication-title: Nature contributor: fullname: Platten – volume: 16 start-page: 959 year: 2017 end-page: 981 ident: bb0070 article-title: Methods, Tools and Current Perspectives in Proteogenomics publication-title: Mol Cell Proteomics contributor: fullname: Mani – volume: 8 start-page: 2281 year: 2013 end-page: 2308 ident: bb0205 article-title: Genome engineering using the CRISPR-Cas9 system publication-title: Nat. Protoc. contributor: fullname: Zhang – volume: 43 year: 2015 ident: bb0080 article-title: PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration publication-title: Nucleic Acids Res. contributor: fullname: Menschaert – volume: 14 start-page: 3729 year: 2015 end-page: 3737 ident: bb0085 article-title: PPLine: An automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics publication-title: J Proteome Res contributor: fullname: Ponomarenko – volume: 109 start-page: 9551 year: 2012 end-page: 9556 ident: bb0175 article-title: Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors publication-title: Proc. Natl. Acad. Sci. U. S. A. contributor: fullname: Soussi – volume: 46 start-page: 837 year: 2014 end-page: 843 ident: bb0190 article-title: O. consortium, Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis publication-title: Nat Genet contributor: fullname: Fitzgerald – volume: 30 start-page: 763 year: 2015 end-page: 770 ident: bb0030 article-title: The genome as a record of environmental exposure publication-title: Mutagenesis contributor: fullname: Phillips – volume: 162 start-page: 1202 year: 2015 end-page: 1205 ident: bb0040 article-title: Checkpoints publication-title: Cell contributor: fullname: Allison – volume: 32 start-page: 511 year: 2016 end-page: 517 ident: bb0200 article-title: Gapped sequence alignment using artificial neural networks: application to the MHC class I system publication-title: Bioinformatics contributor: fullname: Nielsen – volume: 11 year: 2012 ident: bb0225 article-title: Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis publication-title: Mol Cell Proteomics contributor: fullname: Aebersold – volume: 4 year: 2012 ident: bb0060 article-title: Vaccine vectors derived from a large collection of simian adenoviruses induce potent cellular immunity across multiple species publication-title: Sci Transl Med contributor: fullname: Nicosia – volume: 47 start-page: D607 year: 2019 end-page: D613 ident: bb0240 article-title: STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets publication-title: Nucleic Acids Res. contributor: fullname: Mering – volume: 6 start-page: 32417 year: 2016 ident: bb0195 article-title: O. consortium, Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1 publication-title: Sci Rep contributor: fullname: Underwood – volume: 87 start-page: 6319 year: 2015 end-page: 6327 ident: bb0120 article-title: SuperQuant: a data processing approach to increase quantitative proteome coverage publication-title: Anal. Chem. contributor: fullname: Kjeldsen – volume: 17 start-page: 341 year: 2016 ident: bb0125 article-title: Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data publication-title: BMC Bioinformatics contributor: fullname: Castellani – volume: 547 start-page: 217 year: 2017 end-page: 221 ident: bb0165 article-title: An immunogenic personal neoantigen vaccine for patients with melanoma publication-title: Nature contributor: fullname: Wu – volume: 499 start-page: 214 year: 2013 end-page: 218 ident: bb0185 article-title: Mutational heterogeneity in cancer and the search for new cancer-associated genes publication-title: Nature contributor: fullname: Getz – volume: 348 start-page: 803 year: 2015 end-page: 808 ident: bb0050 article-title: Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells publication-title: Science contributor: fullname: Linette – volume: 463 start-page: 893 year: 2010 end-page: 898 ident: bb0005 article-title: Signatures of mutation and selection in the cancer genome publication-title: Nature contributor: fullname: Stratton – volume: 486 start-page: 395 year: 2012 end-page: 399 ident: bb0140 article-title: The clonal and mutational evolution spectrum of primary triple-negative breast cancers publication-title: Nature contributor: fullname: Aparicio – volume: 5 start-page: 169 year: 2013 end-page: 172 ident: bb0010 article-title: Journeys into the genome of cancer cells publication-title: EMBO Mol Med contributor: fullname: Stratton – volume: 9 start-page: 1319 year: 2012 end-page: 1330 ident: bb0055 article-title: Developing mRNA-vaccine technologies publication-title: RNA Biol. contributor: fullname: Kallen – volume: 30 start-page: 3136 year: 2014 end-page: 3138 ident: bb0100 article-title: sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments publication-title: Bioinformatics contributor: fullname: Liu – volume: 47 start-page: 1402 year: 2015 end-page: 1407 ident: bb0025 article-title: Clock-like mutational processes in human somatic cells publication-title: Nat. Genet. contributor: fullname: Stratton – volume: 17 start-page: 1045 year: 1998 end-page: 1052 ident: bb0135 article-title: DNA damage triggers DRB-resistant phosphorylation of human p53 at the CK2 site publication-title: Oncogene contributor: fullname: Hupp – volume: 13 start-page: 6176 year: 2014 end-page: 6186 ident: bb0220 article-title: Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics publication-title: J. Proteome Res. contributor: fullname: Olsen – volume: 31 start-page: i106 year: 2015 end-page: i115 ident: bb0105 article-title: MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms publication-title: Bioinformatics contributor: fullname: Renard – volume: 9 year: 2014 ident: bb0160 article-title: Clonal architectures and driver mutations in metastatic melanomas publication-title: PLoS One contributor: fullname: Weber – volume: 14 start-page: R36 year: 2013 ident: bb0210 article-title: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions publication-title: Genome Biol. contributor: fullname: Salzberg – volume: 32 start-page: 78 year: 2019 end-page: 84 ident: bb0235 article-title: Cooperation of genomic publication-title: Transcriptomics and Proteomic Methods in the Detection of Mutated Proteins, Klin Onkol contributor: fullname: Vojtesek – volume: 513 start-page: 382 year: 2014 end-page: 387 ident: bb0065 article-title: Proteogenomic characterization of human colon and rectal cancer publication-title: Nature contributor: fullname: Nci – volume: 358 start-page: 15 year: 1992 end-page: 16 ident: bb0170 article-title: Cancer. p53, guardian of the genome publication-title: Nature contributor: fullname: Lane – volume: 8 start-page: 42613 year: 2017 end-page: 42620 ident: bb0115 article-title: NGS based identification of mutational hotspots for targeted therapy in anaplastic thyroid carcinoma publication-title: Oncotarget contributor: fullname: Schmid – volume: 16 start-page: 2327 year: 2016 end-page: 2344 ident: bb0230 article-title: Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3 publication-title: Proteomics contributor: fullname: Hupp – volume: 34 start-page: 1859 year: 2018 end-page: 1867 ident: bb0095 article-title: Splice expression variation analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer publication-title: Bioinformatics contributor: fullname: Fertig – volume: 8 start-page: 291 year: 2017 ident: bb0155 article-title: Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry publication-title: Nat. Commun. contributor: fullname: Aebersold – volume: 68 start-page: 68 year: 2015 end-page: 71 ident: bb0075 article-title: Pioneer translation products as an alternative source for MHC-I antigenic peptides publication-title: Mol. Immunol. contributor: fullname: Fahraeus – volume: 476 start-page: 298 year: 2011 end-page: 303 ident: bb0145 article-title: Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma publication-title: Nature contributor: fullname: Marra – volume: 6 start-page: 359 year: 2009 end-page: 362 ident: bb0150 article-title: Universal sample preparation method for proteome analysis publication-title: Nat. Methods contributor: fullname: Mann – volume: 9 year: 2014 ident: bb0110 article-title: Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue publication-title: PLoS One contributor: fullname: Dyrskjot – volume: 22 start-page: 568 year: 2012 end-page: 576 ident: bb0215 article-title: VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing publication-title: Genome Res. contributor: fullname: Wilson – volume: 13 start-page: 1352 year: 2013 end-page: 1357 ident: bb0090 article-title: A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies publication-title: Proteomics contributor: fullname: Griffin – volume: 276 start-page: 4699 year: 2001 end-page: 4708 ident: bb0130 article-title: Stoichiometric phosphorylation of human p53 at Ser315 stimulates p53-dependent transcription publication-title: J. Biol. Chem. contributor: fullname: Hupp – volume: 8 start-page: 147 year: 2008 end-page: 156 ident: bb0020 article-title: Translation of new cancer treatments from pet dogs to humans publication-title: Nat. Rev. Cancer contributor: fullname: Khanna – volume: 183 start-page: 111709 year: 2019 ident: bb0035 article-title: The discovery of a potent and selective third-generation EGFR kinase inhibitor as a therapy for EGFR L858R/T790M double mutant non-small cell lung cancer publication-title: Eur. J. Med. Chem. contributor: fullname: Yan – volume: 16 start-page: 959 year: 2017 ident: 10.1016/j.bbagen.2020.129722_bb0070 article-title: Methods, Tools and Current Perspectives in Proteogenomics publication-title: Mol Cell Proteomics doi: 10.1074/mcp.MR117.000024 contributor: fullname: Ruggles – volume: 109 start-page: 9551 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0175 article-title: Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1200019109 contributor: fullname: Edlund – volume: 162 start-page: 1202 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0040 article-title: Checkpoints publication-title: Cell doi: 10.1016/j.cell.2015.08.047 contributor: fullname: Allison – volume: 9 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0160 article-title: Clonal architectures and driver mutations in metastatic melanomas publication-title: PLoS One doi: 10.1371/journal.pone.0111153 contributor: fullname: Ding – volume: 499 start-page: 214 year: 2013 ident: 10.1016/j.bbagen.2020.129722_bb0185 article-title: Mutational heterogeneity in cancer and the search for new cancer-associated genes publication-title: Nature doi: 10.1038/nature12213 contributor: fullname: Lawrence – volume: 276 start-page: 4699 year: 2001 ident: 10.1016/j.bbagen.2020.129722_bb0130 article-title: Stoichiometric phosphorylation of human p53 at Ser315 stimulates p53-dependent transcription publication-title: J. Biol. Chem. doi: 10.1074/jbc.M003485200 contributor: fullname: Blaydes – volume: 6 start-page: 32417 year: 2016 ident: 10.1016/j.bbagen.2020.129722_bb0195 article-title: O. consortium, Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1 publication-title: Sci Rep doi: 10.1038/srep32417 contributor: fullname: Garcia – volume: 30 start-page: 763 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0030 article-title: The genome as a record of environmental exposure publication-title: Mutagenesis contributor: fullname: Nik-Zainal – volume: 4 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0060 article-title: Vaccine vectors derived from a large collection of simian adenoviruses induce potent cellular immunity across multiple species publication-title: Sci Transl Med doi: 10.1126/scitranslmed.3002925 contributor: fullname: Colloca – volume: 513 start-page: 382 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0065 article-title: Proteogenomic characterization of human colon and rectal cancer publication-title: Nature doi: 10.1038/nature13438 contributor: fullname: Zhang – volume: 9 start-page: 1319 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0055 article-title: Developing mRNA-vaccine technologies publication-title: RNA Biol. doi: 10.4161/rna.22269 contributor: fullname: Schlake – volume: 486 start-page: 395 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0140 article-title: The clonal and mutational evolution spectrum of primary triple-negative breast cancers publication-title: Nature doi: 10.1038/nature10933 contributor: fullname: Shah – volume: 87 start-page: 6319 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0120 article-title: SuperQuant: a data processing approach to increase quantitative proteome coverage publication-title: Anal. Chem. doi: 10.1021/acs.analchem.5b01166 contributor: fullname: Gorshkov – volume: 13 start-page: 1352 year: 2013 ident: 10.1016/j.bbagen.2020.129722_bb0090 article-title: A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies publication-title: Proteomics doi: 10.1002/pmic.201200352 contributor: fullname: Jagtap – volume: 30 start-page: 3136 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0100 article-title: sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu397 contributor: fullname: Wen – volume: 8 start-page: 2281 year: 2013 ident: 10.1016/j.bbagen.2020.129722_bb0205 article-title: Genome engineering using the CRISPR-Cas9 system publication-title: Nat. Protoc. doi: 10.1038/nprot.2013.143 contributor: fullname: Ran – volume: 17 start-page: 341 year: 2016 ident: 10.1016/j.bbagen.2020.129722_bb0125 article-title: Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data publication-title: BMC Bioinformatics doi: 10.1186/s12859-016-1190-7 contributor: fullname: do Valle – volume: 47 start-page: D607 year: 2019 ident: 10.1016/j.bbagen.2020.129722_bb0240 article-title: STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky1131 contributor: fullname: Szklarczyk – volume: 46 start-page: 837 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0190 article-title: O. consortium, Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis publication-title: Nat Genet doi: 10.1038/ng.3013 contributor: fullname: Weaver – volume: 6 start-page: 359 year: 2009 ident: 10.1016/j.bbagen.2020.129722_bb0150 article-title: Universal sample preparation method for proteome analysis publication-title: Nat. Methods doi: 10.1038/nmeth.1322 contributor: fullname: Wisniewski – volume: 11 start-page: 191 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0015 article-title: Diagnosing the decline in pharmaceutical R&D efficiency publication-title: Nat. Rev. Drug Discov. doi: 10.1038/nrd3681 contributor: fullname: Scannell – volume: 16 start-page: 2327 year: 2016 ident: 10.1016/j.bbagen.2020.129722_bb0230 article-title: Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3 publication-title: Proteomics doi: 10.1002/pmic.201500501 contributor: fullname: Way – volume: 547 start-page: 217 year: 2017 ident: 10.1016/j.bbagen.2020.129722_bb0165 article-title: An immunogenic personal neoantigen vaccine for patients with melanoma publication-title: Nature doi: 10.1038/nature22991 contributor: fullname: Ott – volume: 13 start-page: 6176 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0220 article-title: Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics publication-title: J. Proteome Res. doi: 10.1021/pr500893m contributor: fullname: Batth – volume: 31 start-page: i106 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0105 article-title: MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv236 contributor: fullname: Zickmann – volume: 22 start-page: 568 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0215 article-title: VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing publication-title: Genome Res. doi: 10.1101/gr.129684.111 contributor: fullname: Koboldt – volume: 14 start-page: 3729 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0085 article-title: PPLine: An automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics publication-title: J Proteome Res doi: 10.1021/acs.jproteome.5b00490 contributor: fullname: Krasnov – volume: 11 year: 2012 ident: 10.1016/j.bbagen.2020.129722_bb0225 article-title: Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis publication-title: Mol Cell Proteomics doi: 10.1074/mcp.O111.016717 contributor: fullname: Gillet – volume: 68 start-page: 68 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0075 article-title: Pioneer translation products as an alternative source for MHC-I antigenic peptides publication-title: Mol. Immunol. doi: 10.1016/j.molimm.2015.04.019 contributor: fullname: Apcher – volume: 8 start-page: 291 year: 2017 ident: 10.1016/j.bbagen.2020.129722_bb0155 article-title: Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry publication-title: Nat. Commun. doi: 10.1038/s41467-017-00249-5 contributor: fullname: Collins – volume: 34 start-page: 1859 year: 2018 ident: 10.1016/j.bbagen.2020.129722_bb0095 article-title: Splice expression variation analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty004 contributor: fullname: Afsari – volume: 17 start-page: 1045 year: 1998 ident: 10.1016/j.bbagen.2020.129722_bb0135 article-title: DNA damage triggers DRB-resistant phosphorylation of human p53 at the CK2 site publication-title: Oncogene doi: 10.1038/sj.onc.1202014 contributor: fullname: Blaydes – volume: 463 start-page: 893 year: 2010 ident: 10.1016/j.bbagen.2020.129722_bb0005 article-title: Signatures of mutation and selection in the cancer genome publication-title: Nature doi: 10.1038/nature08768 contributor: fullname: Bignell – volume: 32 start-page: 511 year: 2016 ident: 10.1016/j.bbagen.2020.129722_bb0200 article-title: Gapped sequence alignment using artificial neural networks: application to the MHC class I system publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv639 contributor: fullname: Andreatta – volume: 8 start-page: 42613 year: 2017 ident: 10.1016/j.bbagen.2020.129722_bb0115 article-title: NGS based identification of mutational hotspots for targeted therapy in anaplastic thyroid carcinoma publication-title: Oncotarget doi: 10.18632/oncotarget.17300 contributor: fullname: Tiedje – volume: 32 start-page: 78 year: 2019 ident: 10.1016/j.bbagen.2020.129722_bb0235 article-title: Cooperation of genomic publication-title: Transcriptomics and Proteomic Methods in the Detection of Mutated Proteins, Klin Onkol contributor: fullname: Zavadil Kokas – volume: 43 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0080 article-title: PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku1283 contributor: fullname: Crappe – volume: 9 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0110 article-title: Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue publication-title: PLoS One doi: 10.1371/journal.pone.0098187 contributor: fullname: Hedegaard – volume: 5 start-page: 169 year: 2013 ident: 10.1016/j.bbagen.2020.129722_bb0010 article-title: Journeys into the genome of cancer cells publication-title: EMBO Mol Med doi: 10.1002/emmm.201202388 contributor: fullname: Stratton – volume: 8 start-page: 147 year: 2008 ident: 10.1016/j.bbagen.2020.129722_bb0020 article-title: Translation of new cancer treatments from pet dogs to humans publication-title: Nat. Rev. Cancer doi: 10.1038/nrc2273 contributor: fullname: Paoloni – volume: 14 start-page: R36 year: 2013 ident: 10.1016/j.bbagen.2020.129722_bb0210 article-title: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions publication-title: Genome Biol. doi: 10.1186/gb-2013-14-4-r36 contributor: fullname: Kim – volume: 476 start-page: 298 year: 2011 ident: 10.1016/j.bbagen.2020.129722_bb0145 article-title: Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma publication-title: Nature doi: 10.1038/nature10351 contributor: fullname: Morin – volume: 47 start-page: 1402 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0025 article-title: Clock-like mutational processes in human somatic cells publication-title: Nat. Genet. doi: 10.1038/ng.3441 contributor: fullname: Alexandrov – volume: 100 start-page: 11547 year: 2003 ident: 10.1016/j.bbagen.2020.129722_bb0180 article-title: The presence of p53 mutations in human osteosarcomas correlates with high levels of genomic instability publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1934852100 contributor: fullname: Overholtzer – volume: 348 start-page: 803 year: 2015 ident: 10.1016/j.bbagen.2020.129722_bb0050 article-title: Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells publication-title: Science doi: 10.1126/science.aaa3828 contributor: fullname: Carreno – volume: 512 start-page: 324 year: 2014 ident: 10.1016/j.bbagen.2020.129722_bb0045 article-title: A vaccine targeting mutant IDH1 induces antitumour immunity publication-title: Nature doi: 10.1038/nature13387 contributor: fullname: Schumacher – volume: 358 start-page: 15 year: 1992 ident: 10.1016/j.bbagen.2020.129722_bb0170 article-title: Cancer. p53, guardian of the genome publication-title: Nature doi: 10.1038/358015a0 contributor: fullname: Lane – volume: 183 start-page: 111709 year: 2019 ident: 10.1016/j.bbagen.2020.129722_bb0035 article-title: The discovery of a potent and selective third-generation EGFR kinase inhibitor as a therapy for EGFR L858R/T790M double mutant non-small cell lung cancer publication-title: Eur. J. Med. Chem. doi: 10.1016/j.ejmech.2019.111709 contributor: fullname: An |
SSID | ssj0000595 |
Score | 2.403698 |
Snippet | The identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research methodologies... BACKGROUNDThe identification of mutated proteins in human cancer cells-termed proteogenomics, requires several technologically independent research... |
SourceID | proquest crossref pubmed elsevier |
SourceType | Aggregation Database Index Database Publisher |
StartPage | 129722 |
SubjectTerms | Cancer Cell Line, Tumor Gene Expression Regulation, Neoplastic Gene Silencing Humans Melanoma - genetics Mutation p53 Protein mass spectrometry Proteogenomics Proteome - genetics Proteomics Tumor Suppressor Protein p53 - genetics |
Title | The effects of p53 gene inactivation on mutant proteome expression in a human melanoma cell model |
URI | https://dx.doi.org/10.1016/j.bbagen.2020.129722 https://www.ncbi.nlm.nih.gov/pubmed/32866596 https://search.proquest.com/docview/2439622137 |
Volume | 1864 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1LS8QwEB7URfQivl0fSwSvdbdp-jrKoqyKXlTwFvIqrLjtorugF3-7M02reBBBKIWmCQlfkpkhmZkP4CRzoRHWqsAmYhAII3BLmcwFOuOpNoVCFUbRyDe3yehBXD3GjwswbGNhyK2ykf1eptfSuinpN2j2p-Nx_44u9dCciPmAiG9EtggdVEd0V9s5u7we3X4L5LgmX6H6ATVoI-hqNy-tcd9SIlROmRbylPPfNNRvFmitiS7WYa0xIdmZH-UGLLhyE5Y9qeT7JqwMWw63LVC4CljjssGqgk3jiOE4HBuXFNDgj2MZPpM5sQmzOmtDNcE2b42DbIlVmWI1lR-buGdVVhPF6Lif1SQ62_BwcX4_HAUNqUJgxCCbBaEuONfKGBEWLncDbpVwWkWhFTmaQkVeJBz_ZJFOImtzmxvDlU2tjXSmLJp7O7BUVqXbA8YLSiycpEIpLXLuFL2MQSERxxF20IWgBVJOfe4M2TqVPUkPvCTgpQe-C2mLtvyxBiSK9z9aHreTIxFhAkGVrpq_So4GV8J5GKVd2PWz9jWWiFOyvzzZ_3e_B7BKX9695RCWZi9zd4RGykz3YPH0I-w1S_ET8fHmRw |
link.rule.ids | 314,780,784,4502,24116,27924,27925,45585,45679 |
linkProvider | Elsevier |
linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1JS8QwFH64IONF3B3XCF7rtGm6HWVwGNeLDswtZCuM2HbQGdCLv92XplU8iCCUHJqEhC8vLx_JWwDOUhMoprXwdMx8jymGW0qlxpMpTaTKBR5h1hv57j4ejtj1OBovQL_1hbFmlY3udzq91tbNn16DZm86mfQe7KMe0omI-jbxDUsXYZlFyH5RqM8_vu08kD9E7imBebZ56z9XG3lJibvWhkGlNs5CllD62_n0G_-sz6HBOqw1BJJcuDluwIIpN2HFpZR834ROv83gtgUCZYA0Bhukysk0CgnOw5BJad0Z3GUswa-Y21zCpI7ZUBXY560xjy2xKRGkTuRHCvMsyqoQxF72kzqFzjaMBpeP_aHXpFTwFPPTmRfInFIplGJBbjLjUy2YkSIMNMuQCOVZHlOsSUMZh1pnOlOKCp1oHcpUaCR7O7BUVqXZA0JzG1Y4TpgQkmXUCFsohSoiikIcoAteCySfusgZvDUpe-IOeG6B5w74LiQt2vyHBHBU7n_0PG0XhyPCFgRRmmr-yinSrZjSIEy6sOtW7WsuIbWh_rJ4_9_jnkBn-Hh3y2-v7m8OYNXWOEOXQ1iavczNEdKVmTyuxfETBk_nIA |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=The+effects+of+p53+gene+inactivation+on+mutant+proteome+expression+in+a+human+melanoma+cell+model&rft.jtitle=Biochimica+et+biophysica+acta.+General+subjects&rft.au=Faktor%2C+Jakub&rft.au=Grasso%2C+Giuseppa&rft.au=Zavadil+Kokas%2C+Filip&rft.au=Kurkowiak%2C+Ma%C5%82gorzata&rft.date=2020-12-01&rft.eissn=1872-8006&rft.volume=1864&rft.issue=12&rft.spage=129722&rft_id=info:doi/10.1016%2Fj.bbagen.2020.129722&rft_id=info%3Apmid%2F32866596&rft.externalDocID=32866596 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0304-4165&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0304-4165&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0304-4165&client=summon |