How do you predict miRNA target genes?

Stepwise strategy for miRNA target prediction.

1. Assessment of complementarity between miRNA and 3′-UTR target sequences.
2. Evaluation of the free energy (ΔG) of the interaction.
3. Estimate of the evolutionary conservation of the miRNA target across the species.
4. Assessment of target site accessibility.

What is the seed region of miRNA?

The seed sequence of a miRNA is defined as the first 2–8 nucleotides starting at the 5′ end and counting toward the 3′ end (Lewis et al., 2003) (Figure 1). For most tools, a seed match is a Watson-Crick (WC) match between a miRNA and its target in the seed sequence.

How do you find the seed sequence of miRNA?

Seed Match The seed sequence of a miRNA is defined as the first 2–8 nucleotides starting at the 5′ end and counting toward the 3′ end (Lewis et al., 2003) (Figure 1). For most tools, a seed match is a Watson-Crick (WC) match between a miRNA and its target in the seed sequence.

What is miRNA and how does it work?

microRNA is the name of a family of molecules that helps cells control the kinds and amounts of proteins they make. That is, cells use microRNA to help control gene expression. Molecules of microRNA are found in cells and in the bloodstream.

How are miRNAs formed?

MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic.

What are PRI-miRNAs and pre miRNAs?

In animal cells, pri-miRNAs are processed into pre-miRNAs by the Microprocessor complex in the nucleus, and are then transported into the cytoplasm to undergo further processing into mature miRNAs.

What is seed region in miRNA?

The seed sequence or seed region is a conserved heptametrical sequence which is mostly situated at positions 2-7 from the miRNA 5´-end. Even though base pairing of miRNA and its target mRNA does not match perfect, the “seed sequence” has to be perfectly complementary.

How many genes are targeted by miRNA?

MicroRNAs are estimated to regulate 60% of all protein-coding genes and a single miRNA may regulate up to 400 different target mRNAs18.

How are miRNA targets evaluated for target ontology analysis?

For target ontology analysis, predicted targets for a miRNA are \r evaluated as a group using Gene Oncology (GO) terms. Significant GO \r categories are identified by statistics for gene functional enrichment.

What is the mirsnp database?

CREAM (Chemotherapy ResistancE-Associated MiRSNP Database) is a free online database depositing the functional miRSNP associated with chemotherapy resistance.

What is the miRBase database?

miRBase: the microRNA database. The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).

What is mirdb?

miRDB is an online database for miRNA target prediction and functional annotations. All the targets in miRDB were predicted by a bioinformatics tool, MirTarget, which was developed by analyzing thousands of miRNA-target interactions from high-throughput sequencing experiments.