STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts
Nicholas K Akers1, Eric E Schadt1, Bojan Losic1
1Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Bioinformatics (Oxford, England)
|February 24, 2018
Summary
STARChip is a new software for detecting circular RNAs (circRNAs) and gene fusions from chimeric RNA alignments. It offers rapid, efficient, and scalable analysis for large medical datasets, improving upon existing tools.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Chimeric RNA alignments, including chromosomal fusions and circular RNAs (circRNAs), are biologically significant, particularly in cancer.
- Existing software for fusion discovery and circRNA detection suffers from high false positive rates, long runtimes, and limited capabilities, hindering large-scale analysis.
Purpose of the Study:
- To introduce STAR Chimeric Post (STARChip), a novel software package for processing chimeric RNA alignments.
- To enable rapid, efficient, and scalable detection and quantification of circRNAs and high-precision gene fusions.
Main Methods:
- STARChip processes chimeric alignments generated by the STAR aligner.
- The software annotates and quantifies both circRNAs and fusion events.
Main Results:
- STARChip provides annotated circRNA and high-precision fusion detection.
- The software is rapid, efficient, and scalable, suitable for high-dimensional medical omics datasets.
Conclusions:
- STARChip addresses the limitations of existing tools for analyzing chimeric RNA.
- This novel software facilitates robust and scalable discovery of circRNAs and gene fusions in large datasets.
Related Concept Videos
02:45Nuclear Fusion
33.9K
The process of converting very light nuclei into heavier nuclei is also accompanied by the conversion of mass into large amounts of energy, a process called fusion. The principal source of energy in the sun is a net fusion reaction in which four hydrogen nuclei fuse and ultimately produce one helium nucleus and two positrons.
A helium nucleus has a mass that is 0.7% less than that of four hydrogen nuclei; this lost mass is converted into energy during the fusion. This reaction produces about...
A helium nucleus has a mass that is 0.7% less than that of four hydrogen nuclei; this lost mass is converted into energy during the fusion. This reaction produces about...
33.9K
01:10Transcription
157.1K
Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
157.1K
01:58Prokaryotic Transcriptional Activators and Repressors
25.6K
The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
Transcription of prokaryotic...
25.6K
02:16Transcription Factors
82.9K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
82.9K
02:42Eukaryotic Transcription Activators
12.9K
Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
12.9K
02:35Transcription Elongation Factors
14.1K
Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
The transcription elongation is regulated via pausing of RNA polymerase on several occasions during transcription. In bacteria, these halts are necessary because the transcription of DNA into mRNA is coupled to the translation of that mRNA...
14.1K