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Protocols

miRExpress specifications

Information


Unique identifier OMICS_00379
Name miRExpress
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some next-generation sequencing data.
Input format FASTA
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Hsien-Da Huang
  • person_outline Na-Sheng Lin
  • person_outline Feng-Mao Lin

Publication for miRExpress

miRExpress citations

 (19)
library_books

MicroRNA–mRNA expression profiles associated with medulloblastoma subgroup 4

2018
PMCID: 5818864
PMID: 29497332
DOI: 10.2147/CMAR.S156709

[…] Raw reads were processed to trim adaptors and low-quality bases using Trim galore, version 0.4.1. Reads shorter than 15 nucleotides were discarded. The miRExpress tool was used to map reads to precursor miRNAs from miRBase, version 21, and to generate miRNA expression profiles. Expression was computed by summing counts of reads that fell within the l […]

library_books

The Prostate Cancer Cells Resistant to Docetaxel as in vitro Model for Discovering MicroRNAs Predictive of the Onset of Docetaxel Resistance

2017
Int J Mol Sci
PMCID: 5536002
PMID: 28703747
DOI: 10.3390/ijms18071512

[…] .1 []. Remaining reads, with a minimum length of 17 bzp and maximum 35 bp after trimming, were clustered for unique hits and mapped to pre-miRNA sequences present into the miRBase (rel. 21) employing miRExpress tool v 2.1.3 []. […]

library_books

Tumor Cell Derived Microvesicles Induced Not Epithelial Mesenchymal Transition but Apoptosis in Human Proximal Tubular (HK 2) Cells: Implications for Renal Impairment in Multiple Myeloma

2017
Int J Mol Sci
PMCID: 5372529
PMID: 28264449
DOI: 10.3390/ijms18030513

[…] and 3′ adapters, filtered the low-quality reads, and kept the 18~30 nt reads. The reads were mapped to hg19 with BWA []. The remaining reads were mapped to human pre-miRNA miRBase release 20 [] with miRExpress 2.0 []. The expression level of miRNA was normalized with RPM (reads per million mapped reads). […]

library_books

Depletion of tRNA halves enables effective small RNA sequencing of low input murine serum samples

2016
Sci Rep
PMCID: 5129013
PMID: 27901112
DOI: 10.1038/srep37876

[…] For the quantification of small RNAs Biogazelle’s dedicated small RNA seq pipeline was used (part of Cobra), as publically available alternatives we advice the use of miRDeep2 and miRExpress. Adaptor trimming was performed using Cutadapt v1.8.1, reads shorter than 15 bp and those in which no adaptor was found, were discarded. For quality control the FASTX-Toolkit (v0.0.14) was […]

library_books

Wnt signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches

2016
Mol Cancer
PMCID: 5010773
PMID: 27590724
DOI: 10.1186/s12943-016-0541-3

[…] r NGS miRNA databases that can be beneficial in carrying out miRNA expression profiling for identification of Wnt target genes includes, but not restricted to: deepBase [], miRGen 2.0 [], miRBase [], miRExpress [] and CLIPseqtools [].Notwithstanding, traditional platforms for the execution of miRNA expression profiling have also been useful in identifying miRNA targets of the Wnt-signalling pathwa […]

call_split

DICER governs characteristics of glioma stem cells and the resulting tumors in xenograft mouse models of glioblastoma

2016
Oncotarget
PMCID: 5302925
PMID: 27421140
DOI: 10.18632/oncotarget.10570
call_split See protocol

[…] le. We verified the quality of the resultant reads using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Next, we trimmed the adapter sequences and estimated the read counts using miRExpress [], using miRBase 19 as a reference []. Finally, we normalized the counts to reads per million mapped. MiRNAs were determined to be altered by comparing the number of reads for a particular […]

Citations

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miRExpress institution(s)
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan, China; Institute of Biotechnology, National Cheng Kung University, Taiwan, China; Institute of Plant and Microbial Biology, Academia Sinica, Taiwan, China; Department of Biological Science and Technology, National Chiao Tung University, Taiwan, China; Institute of Tropical Plant Science, National Cheng Kung University, Taiwan, China
miRExpress funding source(s)
Supported by the National Science Council of the Republic of China under Contracts No. NSC 98-2311- B-009-004-MY3 and NSC 98-2627-B-009-005, the National Research Program for Genomic Medicine (NRPGM), Taiwan, and in part by MOE ATU.

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