Computational Analysis of “-omics” Data to Identify Transcription Factors Regulating Secondary Metabolism in Rauvolfia serpentina

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Plant Molecular Biology Reporter

• Publication date

  2016-02-01

• Fields of study

  Biology, Chemistry, Computer Science, Environmental Science

• Identifiers
  DOI 10.1007/s11105-015-0919-1
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Comparative Genomics

  2020cited by this paper
• Large-Scale Investigation of Human TF-miRNA Relations Based on Coexpression Profiles

  2014influential reference
• Post-embryonic organogenesis and plant regeneration from tissues: two sides of the same coin?

  2014cited by this paper
• Genome-wide identification of transcription factors and transcription-factor binding sites in oleaginous microalgae Nannochloropsis

  2014cited by this paper
• Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling

  2014influential reference
• Gene clustering in plant specialized metabolism.

  2014cited by this paper
• Visual gene-network analysis reveals the cancer gene co-expression in human endometrial cancer

  2014cited by this paper
• Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

  2014cited by this paper
• Abscisic acid enhanced ajmalicine biosynthesis in hairy roots of Rauvolfia verticillata by upregulating expression of the MEP pathway genes

  2014cited by this paper
• Epigenetic regulation of bud dormancy events in perennial plants

  2014cited by this paper
• Genomic Signatures of Specialized Metabolism in Plants

  2014cited by this paper
• RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters

  2014cited by this paper
• miRNAting control of DNA methylation

  2014cited by this paper
• Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis

  2014cited by this paper
• Reciprocal crosstalk between jasmonate and salicylate defence-signalling pathways modulates plant volatile emission and herbivore host-selection behaviour

  2014cited by this paper
• Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network

  2013cited by this paper
• Recent progress in the metabolic engineering of alkaloids in plant systems.

  2013cited by this paper
• Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics.

  2013cited by this paper
• Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways

  2013cited by this paper
• Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags

  2013cited by this paper
• The remarkable pliability and promiscuity of specialized metabolism

  2013cited by this paper
• Epigenetic Memory and Control in Plants

  2013cited by this paper
• Prospecting for Novel Plant-Derived Molecules of Rauvolfia serpentina as Inhibitors of Aldose Reductase, a Potent Drug Target for Diabetes and Its Complications

  2013cited by this paper
• Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

  2013cited by this paper
• Mapping functional transcription factor networks from gene expression data

  2013cited by this paper
• The ORCA2 transcription factor plays a key role in regulation of the terpenoid indole alkaloid pathway

  2013cited by this paper
• Introduction to Biological Networks

  2013cited by this paper
• iTRAQ protein profile analysis of Citrus sinensis roots in response to long-term boron-deficiency.

  2013cited by this paper
• Transcriptomic analysis highlights epigenetic and transcriptional regulation during zygotic embryo development of Pinus pinaster

  2013cited by this paper
• Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches1[C][W][OA]

  2012cited by this paper
• Methanolic Root Extract of Rauwolfia serpentina Improves the Glucose Tolerance in Wister Mice

  2012cited by this paper
• Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-seq).

  2012cited by this paper
• Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis

  2012cited by this paper
• Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

  2012influential reference
• Transcriptional regulation of plant secondary metabolism.

  2012cited by this paper
• Intraspecific directed deterrence by the mustard oil bomb in a desert plant.

  2012cited by this paper
• clusterMaker: a multi-algorithm clustering plugin for Cytoscape

  2011influential reference
• The Transcription Factor CrWRKY1 Positively Regulates the Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus1[W][OA]

  2011influential reference
• The regulatory epicenter of miRNAs

  2011cited by this paper
• Metabolic engineering of the plant primary-secondary metabolism interface.

  2011cited by this paper
• Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

  2011cited by this paper
• The Transcription Factor CrWRKY1 Positively Regulates the Terpenoid Indole Alkaloid Biosynthesis in

  2011influential reference
• De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

  2011cited by this paper
• Ethnobotanical aspects of Rauvolfia serpentina (L). Benth. ex Kurz. in India, Nepal and Bangladesh

  2011influential reference
• Ensembl BioMarts: a hub for data retrieval across taxonomic space

  2011cited by this paper
• From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants.

  2011cited by this paper
• A general co-expression network-based approach to gene expression analysis: comparison and applications

  2010cited by this paper
• Entropic origin of disassortativity in complex networks.

  2010cited by this paper
• Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana

  2010cited by this paper
• agriGO: a GO analysis toolkit for the agricultural community

  2010cited by this paper
• Functions and biotechnology of plant secondary metabolites

  2010cited by this paper
• Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction

  2010cited by this paper
• Computational identification of plant transcription factors and the construction of the PlantTFDB database.

  2010cited by this paper
• Annual Plant Reviews Volume 39 2nd Edition Functions and Biotechnology of Plant Secondary Metabolites

  2010cited by this paper
• ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

  2009cited by this paper
• Functional analysis of transcription factors in Arabidopsis.

  2009influential reference
• Arabidopsis gene co-expression network and its functional modules

  2009influential reference
• Computational methods for discovering gene networks from expression data

  2009cited by this paper
• Robustness In Scale-Free Networks: Comparing Directed And Undirected Networks

  2008cited by this paper
• Alkaloid biosynthesis: metabolism and trafficking.

  2008cited by this paper
• Graph Clustering Via a Discrete Uncoupling Process

  2008influential reference
• annot8r: GO, EC and KEGG annotation of EST datasets

  2008cited by this paper
• Comprehensive Flavonol Profiling and Transcriptome Coexpression Analysis Leading to Decoding Gene–Metabolite Correlations in Arabidopsis[W][OA]

  2008cited by this paper
• Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants.

  2008cited by this paper
• The Gene Ontology − Providing a Functional Role in Proteomic Studies

  2008cited by this paper
• Light-regulated transcriptional networks in higher plants

  2007cited by this paper
• Statistics IV: Interpreting the results of statistical tests

  2007influential reference
• The iridoid pathway in Catharanthus roseus alkaloid biosynthesis

  2007cited by this paper
• PlnTFDB: an integrative plant transcription factor database

  2007cited by this paper
• Catharanthus terpenoid indole alkaloids: biosynthesis and regulation

  2007cited by this paper
• An Introduction to Systems Biology Design Principles of Biological Circuits

  2007cited by this paper
• Approaches for extracting practical information from gene co-expression networks in plant biology.

  2007influential reference
• Targets of RNA-directed DNA methylation.

  2007cited by this paper
• Chromatin modification and remodeling during early seed development.

  2007cited by this paper
• [Milestones of cardiovascular therapy. IV. Reserpine].

  2007cited by this paper
• Transcription factors involved in terpenoid indole alkaloid biosynthesis in Catharanthus roseus

  2007cited by this paper
• MicroRNA regulation of human protein protein interaction network.

  2007cited by this paper
• Silverleaf Whitefly Induces Salicylic Acid Defenses and Suppresses Effectual Jasmonic Acid Defenses1[W][OA]

  2006cited by this paper
• Transcriptome analysis in Catharanthus roseus leaves and roots for comparative terpenoid indole alkaloid profiles.

  2006cited by this paper
• The igraph software package for complex network research

  2006cited by this paper
• Chemistry and biology of monoterpene indole alkaloid biosynthesis.

  2006cited by this paper
• Isoprenoid biosynthesis in plant chloroplasts via the MEP pathway: Direct thylakoid/ferredoxin‐dependent photoreduction of GcpE/IspG

  2006cited by this paper
• TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes

  2005cited by this paper
• Scale-free networks in cell biology

  2005cited by this paper
• Purification, molecular cloning, and cell-specific gene expression of the alkaloid-accumulation associated protein CrPS in Catharanthus roseus.

  2005cited by this paper
• The kappa statistic in reliability studies: use, interpretation, and sample size requirements.

  2005cited by this paper
• Transport of isoprenoid intermediates across chloroplast envelope membranes.

  2005cited by this paper
• A role for intra- and intercellular translocation in natural product biosynthesis.

  2005cited by this paper
• Reserpine-induced central effects: pharmacological evidence for the lack of central effects of reserpine methiodide.

  2005cited by this paper
• Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks in Arabidopsis by Integration of Metabolomics and Transcriptomics*

  2005cited by this paper
• Functional expression of an ajmaline pathway-specific esterase from Rauvolfia in a novel plant-virus expression system

  2005cited by this paper
• The secondary metabolism of Arabidopsis thaliana: growing like a weed.

  2005cited by this paper
• The Universal Protein Resource (UniProt)

  2004cited by this paper
• Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae

  2004cited by this paper
• Spectrophotometric Determination of Rauwolfia Alkaloids: Estimation of Reserpine in Pharmaceuticals

  2004cited by this paper
• Cytoscape: a software environment for integrated models of biomolecular interaction networks.

  2003influential reference
• A 2-oxoglutarate-dependent dioxygenase is integrated in DIMBOA-biosynthesis.

  2003cited by this paper
• An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants

  2003cited by this paper
• AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors

  2003influential reference
• bZIP transcription factors in Arabidopsis

  2002cited by this paper

• Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa.

  2023cites this paper
• Computational identification of key genes and regulatory miRNAs responsible for differential regulation of host-pathogen response during early and late blight diseases in tomato

  2022cites this paper
• Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids

  2022cites this paper
• Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions

  2022cites this paper
• Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

  2021cites this paper
• Rauwolfia serpentina

  2021cites this paper
• Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge.

  2020cites this paper
• Comparative transcriptomics reveals candidate transcription factors involved in costunolide biosynthesis in medicinal plant-Saussurea lappa.

  2020cites this paper
• UPLC and ESI-MS analysis of metabolites of Rauvol fi a tetraphylla L . and their spatial localization using desorption electrospray ionization ( DESI ) mass spectrometric imaging

  2019cites this paper
• Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology.

  2019cites this paper
• UPLC and ESI-MS analysis of metabolites of Rauvolfia tetraphylla L. and their spatial localization using desorption electrospray ionization (DESI) mass spectrometric imaging.

  2019cites this paper
• Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

  2018cites this paper
• Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.)

  2017cites this paper
• Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus

  2016influential citation