Advanced search
Publication Cover
Cell Cycle Volume 16, 2017 - Issue 19
Submit an article Journal homepage
1,409
Views
42
CrossRef citations to date
0
Altmetric
Reports

Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data

Nicolas BorisovCentre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre “Kurchatov Institute”, Moscow, Russia;Department of R&D, First Oncology Research and Advisory Center, Moscow, RussiaCorrespondence[email protected]
ORCID Iconhttp://orcid.org/0000-0002-1671-5524
ORCID Icon,
Maria SuntsovaDepartment of R&D, Center for Biogerontology and Regenerative Medicine, Moscow, Russia;Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
,
Maxim SorokinCentre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre “Kurchatov Institute”, Moscow, Russia;Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, RussiaORCID Iconhttp://orcid.org/0000-0001-7685-3446
ORCID Icon,
Andrew GarazhaDepartment of R&D, Center for Biogerontology and Regenerative Medicine, Moscow, Russia;Department of R&D, OmicsWay Corporation, Walnut, CA, USA
,
Olga KovalchukDepartment of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
,
Alexander AliperLaboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
,
Elena IlnitskayaDepartment of R&D, Center for Biogerontology and Regenerative Medicine, Moscow, Russia
,
Ksenia LezhninaDepartment of R&D, First Oncology Research and Advisory Center, Moscow, Russia
,
Mikhail KorzinkinDepartment of R&D, Center for Biogerontology and Regenerative Medicine, Moscow, Russia
,
Victor TkachevDepartment of R&D, OmicsWay Corporation, Walnut, CA, USA
,
Vyacheslav SaenkoTechnological Research Institute S.P. Kapitsa, Ulyanovsk State University, Ulyanovsk, Russia
,
Yury SaenkoTechnological Research Institute S.P. Kapitsa, Ulyanovsk State University, Ulyanovsk, Russia
,
Dmitry G. SokovChemotherapy Department, Moscow 1st Oncological Hospital, Moscow, Russia
,
Nurshat M. GaifullinFaculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia;Department of Oncology, Russian Medical Postgraduate Academy, Moscow, RussiaORCID Iconhttp://orcid.org/0000-0003-4312-6730
ORCID Icon,
Kirill KashintsevChemotherapy Department, Moscow Oncological Hospital 62, Stepanovskoye, Russia
,
Valery ShirokoradChemotherapy Department, Moscow Oncological Hospital 62, Stepanovskoye, Russia
,
Irina ShabalinaFaculty of Mathematics and Information Technologies, Petrozavodsk State University, Petrozavodsk, Russia
,
Alex ZhavoronkovLaboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
,
Bhubaneswar MishraCourant Institute, New York University, New York, NY, USAORCID Iconhttp://orcid.org/0000-0003-2126-8711
ORCID Icon,
Charles R. CantorDepartment of Biomedical Engineering, Boston University, Boston, MA, USA
&
Anton BuzdinCentre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, National Research Centre “Kurchatov Institute”, Moscow, Russia;Department of R&D, First Oncology Research and Advisory Center, Moscow, Russia;Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia;Department of R&D, OmicsWay Corporation, Walnut, CA, USAORCID Iconhttp://orcid.org/0000-0001-9866-3424
ORCID Icon show all
Pages 1810-1823 | Received 15 May 2017, Accepted 25 Jul 2017, Published online: 22 Sep 2017

Citations (42)

Keep up to date with the latest research on this topic with citation updates for this article.

Subscribe to citation updates

Read on this site (1)

Nicolas Borisov, Victor Tkachev, Maria Suntsova, Olga Kovalchuk, Alex Zhavoronkov, Ilya Muchnik & Anton Buzdin. (2018) A method of gene expression data transfer from cell lines to cancer patients for machine-learning prediction of drug efficiency. Cell Cycle 17:4, pages 486-491.
Read now

Articles from other publishers (41)

Nicolas Borisov, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Ella Kim, Denis Kuzmin, Betul Karademir-Yilmaz & Anton Buzdin. (2023) Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns. Frontiers in Molecular Biosciences 10.
Crossref
Marianna Zolotovskaia, Maks Kovalenko, Polina Pugacheva, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Alexander Seryakov, Andrew Garazha, Nurshat Gaifullin, Marina Sekacheva, Galina Zakharova & Anton A. Buzdin. (2023) Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers. Proteomes 11:3, pages 26.
Crossref
Hao Liu, Yan Han, Zhantao Liu, Liping Gao, Tienan Yi, Yuandong Yu, Yu Wang, Ping Qu, Longchao Xiang & Yong Li. (2023) Depiction of neuroendocrine features associated with immunotherapy response using a novel one-class predictor in lung adenocarcinoma. Discover Oncology 14:1.
Crossref
Nicolas Borisov, Yaroslav Ilnytskyy, Boseon Byeon, Olga Kovalchuk & Igor Kovalchuk. (2023) Application of Drug Efficiency Index Metric for Analysis of Post-Traumatic Stress Disorder and Treatment Resistant Depression Gene Expression Profiles. Psychoactives 2:2, pages 92-112.
Crossref
Marianna A. Zolotovskaia, Alexander A. Modestov, Maria V. Suntsova, Anastasia A. Rachkova, Elena V. Koroleva, Elena V. Poddubskaya, Marina I. Sekacheva, Victor S. Tkachev, Andrew V. Garazha, Alexander A. Glusker, Aleksander P. Seryakov, Uliana S. Vladimirova, Pavel O. Rumiantsev, Aleksey A. Moisseev, Dmitry O. Zharkov, Denis V. Kuzmin, Xiaowen Zhao, Vladimir S. Prassolov, Petr V. Shegay, Xinmin Li, Teresa B. Steinbichler, Ella Kim, Maxim I. Sorokin, Ye Wang & Anton A. Buzdin. (2023) Pan-cancer antagonistic inhibition pattern of ATM-driven G2/M checkpoint pathway vs other DNA repair pathways. DNA Repair 123, pages 103448.
Crossref
Marianna A. Zolotovskaia, Max A. Kovalenko, Victor S. Tkachev, Alexander M. Simonov, Maxim I. Sorokin, Ella Kim, Denis V. Kuzmin, Betul Karademir-Yilmaz & Anton A. Buzdin. (2022) Next-Generation Grade and Survival Expression Biomarkers of Human Gliomas Based on Algorithmically Reconstructed Molecular Pathways. International Journal of Molecular Sciences 23:13, pages 7330.
Crossref
Nicolas Borisov, Maksim Sorokin, Marianna Zolotovskaya, Constantin Borisov & Anton Buzdin. (2022) Shambhala‐2: A Protocol for Uniformly Shaped Harmonization of Gene Expression Profiles of Various Formats. Current Protocols 2:5.
Crossref
Nikolay Konovalov, Stanislav Timonin, Dmitry Asyutin, Mikhail Raevskiy, Maxim Sorokin, Anton Buzdin & Stanislav Kaprovoy. (2022) Transcriptomic Portraits and Molecular Pathway Activation Features of Adult Spinal Intramedullary Astrocytomas. Frontiers in Oncology 12.
Crossref
Alexander Gudkov, Valery Shirokorad, Kirill Kashintsev, Dmitriy Sokov, Daniil Nikitin, Andrey Anisenko, Nicolas Borisov, Marina Sekacheva, Nurshat Gaifullin, Andrew Garazha, Maria Suntsova, Elena Koroleva, Anton Buzdin & Maksim Sorokin. (2022) Gene Expression-Based Signature Can Predict Sorafenib Response in Kidney Cancer. Frontiers in Molecular Biosciences 9.
Crossref
Mikhail Raevskiy, Maxim Sorokin, Galina Zakharova, Victor Tkachev, Nicolas Borisov, Denis Kuzmin, Kristina Kremenchutckaya, Alexander Gudkov, Dmitry Kamashev & Anton Buzdin. (2022) Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level. International Journal of Molecular Sciences 23:5, pages 2611.
Crossref
Chiara Pastrello, Yun Niu & Igor Jurisica. 2022. Microarray Data Analysis. Microarray Data Analysis 147 159 .
М. Раевский, М. Сорокин, У. Владимирова, М. Сунцова, В. Ефимов, А. Гаража, А. Дробышев, А. Моисеев, П. Румянцев, З. Ли & А. Буздин. (2021) Основанные на молекулярном пути EGFR генные подписи клинически значимых мутаций при раке молочной железы, легких, щитовидной железы и при меланоме. Биохимия 86:11, pages 1719-1732.
Crossref
Mikhail Raevskiy, Maxim Sorokin, Uliana Vladimirova, Maria Suntsova, Victor Efimov, Andrew Garazha, Alexei Drobyshev, Aleksey Moisseev, Pavel Rumiantsev, Xinmin Li & Anton Buzdin. (2021) EGFR Pathway-Based Gene Signatures of Druggable Gene Mutations in Melanoma, Breast, Lung, and Thyroid Cancers. Biochemistry (Moscow) 86:11, pages 1477-1488.
Crossref
Haifeng Wang, Jing Li, Jie Qin, Jie Li, Yishen Chen, Dongliang Song, Haishan Zeng & Shuang Wang. (2021) Confocal Raman microspectral analysis and imaging of the drug response of osteosarcoma to cisplatin. Analytical Methods 13:22, pages 2527-2536.
Crossref
Uliana Vladimirova, Pavel Rumiantsev, Marianna Zolotovskaia, Eugene Albert, Aleksander Abrosimov, Konstantin Slashchuk, Petr Nikiforovich, Olga Chukhacheva, Nurshat Gaifullin, Maria Suntsova, Galina Zakharova, Alexander Glusker, Daniil Nikitin, Andrew Garazha, Xinmin Li, Dmitriy Kamashev, Alexei Drobyshev, Irina Kochergina-Nikitskaya, Maxim Sorokin & Anton Buzdin. (2021) DNA repair pathway activation features in follicular and papillary thyroid tumors, interrogated using 95 experimental RNA sequencing profiles. Heliyon 7:3, pages e06408.
Crossref
Dmitry Kamashev, Maksim Sorokin, Irina Kochergina, Aleksey Drobyshev, Uliana Vladimirova, Marianna Zolotovskaia, Igor Vorotnikov, Nina Shaban, Mikhail Raevskiy, Denis Kuzmin & Anton Buzdin. (2021) Human blood serum can donor-specifically antagonize effects of EGFR-targeted drugs on squamous carcinoma cell growth. Heliyon 7:3, pages e06394.
Crossref
Anton Buzdin, Victor Tkachev, Marianna Zolotovskaia, Andrew Garazha, Sergey Moshkovskii, Nicolas Borisov, Nurshat Gaifullin, Maksim Sorokin & Maria Suntsova. 2021. Proteomics and Systems Biology. Proteomics and Systems Biology 1 53 .
Nicolas Borisov, Yaroslav Ilnytskyy, Boseon Byeon, Olga Kovalchuk & Igor Kovalchuk. (2020) System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation. International Journal of Molecular Sciences 22:1, pages 388.
Crossref
Xiao-Jing Shi, Yongjun Wei & Boyang Ji. (2020) Systems Biology of Gastric Cancer: Perspectives on the Omics-Based Diagnosis and Treatment. Frontiers in Molecular Biosciences 7.
Crossref
M. Sorokin, K. Ignatev, V. Barbara, U. Vladimirova, A. Muraveva, M. Suntsova, N. Gaifullin, I. Vorotnikov, D. Kamashev, A. Bondarenko, M. Baranova, E. Poddubskaya & A. Buzdin. (2020) Molecular Pathway Activation Markers Are Associated with Efficacy of Trastuzumab Therapy in Metastatic HER2-Positive Breast Cancer Better than Individual Gene Expression Levels. Biochemistry (Moscow) 85:7, pages 758-772.
Crossref
Maxim Sorokin, Kirill Ignatev, Elena Poddubskaya, Uliana Vladimirova, Nurshat Gaifullin, Dmitriy Lantsov, Andrew Garazha, Daria Allina, Maria Suntsova, Victoria Barbara & Anton Buzdin. (2020) RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens. Biomedicines 8:5, pages 114.
Crossref
Maxim Sorokin, Elena Poddubskaya, Madina Baranova, Alex Glusker, Lali Kogoniya, Ekaterina Markarova, Daria Allina, Maria Suntsova, Victor Tkachev, Andrew Garazha, Marina Sekacheva & Anton Buzdin. (2020) RNA sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer. Molecular Case Studies 6:2, pages a004945.
Crossref
Ella L. Kim, Maxim Sorokin, Sven Rainer Kantelhardt, Darius Kalasauskas, Bettina Sprang, Julian Fauss, Florian Ringel, Andrew Garazha, Eugene Albert, Nurshat Gaifullin, Christian Hartmann, Nicole Naumann, Sven-Ernö Bikar, Alf Giese & Anton Buzdin. (2020) Intratumoral Heterogeneity and Longitudinal Changes in Gene Expression Predict Differential Drug Sensitivity in Newly Diagnosed and Recurrent Glioblastoma. Cancers 12:2, pages 520.
Crossref
Anton Buzdin, Maxim Sorokin, Andrew Garazha, Alexander Glusker, Alex Aleshin, Elena Poddubskaya, Marina Sekacheva, Ella Kim, Nurshat Gaifullin, Alf Giese, Alexander Seryakov, Pavel Rumiantsev, Sergey Moshkovskii & Alexey Moiseev. (2020) RNA sequencing for research and diagnostics in clinical oncology. Seminars in Cancer Biology 60, pages 311-323.
Crossref
Marianna A. Zolotovskaia, Victor S. Tkachev, Alexander P. Seryakov, Denis V. Kuzmin, Dmitry E. Kamashev, Maxim I. Sorokin, Sergey A. Roumiantsev & Anton A. Buzdin. (2020) Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer. Cancers 12:2, pages 271.
Crossref
Victor Tkachev, Maxim Sorokin, Andrew Garazha, Nicolas Borisov & Anton Buzdin. 2020. Nucleic Acid Detection and Structural Investigations. Nucleic Acid Detection and Structural Investigations 235 255 .
Marianna Zolotovskaia, Maxim Sorokin, Andrew Garazha, Nikolay Borisov & Anton Buzdin. 2020. Nucleic Acid Detection and Structural Investigations. Nucleic Acid Detection and Structural Investigations 207 234 .
Nicolas Borisov, Maxim Sorokin, Andrew Garazha & Anton Buzdin. 2020. Nucleic Acid Detection and Structural Investigations. Nucleic Acid Detection and Structural Investigations 189 206 .
Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin & Anton Buzdin. (2019) Shambhala: a platform-agnostic data harmonizer for gene expression data. BMC Bioinformatics 20:1.
Crossref
Pieter Borger, Marcel Schneider, Lukas Frick, Magda Langiewicz, Maksim Sorokin, Anton Buzdin, Ekaterina Kachaylo, Rolf Graf, Bostjan Humar & Pierre-Alain Clavien. (2019) Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration. Frontiers in Oncology 9.
Crossref
Anna A. Igolkina, Arsenii Zinkevich, Kristina O. Karandasheva, Aleksey A. Popov, Maria V. Selifanova, Daria Nikolaeva, Victor Tkachev, Dmitry Penzar, Daniil M. Nikitin & Anton Buzdin. (2019) H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. Cells 8:9, pages 1034.
Crossref
Daniil Nikitin, Andrew Garazha, Maxim Sorokin, Dmitry Penzar, Victor Tkachev, Alexander Markov, Nurshat Gaifullin, Pieter Borger, Alexander Poltorak & Anton Buzdin. (2019) Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. Cells 8:2, pages 130.
Crossref
Marianna A. Zolotovskaia, Maxim I. Sorokin, Anna A. Emelianova, Nikolay M. Borisov, Denis V. Kuzmin, Pieter Borger, Andrew V. Garazha & Anton A. Buzdin. (2019) Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs. Frontiers in Pharmacology 10.
Crossref
Marianna A. Zolotovskaia, Maxim I. Sorokin, Sergey A. Roumiantsev, Nikolay M. Borisov & Anton A. Buzdin. (2019) Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. Frontiers in Oncology 8.
Crossref
Daniil Nikitin, Maxim Sorokin, Victor Tkachev, Andrew Garazha, Alexander Markov & Anton Buzdin. 2019. Evolution, Origin of Life, Concepts and Methods. Evolution, Origin of Life, Concepts and Methods 85 111 .
Anna A. Emelianova, Denis V. Kuzmin, Pavel V. Panteleev, Maxim Sorokin, Anton A. Buzdin & Tatiana V. Ovchinnikova. (2018) Anticancer Activity of the Goat Antimicrobial Peptide ChMAP-28. Frontiers in Pharmacology 9.
Crossref
Anton Buzdin, Maxim Sorokin, Andrew Garazha, Marina Sekacheva, Ella Kim, Nikolay Zhukov, Ye Wang, Xinmin Li, Souvik Kar, Christian Hartmann, Amir Samii, Alf Giese & Nicolas Borisov. (2018) Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs. Seminars in Cancer Biology 53, pages 110-124.
Crossref
Maxim Sorokin, Roman Kholodenko, Maria Suntsova, Galina Malakhova, Andrew Garazha, Irina Kholodenko, Elena Poddubskaya, Dmitriy Lantsov, Ivan Stilidi, Petr Arhiri, Andreyan Osipov & Anton Buzdin. (2018) Oncobox Bioinformatical Platform for Selecting Potentially Effective Combinations of Target Cancer Drugs Using High-Throughput Gene Expression Data. Cancers 10:10, pages 365.
Crossref
R.O. Aliev & N.M. Borisov. (2018) The Method for Analysis of Expression Data Homogeneity Based On the Student Test. Mathematical Biology and Bioinformatics 13:1, pages 50-67.
Crossref
Daniil Nikitin, Dmitry Penzar, Andrew Garazha, Maxim Sorokin, Victor Tkachev, Nicolas Borisov, Alexander Poltorak, Vladimir Prassolov & Anton A. Buzdin. (2018) Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. Frontiers in Immunology 9.
Crossref
Nicolas Borisov, Victor Tkachev, Anton Buzdin & Ilya Muchnik. 2018. Braverman Readings in Machine Learning. Key Ideas from Inception to Current State. Braverman Readings in Machine Learning. Key Ideas from Inception to Current State 201 212 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.