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Mishra DC, Arora D, Budhlakoti N, Solanke AU, Mithra SVACR, Kumar A, Pandey PS, Srivastava S, Kumar S, Farooqi MS, Lal SB, Rai A, Chaturvedi KK. Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. Front Genet 2022; 12:780599. [PMID: 35198001 PMCID: PMC8859635 DOI: 10.3389/fgene.2021.780599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 02/04/2023] Open
Abstract
Rice is an important staple food grain consumed by most of the population around the world. With climate and environmental changes, rice has undergone a tremendous stress state which has impacted crop production and productivity. Plant growth hormones are essential component that controls the overall outcome of the growth and development of the plant. Cytokinin is a hormone that plays an important role in plant immunity and defense systems. Trans-zeatin is an active form of cytokinin that can affect plant growth which is mediated by a multi-step two-component phosphorelay system that has different roles in various developmental stages. Systems biology is an approach for pathway analysis to trans-zeatin treated rice that could provide a deep understanding of different molecules associated with them. In this study, we have used a weighted gene co-expression network analysis method to identify the functional modules and hub genes involved in the cytokinin pathway. We have identified nine functional modules comprising of different hub genes which contribute to the cytokinin signaling route. The biological significance of these identified hub genes has been tested by applying well-proven statistical techniques to establish the association with the experimentally validated QTLs and annotated by the DAVID server. The establishment of key genes in different pathways has been confirmed. These results will be useful to design new stress-resistant cultivars which can provide sustainable yield in stress-specific conditions.
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Affiliation(s)
- Dwijesh Chandra Mishra
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Devender Arora
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- National Institute of Animal Science, Rural Development Administration, Jeonju, South Korea
| | - Neeraj Budhlakoti
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | | | - Anuj Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - P. S. Pandey
- Agricultural Education Division, Indian Council of Agricultural Research, New Delhi, India
| | - Sudhir Srivastava
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sanjeev Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - M. S. Farooqi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - S. B. Lal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - K. K. Chaturvedi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- *Correspondence: K. K. Chaturvedi,
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Yu C, Qi X, Lin Y, Li Y, Shen B. iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data. J Biomed Inform 2020; 112:103605. [PMID: 33096244 DOI: 10.1016/j.jbi.2020.103605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 02/05/2023]
Abstract
The latest advances in the next generation sequencing technology have greatly facilitated the extensive research of genomics and transcriptomics, thereby promoting the decoding of carcinogenesis with unprecedented resolution. Considering the contribution of analyzing high-throughput multi-omics data to the exploration of cancer molecular mechanisms, an integrated tool for heterogeneous multi-omics data analysis (iODA) is proposed for the systems-level interpretation of multi-omics data, i.e., transcriptomic profiles (mRNA or miRNA expression data) and protein-DNA interactions (ChIP-Seq data). Considering the data heterogeneity, iODA can compare six statistical algorithms in differential analysis for the selected sample data and assist users in choosing the globally optimal one for dysfunctional mRNA or miRNA identification. Since molecular signatures are more consistent at the pathway level than at the gene level, the tool is able to enrich the identified dysfunctional molecules onto the KEGG pathways and extracted the consistent items as key components for further pathogenesis investigation. Compared with other tools, iODA is multi-functional for the systematic analysis of different level of omics data, and its analytical power was demonstrated through case studies of single and cross-level prostate cancer omics data. iODA is open source under GNU GPL and can be downloaded from http://www.sysbio.org.cn/iODA.
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Affiliation(s)
- Chunjiang Yu
- School of Biotechnology, Suzhou Industrial Park Institute of Service Outsourcing, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Xin Qi
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, Suzhou, China; Center for Systems Biology, Soochow University, Suzhou, China
| | - Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Yin Li
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
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Tang J, Wang Y, Luo Y, Fu J, Zhang Y, Li Y, Xiao Z, Lou Y, Qiu Y, Zhu F. Computational advances of tumor marker selection and sample classification in cancer proteomics. Comput Struct Biotechnol J 2020; 18:2012-2025. [PMID: 32802273 PMCID: PMC7403885 DOI: 10.1016/j.csbj.2020.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer proteomics has become a powerful technique for characterizing the protein markers driving transformation of malignancy, tracing proteome variation triggered by therapeutics, and discovering the novel targets and drugs for the treatment of oncologic diseases. To facilitate cancer diagnosis/prognosis and accelerate drug target discovery, a variety of methods for tumor marker identification and sample classification have been developed and successfully applied to cancer proteomic studies. This review article describes the most recent advances in those various approaches together with their current applications in cancer-related studies. Firstly, a number of popular feature selection methods are overviewed with objective evaluation on their advantages and disadvantages. Secondly, these methods are grouped into three major classes based on their underlying algorithms. Finally, a variety of sample separation algorithms are discussed. This review provides a comprehensive overview of the advances on tumor maker identification and patients/samples/tissues separations, which could be guidance to the researches in cancer proteomics.
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Key Words
- ANN, Artificial Neural Network
- ANOVA, Analysis of Variance
- CFS, Correlation-based Feature Selection
- Cancer proteomics
- Computational methods
- DAPC, Discriminant Analysis of Principal Component
- DT, Decision Trees
- EDA, Estimation of Distribution Algorithm
- FC, Fold Change
- GA, Genetic Algorithms
- GR, Gain Ratio
- HC, Hill Climbing
- HCA, Hierarchical Cluster Analysis
- IG, Information Gain
- LDA, Linear Discriminant Analysis
- LIMMA, Linear Models for Microarray Data
- MBF, Markov Blanket Filter
- MWW, Mann–Whitney–Wilcoxon test
- OPLS-DA, Orthogonal Partial Least Squares Discriminant Analysis
- PCA, Principal Component Analysis
- PLS-DA, Partial Least Square Discriminant Analysis
- RF, Random Forest
- RF-RFE, Random Forest with Recursive Feature Elimination
- SA, Simulated Annealing
- SAM, Significance Analysis of Microarrays
- SBE, Sequential Backward Elimination
- SFS, and Sequential Forward Selection
- SOM, Self-organizing Map
- SU, Symmetrical Uncertainty
- SVM, Support Vector Machine
- SVM-RFE, Support Vector Machine with Recursive Feature Elimination
- Sample classification
- Tumor marker selection
- sPLSDA, Sparse Partial Least Squares Discriminant Analysis
- t-SNE, Student t Distribution
- χ2, Chi-square
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Affiliation(s)
- Jing Tang
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziyu Xiao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Feng Zhu
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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Khan A, Rehman Z, Hashmi HF, Khan AA, Junaid M, Sayaf AM, Ali SS, Hassan FU, Heng W, Wei DQ. An Integrated Systems Biology and Network-Based Approaches to Identify Novel Biomarkers in Breast Cancer Cell Lines Using Gene Expression Data. Interdiscip Sci 2020; 12:155-168. [DOI: 10.1007/s12539-020-00360-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 12/31/2019] [Accepted: 01/18/2020] [Indexed: 12/12/2022]
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Jia WQ, Liu YY, Feng XY, Xu WR, Cheng XC. Discovery of novel and highly selective PI3Kδ inhibitors based on the p110δ crystal structure. J Biomol Struct Dyn 2019; 38:2499-2508. [PMID: 31232196 DOI: 10.1080/07391102.2019.1635531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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