Selected article for: "complex structure and high score"

Author: Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano
Title: A high-throughput approach to profile RNA structure
  • Document date: 2017_3_17
  • ID: k23xlzj0_38
    Snippet: We employed CROSS to analyze the structural differences between human coding DNA sequences (CDSs), untranslated regions (UTRs) (total of 217 000 non-redundant sequences each with 3 and 5 UTRs; ENSEMBL 82) and long intergenic non-coding transcripts (14 000 non-redundant sequences; ENSEMBL 82; Supplementary Material; Figure 7B ). In agreement with previous evidence (1), we predict that UTRs are more structured than CDSs (P-value < 2.2e-16; Kolmogor.....
    Document: We employed CROSS to analyze the structural differences between human coding DNA sequences (CDSs), untranslated regions (UTRs) (total of 217 000 non-redundant sequences each with 3 and 5 UTRs; ENSEMBL 82) and long intergenic non-coding transcripts (14 000 non-redundant sequences; ENSEMBL 82; Supplementary Material; Figure 7B ). In agreement with previous evidence (1), we predict that UTRs are more structured than CDSs (P-value < 2.2e-16; Kolmogorov-Smirnov). Long intergenic noncoding transcripts (see Supplementary Material: Long intergenic non-coding RNAs) are found to be less structured, as reported in other studies (25) (P-value < 2.2e-16; Kolmogorov-Smirnov). Indeed, long non-coding RNAs have complex regulatory abilities and their structure could be more flexible and less structured to provide a wide range of interactions (26) . In agreement with previous data (27) , we also observe that the 5 UTR of the amyloid precursor Figure S10 . We note that Rep B contains regions with insufficient sequencing data to determine DMS reactivity (16) that were excluded from the analysis. Our predictions indicate lower structural content at 3 , in line with previous reports indicating poor sequence conservation (only Rep A and B are highly conserved) (24) . The ROC curve of the Z-Score predictions on high-confidence DMS data (10% top and bottom nucleotides, 3 580 fragments) is reported in the corner (AUC 0.75). (B) Predictions of human coding DNA sequences (CDSs), untranslated regions (UTRs) and long-intergenic non-coding RNA (lincRNA) (ENSEMBL version 82; total number of transcripts: 50 000; 14 000 lincRNA isoforms). We predict that the UTRs are more structured than the CDSs, in agreement with previous studies (P-value < 2.2e-16, Kolmogorov-Smirnov) (1) . For each set we show a known example [the APP 5 UTR is more structured, as shown in previous studies (27) ; SERPINE3 has a structured CDS in agreement with PARS data (4); Xist structural content is in agreement with DMSdata (16)].

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