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SANe: The Seed Active Network for Discovering Transcriptional Regulatory Programs of Seed Development

https://doi.org/10.1101/165894
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Cytoscape: Software for Visualization and Analysis of Biological Networks
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ATDOF5.8 protein is the upstream regulator of ANAC069 and is responsive to abiotic stress
inferredcites →https://doi.org/10.1016/j.molp.2017.10.014openalex-snapshot
Regulation of Seed Vigor by Manipulation of Raffinose Family Oligosaccharides in Maize and Arabidopsis thaliana
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Functional symmetry of the B3 network controlling seed development
inferredcites →https://doi.org/10.1016/j.plantsci.2015.03.021openalex-snapshot
Role of B3 domain transcription factors of the AFL family in maize kernel filling
inferredcites →https://doi.org/10.1016/j.plantsci.2016.02.015openalex-snapshot
Galactinol as marker for seed longevity
inferredcites →https://doi.org/10.1016/j.plantsci.2016.06.013openalex-snapshot
Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds
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Carbon dioxide concentrations are very high in developing oilseeds
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From milliseconds to lifetimes: tracking the dynamic behavior of transcription factors in gene networks
inferredcites →https://doi.org/10.1016/s0092-8674(00)81463-4openalex-snapshot
Arabidopsis LEAFY COTYLEDON1 Is Sufficient to Induce Embryo Development in Vegetative Cells
inferredcites →https://doi.org/10.1038/nature03145openalex-snapshot
Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds
inferredcites →https://doi.org/10.1038/nbt.1603openalex-snapshot
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/ncomms6302openalex-snapshot
Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress
inferredcites →https://doi.org/10.1038/ng1532openalex-snapshot
Reverse engineering of regulatory networks in human B cells
inferredcites →https://doi.org/10.1038/nn.4353openalex-snapshot
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder
inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot
Transcription factors: from enhancer binding to developmental control
inferredcites →https://doi.org/10.1038/s41467-018-03013-5openalex-snapshot
Site-specific phosphorylation of TRANSPARENT TESTA GLABRA1 mediates carbon partitioning in Arabidopsis seeds
inferredcites →https://doi.org/10.1038/s41598-017-09542-1openalex-snapshot
GBF3 transcription factor imparts drought tolerance in Arabidopsis thaliana
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FUSCA3encodes a protein with a conserved VP1/ABI3‐like B3 domain which is of functional importance for the regulation of seed maturation inArabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.0508418102openalex-snapshot
MINISEED3 ( MINI3 ), a WRKY family gene, and HAIKU2 ( IKU2 ), a leucine-rich repeat ( LRR ) KINASE gene, are regulators of seed size in Arabidopsis
inferredcites →https://doi.org/10.1073/pnas.1003530107openalex-snapshot
Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors
inferredcites →https://doi.org/10.1073/pnas.1222061110openalex-snapshot
Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed
inferredcites →https://doi.org/10.1073/pnas.1610985113openalex-snapshot
Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.95.25.14863openalex-snapshot
Cluster analysis and display of genome-wide expression patterns
inferredcites →https://doi.org/10.1073/pnas.96.24.13839openalex-snapshot
PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis
inferredcites →https://doi.org/10.1080/15592324.2015.1034421openalex-snapshot
Regulation of grain yield in rice under well-watered and drought stress conditions by GUDK
inferredcites →https://doi.org/10.1093/bioinformatics/17.4.309openalex-snapshot
Validating clustering for gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/bti334openalex-snapshot
DATF: a database of Arabidopsis transcription factors
inferredcites →https://doi.org/10.1093/bioinformatics/btl492openalex-snapshot
A scalable method for integration and functional analysis of multiple microarray datasets
inferredcites →https://doi.org/10.1093/bioinformatics/btn237openalex-snapshot
The Sleipnir library for computational functional genomics
inferredcites →https://doi.org/10.1093/bioinformatics/btp588openalex-snapshot
Detailing regulatory networks through large scale data integration
inferredcites →https://doi.org/10.1093/bioinformatics/btq078openalex-snapshot
SPICi: a fast clustering algorithm for large biological networks
inferredcites →https://doi.org/10.1093/bioinformatics/btq430openalex-snapshot
Cytoscape Web: an interactive web-based network browser
inferredcites →https://doi.org/10.1093/biostatistics/4.2.249openalex-snapshot
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
inferredcites →https://doi.org/10.1093/biostatistics/kxv027openalex-snapshot
Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
inferredcites →https://doi.org/10.1093/emboj/cdg444openalex-snapshot
Arabidopsis MSI1 is a component of the MEA/FIE Polycomb group complex and required for seed development
inferredcites →https://doi.org/10.1093/jxb/erp141openalex-snapshot
The evolution of the starch biosynthetic pathway in cereals and other grasses
inferredcites →https://doi.org/10.1093/mp/ssn081openalex-snapshot
Phosphate Starvation Responses and Gibberellic Acid Biosynthesis are Regulated by the MYB62 Transcription Factor in Arabidopsis
inferredcites →https://doi.org/10.1093/nar/27.1.297openalex-snapshot
Plant cis-acting regulatory DNA elements (PLACE) database: 1999
inferredcites →https://doi.org/10.1093/nar/gkl887openalex-snapshot
NCBI GEO: mining tens of millions of expression profiles--database and tools update
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NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
inferredcites →https://doi.org/10.1093/nar/gkq1120openalex-snapshot
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update
inferredcites →https://doi.org/10.1093/nar/gkq1147openalex-snapshot
COXPRESdb: a database to compare gene coexpression in seven model animals
inferredcites →https://doi.org/10.1093/nar/gks1122openalex-snapshot
RiceFREND: a platform for retrieving coexpressed gene networks in rice
inferredcites →https://doi.org/10.1093/nar/gkt1016openalex-snapshot
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
inferredcites →https://doi.org/10.1093/nar/gkt281openalex-snapshot
PlantGSEA: a gene set enrichment analysis toolkit for plant community
inferredcites →https://doi.org/10.1093/nar/gkv362openalex-snapshot
RSAT 2015: Regulatory Sequence Analysis Tools
inferredcites →https://doi.org/10.1093/pcp/pci048openalex-snapshot
LEAFY COTYLEDON1 Controls Seed Storage Protein Genes through Its Regulation of FUSCA3 and ABSCISIC ACID INSENSITIVE3
inferredcites →https://doi.org/10.1093/pcp/pcv165openalex-snapshot
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
inferredcites →https://doi.org/10.1094/mpmi-20-5-0492openalex-snapshot
OsWRKY13 Mediates Rice Disease Resistance by Regulating Defense-Related Genes in Salicylate- and Jasmonate-Dependent Signaling
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1103/physreve.69.026113openalex-snapshot
Finding and evaluating community structure in networks
inferredcites →https://doi.org/10.1104/pp.104.046367openalex-snapshot
GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox
inferredcites →https://doi.org/10.1104/pp.104.047977openalex-snapshot
The Capacity of Green Oilseeds to Utilize Photosynthesis to Drive Biosynthetic Processes
inferredcites →https://doi.org/10.1104/pp.105.063628openalex-snapshot
Light Enables a Very High Efficiency of Carbon Storage in Developing Embryos of Rapeseed
inferredcites →https://doi.org/10.1104/pp.105.072280openalex-snapshot
AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks
inferredcites →https://doi.org/10.1104/pp.106.077388openalex-snapshot
Characterization of the Class IV Homeodomain-Leucine Zipper Gene Family in Arabidopsis
inferredcites →https://doi.org/10.1104/pp.106.086694openalex-snapshot
Arabidopsis Seed Development and Germination Is Associated with Temporally Distinct Metabolic Switches
inferredcites →https://doi.org/10.1104/pp.106.093013openalex-snapshot
Coordinate Regulation of Phospho enol pyruvate Carboxylase and Phospho enol pyruvate Carboxykinase by Light and CO 2 during C 4 Photosynthesis
inferredcites →https://doi.org/10.1104/pp.109.148494openalex-snapshot
Large-Scale Reverse Genetics in Arabidopsis: Case Studies from the Chloroplast 2010 Project
inferredcites →https://doi.org/10.1104/pp.110.159517openalex-snapshot
Coexpression Analysis Identifies Rice Starch Regulator1, a Rice AP2/EREBP Family Transcription Factor, as a Novel Rice Starch Biosynthesis Regulator
inferredcites →https://doi.org/10.1104/pp.110.161752openalex-snapshot
Molecular and Physiological Analysis of Drought Stress in Arabidopsis Reveals Early Responses Leading to Acclimation in Plant Growth
inferredcites →https://doi.org/10.1104/pp.110.161844openalex-snapshot
A Suite of Lotus japonicus Starch Mutants Reveals Both Conserved and Novel Features of Starch Metabolism
inferredcites →https://doi.org/10.1104/pp.110.168641openalex-snapshot
Coordinated Activation of Cellulose and Repression of Lignin Biosynthesis Pathways in Rice
inferredcites →https://doi.org/10.1104/pp.113.220988openalex-snapshot
Distinct Roles of LAFL Network Genes in Promoting the Embryonic Seedling Fate in the Absence of VAL Repression
inferredcites →https://doi.org/10.1104/pp.113.226019openalex-snapshot
Rice WRKY13 Regulates Cross Talk between Abiotic and Biotic Stress Signaling Pathways by Selective Binding to Different cis-Elements
inferredcites →https://doi.org/10.1104/pp.15.00943openalex-snapshot
TRANSPARENT TESTA GLABRA1 Regulates the Accumulation of Seed Storage Reserves in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.000877openalex-snapshot
Contrapuntal Networks of Gene Expression during Arabidopsis Seed Filling[W]
inferredcites →https://doi.org/10.1105/tpc.001404openalex-snapshot
TRANSPARENT TESTA GLABRA2 , a Trichome and Seed Coat Development Gene of Arabidopsis, Encodes a WRKY Transcription Factor
inferredcites →https://doi.org/10.1105/tpc.001941openalex-snapshot
Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth
inferredcites →https://doi.org/10.1105/tpc.006973openalex-snapshot
LEAFY COTYLEDON1-LIKE Defines a Class of Regulators Essential for Embryo Development
inferredcites →https://doi.org/10.1105/tpc.010098openalex-snapshot
The Arabidopsis TT2 Gene Encodes an R2R3 MYB Domain Protein That Acts as a Key Determinant for Proanthocyanidin Accumulation in Developing Seed
inferredcites →https://doi.org/10.1105/tpc.10.3.383openalex-snapshot
PEI1, an Embryo-Specific Zinc Finger Protein Gene Required for Heart-Stage Embryo Formation in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.105.039925openalex-snapshot
A Network of Local and Redundant Gene Regulation Governs Arabidopsis Seed Maturation
inferredcites →https://doi.org/10.1105/tpc.106.040824openalex-snapshot
AGL80 Is Required for Central Cell and Endosperm Development in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.106.043018openalex-snapshot
A Membrane-Bound NAC Transcription Factor Regulates Cell Division inArabidopsis
inferredcites →https://doi.org/10.1105/tpc.106.047472openalex-snapshot
KANADI and Class III HD-Zip Gene Families Regulate Embryo Patterning and Modulate Auxin Flow during Embryogenesis in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.106.048165openalex-snapshot
A Novel Transcriptional Cascade Regulating Expression of Heat Stress Proteins during Seed Development of Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.114.130021openalex-snapshot
MYB118 Represses Endosperm Maturation in Seeds of Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.114.131417openalex-snapshot
Arabidopsis Ensemble Reverse-Engineered Gene Regulatory Network Discloses Interconnected Transcription Factors in Oxidative Stress
inferredcites →https://doi.org/10.1105/tpc.114.134585openalex-snapshot
A Cascade of Sequentially Expressed Sucrose Transporters in the Seed Coat and Endosperm Provides Nutrition for the Arabidopsis Embryo
inferredcites →https://doi.org/10.1105/tpc.15.00454openalex-snapshot
The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity
inferredcites →https://doi.org/10.1105/tpc.16.00158openalex-snapshot
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments
inferredcites →https://doi.org/10.1105/tpc.16.00490openalex-snapshot
MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms
inferredcites →https://doi.org/10.1105/tpc.16.00612openalex-snapshot
Transcriptional Activation of Two Delta-9 Palmitoyl-ACP Desaturase Genes by MYB115 and MYB118 Is Critical for Biosynthesis of Omega-7 Monounsaturated Fatty Acids in the Endosperm of Arabidopsis Seeds
inferredcites →https://doi.org/10.1105/tpc.6.5.589openalex-snapshot
fusca3: A Heterochronic Mutation Affecting Late Embryo Development in Arabidopsis
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ABERRANT TESTA SHAPE encodes a KANADI family member, linking polarity determination to separation and growth of Arabidopsis ovule integuments
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03092.xopenalex-snapshot
WRINKLED1 specifies the regulatory action of LEAFY COTYLEDON2 towards fatty acid metabolism during seed maturation in Arabidopsis
inferredcites →https://doi.org/10.1111/j.1365-313x.2009.03817.xopenalex-snapshot
Arabidopsis NF‐YB subunits LEC1 and LEC1‐LIKE activate transcription by interacting with seed‐specific ABRE‐binding factors
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A brassinosteroid transcriptional network revealed by genome‐wide identification of BESI target genes in Arabidopsis thaliana
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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The A rabidopsis embryo as a miniature morphogenesis model
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Adjustments of embryonic photosynthetic activity modulate seed fitness in A rabidopsis thaliana
inferredcites →https://doi.org/10.1111/tpj.13106openalex-snapshot
Potential targets of VIVIPAROUS 1/ ABI 3‐ LIKE 1 ( VAL 1) repression in developing Arabidopsis thaliana embryos
inferredcites →https://doi.org/10.1126/science.280.5362.446openalex-snapshot
Maternal Control of Embryogenesis by MEDEA , a Polycomb Group Gene in Arabidopsis
inferredcites →https://doi.org/10.1128/mcb.01490-07openalex-snapshot
Dyskerin Is a Component of the Arabidopsis Telomerase RNP Required for Telomere Maintenance
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Seed-Development Programs: A Systems Biology–Based Comparison Between Dicots and Monocots
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Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
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PAGE: Parametric Analysis of Gene Set Enrichment
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WGCNA: an R package for weighted correlation network analysis
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PLANEX: the plant co-expression database
inferredcites →https://doi.org/10.1186/1471-2229-14-97openalex-snapshot
ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks
inferredcites →https://doi.org/10.1242/dev.01186openalex-snapshot
Asymmetric leaf development and blade expansion in Arabidopsis are mediated by KANADI and YABBY activities
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Scale-free networks in cell biology
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Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
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Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
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Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods
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Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes
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Seed Embryo Development Is Regulated via an AN3-MINI3 Gene Cascade
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A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis
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RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response
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Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos
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Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages
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ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.pbi.2018.10.005openalex-snapshot
Computational prediction of gene regulatory networks in plant growth and development
inferred← citeshttps://doi.org/10.1016/j.plantsci.2018.03.011openalex-snapshot
Metabolic engineering to increase crop yield: From concept to execution
inferred← citeshttps://doi.org/10.1093/gigascience/giz151openalex-snapshot
Retracted: Dissection of soybean populations according to selection signatures based on whole-genome sequences
inferred← citeshttps://doi.org/10.12688/f1000research.17207.1openalex-snapshot
Recent advances in gene function prediction using context-specific coexpression networks in plants
inferred← citeshttps://doi.org/10.2174/0115748936304167240530091051openalex-snapshot
Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development
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