Abstract 4447: Analysis of small RNA-seq data for differential expression of small noncoding RNAs in human colorectal cancer

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease.

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Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽

10.12688/f1000research.18142.1 ◽

2019 ◽

Vol 8 ◽

pp. 232

Author(s):

Lorena Pantano ◽

Francisco Pantano ◽

Eulalia Marti ◽

Shannan Ho Sui

Keyword(s):

Gene Regulation ◽

Small Rna ◽

Small Rnas ◽

Noncoding Rnas ◽

Model Organisms ◽

Visualization Tool ◽

Rna Seq ◽

Small Noncoding Rnas ◽

Different Types ◽

Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

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DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

Non-Coding RNA ◽

10.3390/ncrna8010009 ◽

2022 ◽

Vol 8 (1) ◽

pp. 9

Author(s):

Jin Zhang ◽

Abdallah M. Eteleeb ◽

Emily B. Rozycki ◽

Matthew J. Inkman ◽

Amy Ly ◽

...

Keyword(s):

Colorectal Cancer ◽

Small Rna ◽

Small Rnas ◽

Noncoding Rna ◽

Noncoding Rnas ◽

Biologically Relevant ◽

Small Noncoding Rna ◽

Small Noncoding Rnas ◽

Rna Analysis ◽

Length Range

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

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