initial analysis- known srilankan SNPs

initial part of analysis starts with identification of srilankan genome SNPs falling withing microRNA predicted targets by 'targetScan'.Results shown 6163 SNPs fall within targets.

It took 5HRS to execute.

methodology - continues

Administrator level:

Creating database : myproject

Table 1:hmdd2011 – from manually retrieved the associations of miRNA and disease from literatures. Using human miRNA disease database (HMDD), which contains miRNA names, disease names, dysfunction evidences, and the literature PubMed ID (http://202.38.126.151/hmdd)

Table 2:mirtag – all predicted miRNA by TargetScan(http://www.targetscan.org/) and their target genes with UTR locations from UCSC table browser(http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=214845735&clade=mammal&org=Human&db=hg19&hgta_group=allTracks&hgta_track=targetScanS&hgta_table=0&hgta_regionType=genome&position=chr21%3A33031597-33041570&hgta_outputType=selectedFields&hgta_outFileName=enst_loc)

Table 3:srilanka, Table 4:slgnovel – all Sri Lankan Genome SNP profile with locations

Table 5:family_info_human – miRNA family name and miRbase IDs from SigTerms(http://sigterms.sourceforge.net/).to be used to map miRNA names

***Table 6:SLG_mirna – to be created by administrator by following method: both Tables 3 & 4 locations mapped with table 2.Result will be as Table 6

User level:

Query disease as input using GUI? And output of either ALL or Si Lankan genome specific miRNA catalogues and their features explicitly linked to relevant databases

SLG-mirna will be categorized using variation either present within target (RED color code) or 100 nt up/down stream of target region (YELLOW color code)

Objectives

• General Objective:

– To propose the disease specific microRNA in regards to sri lankan genome

• Specific objectives:

– To identify disease specific miRNA gene

– to find disease specific experimentally validated microRNAs and their target genes

– To find SNPs exist within microRNA gene

– To find SNPs exist within and around in proximity of microRNA target gene

– To find target genes SNPs which are located within target UTR , found in Sri Lankan genome and their relevant microRNAs

introduction

microRNAs are a large class of non-coding ~22 nucleotide RNAs.One miRNA can target many different sites on the same mRNA or on many different mRNAs.About 1% of human genes encode for miRNAs, and up to 30% of human protein-coding genes may be regulated by miRNAs.Over 1400 human miRNAs are identified (http://www.mirbase.org), which regulate gene expression at the post-transcriptional level by binding to 3 prime untranslated region(UTR) of mRNA transcript. MicroRNAs have been implicated in numerous developmental and adult diseases, but disease specific microRNAs and proposing them to use as biomarkers in relation to personal genome is lacking. Therefore, in my project using Sri Lankan genome as a reference of whole population, I am going to develop a web based database of disease specific microRNA by mining existing evidence of how variation in 3’ UTR of target transcript will affect binding of microRNA and gene expression. This database will assist the wet lab people on further studying human disease and microRNA association.