microRNA.org: A resource for predicted microRNA targets and expression

About this document

MicroRNA.org is a web-accessible information resource produced and maintained at cBio, the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). This document details changes in data, programs, and interface for each release, and also contains general information and references about this resource.

Hyperlinks to document sections:

General Information

September 2008 (current) release notes

January 2008 release notes

General Information

Summary

The MicroRNA.org website is a comprehensive resource of microRNA target predictions and expression profiles. Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs. MicroRNA expression profiles are derived from a comprehensive sequencing project of a large set of mammalian tissues and cell lines of normal and disease origin. This website enables users to explore:

• The set of genes that are potentially regulated by a particular microRNA.
• The implied cooperativity of multiple microRNAs on a particular mRNA.
• MicroRNA expression profiles in various mammalian tissues.

The website interface currently makes available:

• 1934522 predicted microRNA target sites in 31869 human gene isoforms.
• 1209841 predicted microRNA target sites in 26697 mouse gene isoforms.
• 84264 predicted microRNA target sites in 4886 rat gene isoforms.
• target sites for 677 human microRNAs.
• target sites for 491 mouse microRNAs.
• target sites for 286 rat microRNAs.

Software and data files

The miRanda source code is available under the LGPL open source license. The microRNA target predictions and expression data are available as tab delimited files. See the Downloads tab of the MicroRNA.org website.

Previous releases

Previous releases are available as tab delimited files through the Downloads tab of the website. Additionally, the previous release (jan2008) is available through the website interface for a limited time at http://cbio.mskcc.org/microrna-previous

Contact

Send comments and questions to

References

• MicroRNA target predictions with expression profiles.
  The microRNA.org resource: targets and expression.
  Betel D, Wilson M, Gabow A, Marks DS, Sander C.,
  Nucleic Acids Res. 2008 Jan; 36(Database Issue): D149-53.
• Comprehensive cloning and sequencing effort of 172 human, 64 mouse and 16 rat small RNA libraries extracted from major organs and cell types.
  A mammalian microRNA expression atlas based on small RNA library sequencing.
  Landgraf P., et al., Cell 2007 Jun 29;129(7):1401-14.
• First comprehensive computational prediction of microRNA targets in the human genome and first publication of the hypothesis that a large fraction of human genes (more than 10%) may be regulated by microRNAs.
  Human MicroRNA targets.
  John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS.
  PLoS Biology 2005 Jul;3(7):e264.
• First implementation of the miRanda dynamic programming algorithm and comprehensive application to the drosophila genome.
  MicroRNA targets in Drosophila.
  Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS
  Genome Biology (2003) 5;R1

September 2008 release notes

Data Sources

• Mature microRNA sequences for human, mouse, and rat were downloaded from mirBASE 11.0 (April 2008).
• 3' UTR sequences were downloaded from ucsc genome assemblies: human: hg18 (Mar. 2006), mouse: mm9 (July 2007), rat: rn4 (Nov 2004).

Changes to the website interface

• User selected microRNAs can be highlighted in the alignment view.
• A toggle checkbox allows users to hide non-highlighted microRNAs.

Changes to microRNA target prediction algorithm

The terminal microRNA nucleotides (first nucleotide and last two nucleotides) no longer contribute to the alignment score, regardless of base pairing.

For example, in the following alignment:

        3' uuCUUUCUCAGA-ACGAAACAGCGGg 5'    hsa-miR-1273
             |||:|: | | || | |||||:|  
        5' aaGAAGGGAUGUCUG-UCUGUCGUCc 3'    MEX3A
           ^^                       ^
    

the 3'-end uu nucleotides and the 5'-end g nucleotide do not contribute to the alignment score even though they are complementary to nucleotides in the mRNA.

Recent structural data show that these nucleotides are inaccessible to base-pairing and therefore, are not likely to contribute to target specificity. [Structure of the guide-strand-containing argonaute silencing complex. Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ. Nature advance online publication 27 August 2008]

Change in conservation score cutoff

For microRNA target predictions in mouse, the cutoff for minimum phastCons conservation score at the predicted target site has been changed from .57 to .566. The current mm9 phastCons conservation score is based on 30 aligned genomes, while the mm8 phastCons conservation score is based on 17 aligned genomes. The new threshold is based on a comparison of 30way to 17way conservation scores for all target sites that map to both mm9 and mm8 genome coordinates using liftOver chains.

Figure: Scatterplot of Target Site Conservation Scores
(phastCons 30way v. phastCons 17way)

January 2008 release notes

Data

MicroRNA sequences were collected from MirBase release 10.0. Mammalian 3'UTR sequences from the rat (rno4), mouse (mm7) and human (hg18) genomes were downloaded from the UCSC genome browser.

MicroRNA expression profiles were collected from a recently published comprehensive cloning and sequencing effort of 172 human, 64 mouse and 16 rat small RNA libraries extracted from major organs and cell types (Landgraf et al., Cell, 129, (2007), 1401-1414). Expression values represent the number of cloned mature microRNAs that were sequenced in each library and reported as clone counts. The counts are normalized by the total number of microRNAs that were cloned in each library.

Prediction parameters

Predictions were generated using the 2004 version of the miRanda algorithm (John et al., PLoS Biology, 2, (2004), e363) with the following command-line options:

Score cutoff S>= 140
Energy cutoff E<= -7.0
Gap opening: -9.0
Gap extension -4.0
5' scaling: 4

The miRNA:mRNA alignment scores are based on optimization of a sum of match values using a dynamic programming algorithm using the following single-position match values (base-pairing values):
A:U = 5
G:C = 5
G:U = 1
All other base pairs (mismatches) = -3

The match value s(i) is multiplied by a position specific weight w(i) before being evaluated in the alignment algorithm. The position specific weights reflect the non-homogeneous effect of different positions, such as the importance of the 'seed' or 'nucleus' generally defined as positions 2-8. Thus the total score S for a particular alignment is

S = SUM(over i) [ w(i) s(i) ]

where the sum is taken along the alignment trace (which may include bulges, i.e., unpaired nucleotides, in one of the sequences, evaluated as 'gaps').

Position s(i)	Weight w(i)
1	1.0
2-8	4.0
9-21	1.0

Note that a perfect heptamer match in positions 2-8 corresponds to a score of 140 (5*4*7), where 5 reflects a match, 4 the positional weight and 7 the number of positions.

Caveat:

These base-pairing scores were optimized against a limited set of validated targets. We are currently (early 2008) in the process of refining these values and will probably refine the parameters by mid-2008. Therefore, target predictions may differ in subsequent releases. Users will have access to previous, archived releases through links on the website.

Conservation

We used PhastCons conservation score, which measures the evolutionary conservation of sequence blocks across multiple vertebrates using a phylogenetic hidden Markov model (Siepel et al., Genome research, 15, (2005), 1034-1050.), to filter out less conserved predicted target sites. Target sites are filtered for PhastCons 0.57, which roughly corresponds to conservation across all mammals.