Another class of regulatory non-coding RNAs, miRNAs, have gained significant importance in the past decades as master regulators of gene expression7. MiRNAs bind to the 3’UTR of target genes inhibiting their t
The Ensembl and human genes (GRCh38.p13) (as mart databases), as well as transcript type (as an attribute), were utilized for annotation to categorize the differentially-expressed Ensembl gene IDs into coding genes and non-coding RNAs. Hierarchical cluster analysis was performed to distinguish ...
In this study, we screened a human-specific lncRNA transcript, namely, lymphocyte-specific protein 1 pseudogene 5 (LSP1P5), that functions to maintain fibrosis in keloids. First, we observed that nuclear LSP1P5 is upregulated in both keloid tissue and fibroblasts. Functional analysis revealed th...
If this is true, the abundance of NAT s (cis and trans) may be higher yet, since nuclear non-polyadenylated transcripts are underrepresented in transcript sequence databases. This fact may have important implications for researchers, not only because of their potential biological function but they...
, andpiRNAs, which bind PIWI proteins to induce gene silencing at the transcriptional and post-translational levels. Long non-coding RNAs (longer than 200 nucleotides) are often involved in recruitment of chromatin-remodeling complexes. Historic examples are the X-inactive specific transcript (Xist) ...
(whereskwas the total number of times that the sliding-window of sizek-nt could slide along the transcript,sk= l-k + 1); however, we calibrated it asfiby a factor relating to the length of the pattern,wk, as the features of the transcript for prediction. The features used ...
(Required.) The path of coding reference gtf file. Two mandatory attributes (gene_id "value"; transcript_id "value") should be provided in the file. Some files which has been prepared could be download athttp://www.bioinfo.org/np/ ...
(Additional file2: Tables S5 and S6). mencRNA transcript lengths ranged from 143 to 35,678 bp with a median length of 1550 bp (Fig.1c). The Coding Potential Calculator [14] predicted a high proportion of the transcripts (94.03%) as “non-coding,” significantly more than GENCODE ...
Finally, the merged transcript file along with the original alignment files produced from Tophat were analyzed using Cuffdiff. Libraries were quantile-normalized and differential expression analysis was performed considering genes with FPKM >1 in at least one of the sample groups. Small RNA count ...
Catalogue of gene loci comprising detailed and hierarchical information on their genomic coordinates and that of their constituent transcript isoforms and exons, all of which are assigned unique and stable identifiers. Transcriptome assembly The use of bioinformatic algorithms to reconstruct gene and transcr...