# Tools for downstream analysis

## Web-servers

TFmiR: disease-specific miRNA/transcription factor co-regulatory networks v1.2. It uses results from UP/DOWN regulated miRNA/Genes and allows to focus in only one disease to create different type of relationships between miRNA/TF/Gene. Easy to use. Probably need to filter the output sometime due to the big networks that can result from an analysis.

Diana-TarBase v7.0: Database for validated miRNA targets. Many filter options. Good for small candidate miRNAs set studies.

StarScan: Database to browse the targets of miRNAs from degradome data. It has a fancy interface, and many species and data from GEO.

miRtex gives targets from literature. Good for finding validated targets to help discussion in papers or further functional experiment based on new hypothesis.

piRBase: Database for piRNA annotation and function. Published last year, for now the best I can find out there.

chimira: Web tool to analyze isomiR. It gives you a quick idea of you samples.

MicroCosm: MiRNA target database. Updated and download option.

IsomiR Bank: isomiR database from many species and tissues. For single queries is useful.

## Command-lines

miRVaS : tools to predict the functional changed due to nt changes in the miRNA sequence.