Valmei lab

Pra-GE-ATLAS



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  1. CoreSet_* Analysis: includes a set of files listing the genes and events used to describe transcriptional landscape in the manuscript. A total of 6 files are available taking into account three core sets (Pan = alternatively spliced/expressed in the vast majority of samples, Stress = stress-specific, Tissue = tissue-specific) for two regulatory layers (alternative splicing (AS) and gene expression (GE)).
  2. MOFA_* Analysis: MOFA models used in the manuscript to infer shared and unique sources of transcriptional/protein variation across tissues and stressors.
  3. Pra-GE-ATLAS_ConsensusAssembly.* Resource: best set of primary transcripts based on EvidentialGene coding potential. A total of 3 files are available considering coding regions (.cds), proteins (.aa), and transcripts (.fasta).
  4. Pra-GE-ATLAS_EvidentialGene_Alt.* Resource: best set of alternative transcripts based on EvidentialGene coding potential. A total of 3 files are available considering coding regions (.cds), proteins (.aa), and transcripts (.fasta).
  5. Pra-GE-ATLAS_FinalAssembly* Resource: transcript sequences and annotation of the final assembly used for protein analyses constituted by consensus assembly + cdhit 0.905 identity alternative sequences.
  6. Pra-GE-ATLAS_GenEra_PraProteins_* Resource: genEra outputs derived from Pinus radiata protein sequences. Include gen ages, gene family founder events and summaries.
  7. Pra-GE-ATLAS_ProteinModule_* Resource: Information associated with Pra-GE-ATLAS database protein module. Include two files, annotations (*Annotation.tsv) and preprocessed abundance table (*Preprocessed_Abundance.txt).
  8. Pra-GE-ATLAS_TranscriptionalModule_* Resource: Information associated with Pra-GE-ATLAS database transcriptional module. Include four files, gene/event-level annotations (*Pinustaeda_Gene_annotation.txt; *ASEvent_annotation.txt) and expression/splicing table (*Pta_Expression_VST.txt; *Splicing_PSI.txt) computed using Pinus taeda genome.