Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

Ballouz, S., Verleyen, W., Gillis, J.·2015·Bioinformatics
DOI 10.1093/bioinformatics/btv118

Cited by (261)

Items 101–200 of 261

  1. Whole Transcriptome Profiling: An RNA‐Seq Primer and Implications for Pharmacogenomics Research
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  2. Physiological RNA dynamics in RNA-Seq analysis
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  3. AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
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  4. Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks
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  5. A Comprehensive Coexpression Network Analysis in Vibrio cholerae
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  6. Functional characterization of co-phosphorylation networks
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  8. A time-resolved transcriptome landscape of the developing mouse ovary
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  9. Co-phosphorylation networks reveal subtype-specific signaling modules in breast cancer
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  10. HetIG-PreDiG: A Heterogeneous Integrated Graph Model for Predicting Human Disease Genes based on gene expression
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  11. Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia
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  12. CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair
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  13. Accelerated brain aging towards transcriptional inversion in a zebrafish model of familial Alzheimer’s disease
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  14. Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava
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  15. Multiple hot-deck imputation for network inference from RNA sequencing data
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  16. Integrating barcoded neuroanatomy with spatial transcriptional profiling reveals cadherin correlates of projections shared across the cortex
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  17. Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma
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  18. Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters
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  19. The impact of sample size and tissue type on the reproducibility of gene co-expression networks
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  20. A study of tools for differential co-expression analysis for RNA-Seq data
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  21. Voluntary exposure to a toxin: the genetic influence on ethanol consumption
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  23. The fusiform gyrus exhibits differential gene-gene co-expression in Alzheimer's disease
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  24. Cheminformatics and Bioinformatics at the Interface with Systems Biology
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  26. A Framework for Comparison and Assessment of Synthetic RNA-Seq Data
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  27. A global co-expression network approach for connecting genes to specialized metabolic pathways in plants
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  28. Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML
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  29. AuPairWise: a method to estimate RNA-seq replicability through co-expression
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  30. RapaNet: A Web Tool for the Co-Expression Analysis of Brassica rapa Genes
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  31. Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer
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  32. Addressing the looming identity crisis in single cell RNA-seq
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  33. DysRegNet: Patient-specific and confounder-aware dysregulated network inference
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  34. Gene Regulatory Networks: Current Updates and Applications in Plant Biology
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  35. dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data
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  36. Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data
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  37. Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells
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  38. TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework
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  39. High-quality co-expression networks for accurate gene function predictions in the fungal cell factory Aspergillus niger and beyond
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  40. Transcriptional Profiling Reveals the Transcription Factor Networks Regulating the Survival of Striatal Neurons
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  41. HCNetlas: A reference database of human cell type-specific gene networks to aid disease genetic analyses
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  42. Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters
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  43. Data generation and network reconstruction strategies for single cell transcriptomic profiles of CRISPR-mediated gene perturbations
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  44. CoPhosK: A Method for Comprehensive Kinase Substrate Annotation Using Co-phosphorylation Analysis
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  45. Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
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  46. Exploring the role of transcriptional and post‐transcriptional processes in mRNA co‐expression
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  47. Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species
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  48. Constructing Gene Co-functional and Co-regulatory Networks from Public Transcriptomes using Condition-Specific Ensemble Co-expression
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  49. The Performance Comparison of Gene Co-expression Networks of Breast and Prostate Cancer using Different Selection Criteria
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  50. Identification of a global gene expression signature associated with the genetic risk of catastrophic fracture in iPSC ‐derived osteoblasts from Thoroughbred horses
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  51. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes
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  52. Gene Co-expression Network Analysis and Linking Modules to Phenotyping Response in Plants
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  53. A framework for robust differential network modular structure discovery from RNA-seq data
    Tianle Ma, Aidong Zhang · 2016 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  54. Modern Approaches for Transcriptome Analyses in Plants.
    D. Riaño-Pachón, Hector F. Espitia-Navarro, J. J. Riascos, G. Margarido · 2021 · Advances in Experimental Medicine and Biology
  55. Uncovering the transcriptional landscape of Fomes fomentarius during fungal-based material production through gene co-expression network analysis
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  56. Co-Expression Network Modeling Identifies Specific Inflammation and Neurological Disease-Related Genes mRNA Modules in Mood Disorder
    Chunxia Yang, Kun Zhang, Ai‐Xia Zhang, Ning Sun, Zhifen Liu, Kerang Zhang · 2022 · Frontiers in Genetics
  57. Loss of CD98HC phosphorylation by ATM impairs antiporter trafficking and drives glutamate toxicity in Ataxia telangiectasia
    July Carolina Romero, Sonal S. Tonapi, Manish Parihar, Eva Loranc, Henry E. Miller, Liesl A. Lawrence, Nicklas Bassani, Daniel G Robledo, Lin Cao, Jia Nie et al. · 2025 · Nature Communications
  58. Molecular biology and functional genomics of immune-endocrine interactions in the Japanese eel, Anguilla japonica
    Takashi Yada, Miyuki Mekuchi, Nobuhiko Ojima · 2017 · General and Comparative Endocrinology
  59. PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants
    2018
  60. Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data
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  61. Using cross-species co-expression to predict metabolic interactions in microbiomes
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  62. A multi-layered systems biology framework reveals dual-phased regulators and hormonal crosstalk underlying soybean cold tolerance
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  64. Flexibility in Gene Coexpression at Developmental and Evolutionary Timescales
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  65. Construction of Gene Networks Using Expression Profiles
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  68. JEBIN: analyzing gene co-expressions across multiple datasets by joint network embedding
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  69. DysRegNet: Patient‐specific and confounder‐aware dysregulated network inference towards precision therapeutics
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  71. Multimodal bioinformatic analyses of genome-scale expression beyond gene-centric differential expression
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  72. Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics
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  73. Two-tier combinatorial structure to integrate various gene co-expression networks of prostate cancer
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  74. CoCoCoNet: Conserved and Comparative Co-expression Across a Diverse Set of Species
    2020
  75. Not by systems alone: replicability assessment of disease expression signals
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  77. Characterization of Analytic and Experimental Uncertainty of RNA-seq Co-expression Network Determination: Application to SCA2
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  78. Fine construction of gene coexpression network analysis using GTOM and RECODE detected a critical module of neuroblastoma stages 4 and 4S
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  79. Mining of Stress-related Genes in Pigmented and Non-pigmented Rice using Gene Co-expression Network and Clustering Approaches
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  80. PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum
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  81. Deeper insights into long-term survival heterogeneity of Pancreatic Ductal Adenocarcinoma (PDAC) patients using integrative individual- and group-level transcriptome network analyses
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  82. Probabilistic Graphical Models Applied to Biological Networks
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  83. Inferring Gene Regulatory Networks from RNA-seq Data Using Kernel Classification
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  85. Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the noncanonical translatome
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  86. Systems Integration Tool: uma ferramenta para integração e visualização de dados em larga escala e sua aplicação em cana-de-açúcar
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  88. Integrative gene co-expression network analysis reveals protein-coding and LncRNA genes associated with Alzheimer’s disease pathology
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  92. Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data
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  93. Temporal Gene Coexpression Network Analysis Using A Low-rank plus Sparse Framework
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  94. ATM phosphorylation of CD98HC increases antiporter membrane localization and prevents chronic toxic glutamate accumulation in Ataxia telangiectasia
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  95. Cell-type resolved transcriptional network analysis of in vivo cellular senescence following injury
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