The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
miRNAkey: a software for microRNA deep sequencing analysis
Abstract
Motivation: MicroRNAs (miRNAs) are short abundant non-coding RNAs critical for many cellular processes. Deep sequencing (next-generation sequencing) technologies are being readily used to receive a more accurate depiction of miRNA expression profiles in living cells. This type of analysis is a key step towards improving our understanding of the complexity and mode of miRNA regulation. Results: miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. The package implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple read determination, generating a novel platform for the analysis of miRNA expression. A user-friendly graphical interface is applied to determine the analysis steps. The tabular and graphical output contains general and detailed reports on the sequence reads and provides an accurate picture of the differentially expressed miRNAs in paired samples. Availability and implementation: See http://ibis.tau.ac.il/miRNAkey Contact: nshomron@post.tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“we used the miRNAkey pipeline, implementing the SeqEM option to account for reads mapping to multiple miRNAs [32].”
From Reduced Expression of Brain-Enriched microRNAs in Glioblastomas Permits Targeted Regulation of a Cell Death Gene (2011) · cites this paper as [32]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Research works printed but not linked: 13
- Bushati, 2007, microRNA functions, Annu. Rev. Cell Dev. Biol., 23, 175, 10.1146/annurev.cellbio.23.090506.123406 · DOI · Paper page
- Calin, 2006, MicroRNA signatures in human cancers, Nat. Rev. Cancer, 6, 857, 10.1038/nrc1997 · DOI
- Friedländer, 2008, Discovering microRNAs from deep sequencing data using miRDeep, Nat. Biotechnol., 26, 407, 10.1038/nbt1394 · DOI
- Golan, 2010, Biased hosting of intronic microRNA genes, Bioinformatics, 26, 992, 10.1093/bioinformatics/btq077 · DOI
- Hackenberg, 2009, miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments, Nucleic Acids Res., 37, W68, 10.1093/nar/gkp347 · DOI
- Huang, 2010, DSAP: deep-sequencing small RNA analysis pipeline, Nucleic Acids Res., 38, W385, 10.1093/nar/gkq392 · DOI
- Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 · DOI · Paper page
- Moxon, 2008, A toolkit for analysing large-scale plant small RNA datasets, Bioinformatics, 24, 2252, 10.1093/bioinformatics/btn428 · DOI
- Pantano, 2010, SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells, Nucleic Acids Res., 38, e34, 10.1093/nar/gkp1127 · DOI
- Pasaniuc, 2010, Accurate estimation of expression levels of homologous genes in RNA-seq experiments, 397, 10.1007/978-3-642-12683-3_26 · DOI
- Shomron, 2009, An evolutionary perspective of animal microRNAs and their targets, J. Biomed. Biotechnol., 2009, 594738, 10.1155/2009/594738 · DOI
- Wang, 2009, miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression, BMC Bioinformatics, 10, 328, 10.1186/1471-2105-10-328 · DOI
- Zhu, 2010, mirTools: microRNA profiling and discovery based on high-throughput sequencing, Nucleic Acids Res., 38, W392, 10.1093/nar/gkq393 · DOI
Cited by
Sorted by citations
Skalsky, R. L., & Cullen, B. R. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024248 · Cited by 170
Metadata
- Authors
- Ronen, R., Gan, I., Modai, S., Sukacheov, A., Dror, G., Halperin, E., & Shomron, N.
- Affiliations
- 1 Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, 2The Academic College of Tel-Aviv-Yaffo, Tel−Aviv, Israel, 3International Computer Science Institute, Berkeley, CA, USA and 4School of Computer Science and Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Science, Tel-Aviv University, Tel-Aviv, Israel
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-08-27
- Volume
- 26
- Issue
- 20
- Pages
- 2615-2616
- ISSN
- 1367-4811
- 1367-4803
- Cited by
- 74
- References
- 1
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
