Abstract
BackgroundThe ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood. Currently, a database that integrates information on TM relevant genes is missing.DescriptionTo provide a resource for studies that dissect TM features, we here introduce the TelNet database at http://www.cancertelsys.org/telnet/. It offers a comprehensive compilation of more than 2000 human and 1100 yeast genes linked to telomere maintenance. These genes were annotated in terms of TM mechanism, associated specific functions and orthologous genes, a TM significance score and information from peer-reviewed literature. This TM information can be retrieved via different search and view modes and evaluated for a set of genes as demonstrated for an exemplary application.ConclusionTelNet supports the annotation of genes identified from bioinformatics analysis pipelines to reveal possible connections with TM networks. We anticipate that TelNet will be a helpful resource for researchers that study telomeres.
Highlights
The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery
TelNet supports the annotation of genes identified from bioinformatics analysis pipelines to reveal possible connections with telomere maintenance (TM) networks
To quantify the significance of a given gene for TM we introduced the TelNet score ranging from 1 to 10 that was automatically calculated from information entered into the TelNet database (Table 2)
Summary
The gene annotations provided by TelNet largely facilitate a distinction between different TM mechanisms for a gene set of interest by providing corresponding functional terms and a significance ranking With these features, TelNet supports the identification of TM networks in various ways. Additional file 1: The table lists the 1022 genes identified in the pancancer analyis described in the context of Fig. 4. These genes have either significant changes of gene expression in tumor over normal cells (p-value < 0.01, log ratio below − 0.782 or above 0.852) or an (anti-) correlation of gene expression and telomere length ratios
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