Limits...
OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.

Khurana R, Verma VK, Rawoof A, Tiwari S, Nair RA, Mahidhara G, Idris MM, Clarke AR, Kumar LD - BMC Bioinformatics (2014)

Bottom Line: We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples.The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm.OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Biology, Centre for Cellular & Molecular Biology, Council of scientific and Industrial Research, Hyderabad, A,P, India. lekha@ccmb.res.in

ABSTRACT

Background: Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet no comprehensive compilation of this data which has rendered it underutilized by cancer biologists. There is therefore an unmet need in generating bioinformatic platforms to speed the identification of novel therapeutic targets.

Description: We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm.

Conclusion: OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance. OncomiRdbB is freely available for download through the URL link http://tdb.ccmb.res.in/OncomiRdbB/index.htm.

Show MeSH

Related in: MedlinePlus

Schematic illustration of construction of OncomirdbB using different bioinformatics approaches. MicroRNAs were mined from different databases like miRbase, PhenomiR2.0 and miR2Disease. In order to find targets for these miRNAs, different pathway genes were downloaded from KEGG database and removed the repeated entries by using Perl script. We used miRanda for finding the targets at different energy levels.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3926854&req=5

Figure 1: Schematic illustration of construction of OncomirdbB using different bioinformatics approaches. MicroRNAs were mined from different databases like miRbase, PhenomiR2.0 and miR2Disease. In order to find targets for these miRNAs, different pathway genes were downloaded from KEGG database and removed the repeated entries by using Perl script. We used miRanda for finding the targets at different energy levels.

Mentions: The mined miRNAs were classified as breast cancer miRNAs based on their complementarity to the target genes of different oncogenic pathways (MicroCosm) deregulated in breast cancer. This was further confirmed using miRanda, TargetScan and PicTar (Figure 1). A comparison between OncomiRdbB and existing databases demonstrated the utility of integrating various databases into one comprehensive database (Figure 2). A phylogenetic functional relationship between microRNAs of human and mouse was established by aligning the sequences using ClustalX. A conserved biological function of breast cancer microRNAs between mice and human genomes was observed after clustering both data sets. In the cladogram, branches from the same node represent descendents of a similar ancestor or cluster of the same family indicating their origin from a common ancestor. For example, hsa-miR-145, miR-151-3p and miR-30 families align with their mmu-miR counterparts indicating a conserved biological function in breast cancer development in both the genomes (Additional file 1: Figure S1). We retrieved a total of 782 human and 246 mouse microRNAs and their respective sequences associated with breast cancer from existing miRNA databases including miRBase, miR2Disease and PhenomiR. We have validated these miRNAs with two different platforms, Taqman low density arrays consisting of 667 human microRNAs (version 10) and LNA arrays using human breast cancer samples of grade 2 and grade 3 each consisting of Stages I to III. Approximately 400 significant and valid miRNAs lighted up in one or the other grades/stages classifying them as breast cancer microRNAs.


OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer.

Khurana R, Verma VK, Rawoof A, Tiwari S, Nair RA, Mahidhara G, Idris MM, Clarke AR, Kumar LD - BMC Bioinformatics (2014)

Schematic illustration of construction of OncomirdbB using different bioinformatics approaches. MicroRNAs were mined from different databases like miRbase, PhenomiR2.0 and miR2Disease. In order to find targets for these miRNAs, different pathway genes were downloaded from KEGG database and removed the repeated entries by using Perl script. We used miRanda for finding the targets at different energy levels.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3926854&req=5

Figure 1: Schematic illustration of construction of OncomirdbB using different bioinformatics approaches. MicroRNAs were mined from different databases like miRbase, PhenomiR2.0 and miR2Disease. In order to find targets for these miRNAs, different pathway genes were downloaded from KEGG database and removed the repeated entries by using Perl script. We used miRanda for finding the targets at different energy levels.
Mentions: The mined miRNAs were classified as breast cancer miRNAs based on their complementarity to the target genes of different oncogenic pathways (MicroCosm) deregulated in breast cancer. This was further confirmed using miRanda, TargetScan and PicTar (Figure 1). A comparison between OncomiRdbB and existing databases demonstrated the utility of integrating various databases into one comprehensive database (Figure 2). A phylogenetic functional relationship between microRNAs of human and mouse was established by aligning the sequences using ClustalX. A conserved biological function of breast cancer microRNAs between mice and human genomes was observed after clustering both data sets. In the cladogram, branches from the same node represent descendents of a similar ancestor or cluster of the same family indicating their origin from a common ancestor. For example, hsa-miR-145, miR-151-3p and miR-30 families align with their mmu-miR counterparts indicating a conserved biological function in breast cancer development in both the genomes (Additional file 1: Figure S1). We retrieved a total of 782 human and 246 mouse microRNAs and their respective sequences associated with breast cancer from existing miRNA databases including miRBase, miR2Disease and PhenomiR. We have validated these miRNAs with two different platforms, Taqman low density arrays consisting of 667 human microRNAs (version 10) and LNA arrays using human breast cancer samples of grade 2 and grade 3 each consisting of Stages I to III. Approximately 400 significant and valid miRNAs lighted up in one or the other grades/stages classifying them as breast cancer microRNAs.

Bottom Line: We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples.The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm.OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cancer Biology, Centre for Cellular & Molecular Biology, Council of scientific and Industrial Research, Hyderabad, A,P, India. lekha@ccmb.res.in

ABSTRACT

Background: Given the estimate that 30% of our genes are controlled by microRNAs, it is essential that we understand the precise relationship between microRNAs and their targets. OncomiRs are microRNAs (miRNAs) that have been frequently shown to be deregulated in cancer. However, although several oncomiRs have been identified and characterized, there is as yet no comprehensive compilation of this data which has rendered it underutilized by cancer biologists. There is therefore an unmet need in generating bioinformatic platforms to speed the identification of novel therapeutic targets.

Description: We describe here OncomiRdbB, a comprehensive database of oncomiRs mined from different existing databases for mouse and humans along with novel oncomiRs that we have validated in human breast cancer samples. The database also lists their respective predicted targets, identified using miRanda, along with their IDs, sequences, chromosome location and detailed description. This database facilitates querying by search strings including microRNA name, sequence, accession number, target genes and organisms. The microRNA networks and their hubs with respective targets at 3'UTR, 5'UTR and exons of different pathway genes were also deciphered using the 'R' algorithm.

Conclusion: OncomiRdbB is a comprehensive and integrated database of oncomiRs and their targets in breast cancer with multiple query options which will help enhance both understanding of the biology of breast cancer and the development of new and innovative microRNA based diagnostic tools and targets of therapeutic significance. OncomiRdbB is freely available for download through the URL link http://tdb.ccmb.res.in/OncomiRdbB/index.htm.

Show MeSH
Related in: MedlinePlus