JustRNA

JustRNA provides an extensive expression-profiling database and analysis resources for plant long noncoding RNAs (lncRNAs), enabling investigation of their expression patterns, microRNA targeting, genomic associations, co-expression networks, and transcriptional regulation.

Key Features:

• Extensive annotation database: 1,088,565 annotated lncRNAs across 80 plant species.
• RNA-seq dataset: 3,692 RNA-seq samples from 825 distinct conditions in six model plants for expression profiling.
• Functional network reconstruction: Reconstruction of lncRNA-associated functional networks to infer regulatory relationships.
• Genomic association analysis: Analysis of genomic proximity and associations between lncRNAs and nearby genes.
• MicroRNA target prediction: Prediction of microRNA targets involving lncRNAs.
• Co-expression analysis: Co-expression analysis between lncRNAs and protein-coding genes to support interaction inference.
• ChIP-seq integration: Integration of ChIP-seq data for transcription factors and histone modifications across plant species.

Scientific Applications:

• Regulatory mechanism elucidation: Use of co-expression and network data to infer lncRNA roles in gene regulation.
• Gene interaction studies: Investigation of lncRNA–gene and lncRNA–microRNA interactions via genomic association and target prediction.
• Transcriptional regulation insights: Analysis of ChIP-seq and expression data to study transcription factor and histone-modification influences on lncRNA expression.

Methodology:

Functional network reconstruction, genomic association analysis, microRNA target prediction, co-expression analysis, and integration of RNA-seq and ChIP-seq data.