MicroRNA

Post-analysis categorization
- Literature search
Post-survey categorization
- Features validated in most cases
- Features not validated
Simple lists
Preliminary lists

Tool name

Patrocles

URL

http://www.patrocles.org

Important features

Database on DNA sequence polymorphisms (DSPs) that are likely to affect microRNA-directed gene regulation.

Citations

Hiard S, Charlier C, Coppieters W, Georges M, Baurain D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. Epub 2009 Nov 11. PubMed PMID: 19906729

Year of publication

2010

Rank by usage frequency

100

Comments

Function

FUNCTIONAL ANALYSIS: SNP/ genetic variations, SPECIES: miscellaneous, http://www.patrocles.org, Database on DNA sequence polymorphisms (DSPs) that are likely to affect microRNA-directed gene regulation. , Hiard S- Charlier C- Coppieters W- Georges M- Baurain D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. Epub 2009 Nov 11. PubMed PMID: 19906729 , 2010, 100, Online, I. SPECIES SUPPORTED INCLUDE: chicken- chimpanzee- cow- dog- human- mouse- rat II. QUERY OR INPUT DATA: For polymorphic miRNAs: 1. Choose species 2. Enter miRNAs (miRNA id- miRNA position-chromosome start and end position) 3. Select type of polymorphism: SNP or CNV + eQTL (Expression quantitative trait loci ) 4. Choose SNP parameters: a. SNP position: All- Seed- mature miRNA- pre-miRNA; b. SNP status: all or validated; 3. Enter SNP ID 5. Choose output: HTML or Text file (download) or Text file (Browser). For Polymorphic targets: 1. Select species 2. Select seed type: 8 mer or 7 mer 3. Select target sites: XI et al or lewis et al or both as the source; Enter microRNA ID- Octamer motif(in target) 4. Select target genes (enter target gene id- target gene position-chromosome- start and end position) 5. Select SNP parameters: a. SNP effect (choose from given options) b. SNP status: all or validated c. Enter SNP ID. Polymorphic silencing machinery: 1. Select species 2. Select genes: a. Functional compartment- all/ miRNA processing/ RISC/ MiRNP complex- P-body b. Gene id: Select from list c. Gene position: chromosome- start and end position 3. Select type of polymorphism 4. Select SNPs: a. SNP effect: all/ essential splice site/ frameshift-coding/ non-synonymous-splice-site/ splice-site/ splice site-non-synonymous/ stop-gained b. SNP status c. SNP ID Finder:: a. - Compare 2 sequences: Select species- Select motif length- enter sequence or alignment in Pearson/FASTA format or Follow the given link to convert the alignment if necessary b. analyze 1 sequence III. OUTPUT DATA depends on the type of analysis selected and may depict motifs or target sites within submitted sequences.