KTCNlncDB: a database of long non-coding RNAs in human cornea

What is KTCNlncDB?

This database collects long non-coding RNA (lncRNA) data obtained from the analysis of RNA-Seq data from 50 samples. The samples came from KTCN (keratoconus) and non-KTCN human corneas. First of all, it collects 16,331 lncRNAs that we found in the KTCN and non-KTCN transcriptomes. Also, we investigated potential functions of these lncRNAs in the context of lncRNA-RNA interactions. As a result we assigned functions to transcripts coming from 519 genes that are differentially expressed between KTCN and non-KTCN samples. Finally, the database enables BLAST search of lncRNA sequences.

Why we developed KTCNlncDB?

Our motivation was to build a catalogue of human long non-coding RNAs and their functions, with much attention paid to their keratoconus-related regulatory roles. Therefore, we linked differentially expressed genes to one of the following lncRNA-mediated mechanisms:

  • modulating splicing by masking splicing signals
  • triggering RNA editing events
  • guiding protein-coding transcripts to decay in a Staufen-mediated decay (SMD) pathway
  • deregulating miRNA functions by masking miRNA target sites in 3' UTRs of protein-coding genes

How to cite KTCNlncDB?

If you find this resource helpful, please cite:

Szcześniak MW, Kabza M, Karolak JA, Rydzanicz M, Nowak DM, Ginter-Matuszewska 
B, Polakowski P, Ploski R, Szaflik JP, Gajecka M. KTCNlncDB-a first platform to
investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas.
Database (Oxford). 2017 Jan 10;2017. pii: baw168. doi: 10.1093/database/baw168.
PubMed PMID: 28077570; PubMed Central PMCID: PMC5225396

Contact information

The database was developed at the Poznan University of Medical Sciences (Department of Genetics and Pharmaceutical Microbiology) and Polish Academy of Sciences (Institute of Human Genetics) under supervision of prof. Marzena Gajęcka.

For technical issues please contact Michał W. Szcześniak: miszcz@amu.edu.pl.

Important: please note that your results that in whole or part are based upon data from KTCNlncDB can not be published until we provide detailed citation data. This should happen as soon as the database and associated manuscript are accepted for publication.

Copyright © KTCNlncDB 2016