박사

Development of proteogenomics pipeline for identifying fusion proteoforms

김채연 2019년
논문상세정보
' Development of proteogenomics pipeline for identifying fusion proteoforms' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • Customized DB
  • Genomics
  • Mass spectrometry
  • Mutation
  • Proteoform
  • Proteogenomics
  • Proteomics
  • Transcriptomics
  • Variant
  • peptide
  • protein
  • 단백유전체학
  • 생물정보학
  • 융합 단백체폼
  • 융합 전사체
  • 주문형 데이터베이스
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
511 0

0.0%

' Development of proteogenomics pipeline for identifying fusion proteoforms' 의 참고문헌

  • Zhang, H., Liu, T., Zhang, Z., Payne, S.H., Zhang, B., McDermott, J.E., Zhou, J.Y., Petyuk, V.A., Chen, L., Ray, D., et al. (2016). Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell 166, 755-765.
  • Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H., and Verhaak, R.G. (2015). The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene 34, 4845-4854.
  • Woo, S., Cha, S.W., Na, S., Guest, C., Liu, T., Smith, R.D., Rodland, K.D., Payne, S., and Bafna, V. (2014). Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics 14, 2719-2730.
  • Wang, X., Codreanu, S.G., Wen, B., Li, K., Chambers, M.C., Liebler, D.C., and Zhang, B. (2018). Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity. Mol Cell Proteomics 17, 422-430.
  • Wang, Q., Xia, J., Jia, P., Pao, W., and Zhao, Z. (2013). Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform 14, 506-519.
  • Wang, K., Singh, D., Zeng, Z., Coleman, S.J., Huang, Y., Savich, G.L., He, X., Mieczkowski, P., Grimm, S.A., Perou, C.M., et al. (2010). MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38, e178.
  • Veeraraghavan, J., Tan, Y., Cao, X.X., Kim, J.A., Wang, X., Chamness, G.C., Maiti, S.N., Cooper, L.J., Edwards, D.P., Contreras, A., et al. (2014). Recurrent ESR1-CCDC170 rearrangements in an aggressive subset of oestrogen receptor-positive breast cancers. Nat Commun 5, 4577.
  • Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511-515.
  • Torres-Garcia, W., Zheng, S., Sivachenko, A., Vegesna, R., Wang, Q., Yao, R., Berger, M.F., Weinstein, J.N., Getz, G., and Verhaak, R.G. (2014). PRADA: pipeline for RNA sequencing data analysis. Bioinformatics 30, 2224-2226.
  • Sun, H., Xing, X., Li, J., Zhou, F., Chen, Y., He, Y., Li, W., Wei, G., Chang, X., Jia, J., et al. (2013). Identification of gene fusions from human lung cancer mass spectrometry data. BMC Genomics 14 Suppl 8, S5.
  • Smith, L.M., Kelleher, N.L., and Consortium for Top Down, P. (2013). Proteoform: a single term describing protein complexity. Nat Methods 10, 186-187.
  • Slavoff, S.A., Mitchell, A.J., Schwaid, A.G., Cabili, M.N., Ma, J., Levin, J.Z., Karger, A.D., Budnik, B.A., Rinn, J.L., and Saghatelian, A. (2013). Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol 9, 59-64.
  • Sisu, C., Pei, B., Leng, J., Frankish, A., Zhang, Y., Balasubramanian, S., Harte, R., Wang, D., Rutenberg-Schoenberg, M., Clark, W., et al. (2014). Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci U S A 111, 13361-13366.
  • Sheynkman, G.M., Shortreed, M.R., Frey, B.L., and Smith, L.M. (2013). Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol Cell Proteomics 12, 2341-2353.
  • Sakarya, O., Breu, H., Radovich, M., Chen, Y., Wang, Y.N., Barbacioru, C., Utiramerur, S., Whitley, P.P., Brockman, J.P., Vatta, P., et al. (2012). RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput Biol 8, e1002464.
  • Russo, A.A., Tong, L., Lee, J.O., Jeffrey, P.D., and Pavletich, N.P. (1998). Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a. Nature 395, 237-243.
  • Rodriguez-Martin, B., Palumbo, E., Marco-Sola, S., Griebel, T., Ribeca, P., Alonso, G., Rastrojo, A., Aguado, B., Guigo, R., and Djebali, S. (2017). ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. BMC Genomics 18, 7.
  • Robinson, D.R., Kalyana-Sundaram, S., Wu, Y.M., Shankar, S., Cao, X., Ateeq, B., Asangani, I.A., Iyer, M., Maher, C.A., Grasso, C.S., et al. (2011). Functionally recurrent rearrangements of the MAST kinase and Notch gene families in breast cancer. Nat Med 17, 1646-1651.
  • Pathak, E., Bhavya, Mishra, D., Atri, N., and Mishra, R. (2017). Deciphering the Role of microRNAs in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma. Bioinformation 13, 209-213.
  • Parker, E.P., Siebert, R., Oo, T.H., Schneider, D., Hayette, S., and Wang, C. (2013). Sequencing of t(2;7) translocations reveals a consistent breakpoint linking CDK6 to the IGK locus in indolent B-cell neoplasia. J Mol Diagn 15, 101-109.
  • Paik, Y.K., Omenn, G.S., Hancock, W.S., Lane, L., and Overall, C.M. (2017). Advances in the Chromosome-Centric Human Proteome Project: looking to the future. Expert Rev Proteomics 14, 1059.
  • Paik, Y.K., Jeong, S.K., Omenn, G.S., Uhlen, M., and Hanash, S. (2012). The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol 30, 221.
  • Paik, Y.-K., Lane, L., Kawamura, T., Chen, Y.-J., Cho, J.-Y., LaBaer, J., Yoo, J.S., Domont, G., Corrales, F., Omenn, G.S., et al. (2018). Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function. Journal of Proteome Research 17, 4042-4050.
  • Nome, T., Thomassen, G.O., Bruun, J., Ahlquist, T., Bakken, A.C., Hoff, A.M., Rognum, T., Nesbakken, A., Lorenz, S., Sun, J., et al. (2013). Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing. Transl Oncol 6, 546- 553.
  • Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., Martincorena, I., Alexandrov, L.B., Martin, S., Wedge, D.C., et al. (2016). Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47-54.
  • Nicorici, D., Satalan, M., Edgren, H., Kangaspeska, S., Murumagi, A., Kallioniemi, O., Virtanen, S., and Kilkku, O. (2014). FusionCatcher - a tool for finding somatic fusion genes in paired-end RNA-sequencing data. bioRxiv.
  • Nesvizhskii, A.I. (2014). Proteogenomics: concepts, applications and computational strategies. Nat Methods 11, 1114-1125.
  • Mitelman, F., Johansson, B., and Mertens, F. (2007). The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7, 233-245.
  • Liu, Y., Easton, J., Shao, Y., Maciaszek, J., Wang, Z., Wilkinson, M.R., McCastlain, K., Edmonson, M., Pounds, S.B., Shi, L., et al. (2017). The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet 49, 1211-1218.
  • Liu, S., Tsai, W.H., Ding, Y., Chen, R., Fang, Z., Huo, Z., Kim, S., Ma, T., Chang, T.Y., Priedigkeit, N.M., et al. (2016). Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res 44, e47.
  • Lin, Y.Y., Gawronski, A., Hach, F., Li, S., Numanagic, I., Sarrafi, I., Mishra, S., McPherson, A., Collins, C.C., Radovich, M., et al. (2018). Computational identification of microstructural variations and their proteogenomic consequences in cancer. Bioinformatics 34, 1672-1681.
  • Lee, M., Lee, K., Yu, N., Jang, I., Choi, I., Kim, P., Jang, Y.E., Kim, B., Kim, S., Lee, B., et al. (2017). ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. Nucleic Acids Res 45, D784-D789.
  • Laurent, E., Talpaz, M., Kantarjian, H., and Kurzrock, R. (2001). The BCR gene and philadelphia chromosome-positive leukemogenesis. Cancer Res 61, 2343-2355.
  • Latysheva, N.S., and Babu, M.M. (2016). Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 44, 4487- 4503.
  • Lane, L., Argoud-Puy, G., Britan, A., Cusin, I., Duek, P.D., Evalet, O., Gateau, A., Gaudet, P., Gleizes, A., Masselot, A., et al. (2012). neXtProt: a knowledge platform for human proteins. Nucleic Acids Res 40, D76-83.
  • Lai, J., An, J., Seim, I., Walpole, C., Hoffman, A., Moya, L., Srinivasan, S., Perry-Keene, J.L., Australian Prostate Cancer, B., Wang, C., et al. (2015). Fusion transcript loci share many genomic features with non-fusion loci. BMC Genomics 16, 1021.
  • Kollmann, K., Heller, G., and Sexl, V. (2011b). c-JUN prevents methylation of p16(INK4a) (and Cdk6): the villain turned bodyguard. Oncotarget 2, 422-427.
  • Kollmann, K., Heller, G., Schneckenleithner, C., Warsch, W., Scheicher, R., Ott, R.G., Schafer, M., Fajmann, S., Schlederer, M., Schiefer, A.I., et al. (2013). A kinase-independent function of CDK6 links the cell cycle to tumor angiogenesis. Cancer Cell 24, 167-181.
  • Kollmann, K., Heller, G., Ott, R.G., Scheicher, R., Zebedin-Brandl, E., Schneckenleithner, C., Simma, O., Warsch, W., Eckelhart, E., Hoelbl, A., et al. (2011a). c-JUN promotes BCRABL- induced lymphoid leukemia by inhibiting methylation of the 5' region of Cdk6. Blood 117, 4065-4075.
  • Kim, D., and Salzberg, S.L. (2011). TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12, R72.
  • Kangaspeska, S., Hultsch, S., Edgren, H., Nicorici, D., Murumagi, A., and Kallioniemi, O. (2012). Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One 7, e48745.
  • Kalyana-Sundaram, S., Shankar, S., Deroo, S., Iyer, M.K., Palanisamy, N., Chinnaiyan, A.M., and Kumar-Sinha, C. (2012). Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer. Neoplasia 14, 702-708.
  • Jia, W., Qiu, K., He, M., Song, P., Zhou, Q., Zhou, F., Yu, Y., Zhu, D., Nickerson, M.L., Wan, S., et al. (2013). SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol 14, R12.
  • Ivanov, M.V., Lobas, A.A., Karpov, D.S., Moshkovskii, S.A., and Gorshkov, M.V. (2017). Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics. J Proteome Res 16, 1936-1943.
  • Inaki, K., Hillmer, A.M., Ukil, L., Yao, F., Woo, X.Y., Vardy, L.A., Zawack, K.F., Lee, C.W., Ariyaratne, P.N., Chan, Y.S., et al. (2011). Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res 21, 676-687.
  • Huang, W., Li, L., Myers, J.R., and Marth, G.T. (2012). ART: a next-generation sequencing read simulator. Bioinformatics 28, 593-594.
  • Hu, X., Wang, Q., Tang, M., Barthel, F., Amin, S., Yoshihara, K., Lang, F.M., Martinez- Ledesma, E., Lee, S.H., Zheng, S., et al. (2018). TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Res 46, D1144-D1149.
  • Hayette, S., Tigaud, I., Callet-Bauchu, E., Ffrench, M., Gazzo, S., Wahbi, K., Callanan, M., Felman, P., Dumontet, C., Magaud, J.P., et al. (2003). In B-cell chronic lymphocytic leukemias, 7q21 translocations lead to overexpression of the CDK6 gene. Blood 102, 1549- 1550.
  • Hampton, O.A., Den Hollander, P., Miller, C.A., Delgado, D.A., Li, J., Coarfa, C., Harris, R.A., Richards, S., Scherer, S.E., Muzny, D.M., et al. (2009). A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res 19, 167-177.
  • Giacomini, C.P., Sun, S., Varma, S., Shain, A.H., Giacomini, M.M., Balagtas, J., Sweeney, R.T., Lai, E., Del Vecchio, C.A., Forster, A.D., et al. (2013). Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 9, e1003464.
  • Geiger, T., Wehner, A., Schaab, C., Cox, J., and Mann, M. (2012). Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics 11, M111 014050.
  • Frenkel-Morgenstern, M., Lacroix, V., Ezkurdia, I., Levin, Y., Gabashvili, A., Prilusky, J., Del Pozo, A., Tress, M., Johnson, R., Guigo, R., et al. (2012). Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res 22, 1231-1242.
  • French, C.A., Miyoshi, I., Kubonishi, I., Grier, H.E., Perez-Atayde, A.R., and Fletcher, J.A. (2003). BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. Cancer Res 63, 304-307.
  • Finn, R.D., Attwood, T.K., Babbitt, P.C., Bateman, A., Bork, P., Bridge, A.J., Chang, H.Y., Dosztanyi, Z., El-Gebali, S., Fraser, M., et al. (2017). InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45, D190-D199.
  • Ellis, M.J., Gillette, M., Carr, S.A., Paulovich, A.G., Smith, R.D., Rodland, K.K., Townsend, R.R., Kinsinger, C., Mesri, M., Rodriguez, H., et al. (2013). Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium. Cancer Discov 3, 1108-1112.
  • Edwards, N.J., Oberti, M., Thangudu, R.R., Cai, S., McGarvey, P.B., Jacob, S., Madhavan, S., and Ketchum, K.A. (2015). The CPTAC Data Portal: A Resource for Cancer Proteomics Research. J Proteome Res 14, 2707-2713.
  • Edgren, H., Murumagi, A., Kangaspeska, S., Nicorici, D., Hongisto, V., Kleivi, K., Rye, I.H., Nyberg, S., Wolf, M., Borresen-Dale, A.L., et al. (2011). Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 12, R6.
  • Druker, B.J., and Lydon, N.B. (2000). Lessons learned from the development of an abl tyrosine kinase inhibitor for chronic myelogenous leukemia. J Clin Invest 105, 3-7.
  • Davidson, N.M., Majewski, I.J., and Oshlack, A. (2015). JAFFA: High sensitivity transcriptome-focused fusion gene detection. Genome Med 7, 43.
  • Casado-Vela, J., Lacal, J.C., and Elortza, F. (2013). Protein chimerism: novel source of protein diversity in humans adds complexity to bottom-up proteomics. Proteomics 13, 5- 11.
  • Carrara, M., Beccuti, M., Lazzarato, F., Cavallo, F., Cordero, F., Donatelli, S., and Calogero, R.A. (2013). State-of-the-art fusion-finder algorithms sensitivity and specificity. Biomed Res Int 2013, 340620.
  • Cagney, G., Amiri, S., Premawaradena, T., Lindo, M., and Emili, A. (2003). In silico proteome analysis to facilitate proteomics experiments using mass spectrometry. Proteome Sci 1, 5.
  • Berger, M.F., Levin, J.Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L.A., Robinson, J., Verhaak, R.G., Sougnez, C., et al. (2010). Integrative analysis of the melanoma transcriptome. Genome Res 20, 413-427.
  • Bassani-Sternberg, M., Braunlein, E., Klar, R., Engleitner, T., Sinitcyn, P., Audehm, S., Straub, M., Weber, J., Slotta-Huspenina, J., Specht, K., et al. (2016). Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat Commun 7, 13404.
  • Bao, Z.S., Chen, H.M., Yang, M.Y., Zhang, C.B., Yu, K., Ye, W.L., Hu, B.Q., Yan, W., Zhang, W., Akers, J., et al. (2014). RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas. Genome Res 24, 1765-1773.
  • Annala, M.J., Parker, B.C., Zhang, W., and Nykter, M. (2013). Fusion genes and their discovery using high throughput sequencing. Cancer Lett 340, 192-200.
  • Adusumilli, R., and Mallick, P. (2017). Data Conversion with ProteoWizard msConvert. Methods Mol Biol 1550, 339-368.
  • Abmayr, S.M., Yao, T., Parmely, T., and Workman, J.L. (2006). Preparation of nuclear and cytoplasmic extracts from mammalian cells. Curr Protoc Mol Biol Chapter 12, Unit 12 11.