Version History

LNCipedia 5.0 - Dec 15, 2017

Warning: Some transcript and gene IDs have changed in this update. To convert your LNCipedia 4.1 IDs to 5.0, use the “ID history converter” on the search page or this convertion table.

  • Revised filtering pipeline:
    • Removes transcripts that share sequence with coding ORFs (Ensembl)
    • Removes transcripts that are shorter than 200 nt
    • Removes transcripts without GRCh38/hg38 annotation
  • Ensembl updated to most recent version (release 90). Now includes biotypes 'bidirectional_promoter_lncRNA' and 'antisense_RNA'
  • Refseq updated to most recent version (NCBI Annotation Release 106)
  • PRIDE reprocesing pipeline updated
  • Gene and transcript names updated:
    • Over 30,000 transcripts (25% ~ 3,500 genes) now have an official HGNC gene symbol
    • Gene name is now based on Ensembl release 90 protein-coding genes

LNCipedia 4.1 - May 4, 2017

  • FANTOM CAT resource added
  • Ensembl updated to most recent version

LNCipedia 4.0 - May 25, 2016

Warning: Some transcript and gene IDs have changed in this update. To convert your LNCipedia 3.1 IDs to 4.0, use the “ID history converter” on the search page or this convertion table.

  • GRCh38/hg38 reference genome support
  • UCSC trackhub
  • Support for official (HGNC) gene symbols of lncRNAs
  • New tool for coding-potential assessment; CPAT: Coding-Potential Assessment Tool
  • Over 1,500 new PubMed articles linked
  • REST API (for now in beta)
  • Transcript classification based on chromosomal position and orientation
  • New reCAPTCHA
  • Ensembl lncRNAs updated to version 83
  • New source: Sun and Gadad et al., 2015
  • Numerous small improvements to the website and database