TY - JOUR
T1 - CmirC
T2 - an integrated database of clustered miRNAs co-localized with copy number variations in cancer
AU - Ware, Akshay Pramod
AU - Satyamoorthy, Kapaettu
AU - Paul, Bobby
N1 - Funding Information:
The authors would like to thank DST-FIST, the Government of India, TIFAC-CORE in Pharmacogenomics, and Manipal Academy of Higher Education (MAHE), Manipal, for the support and facilities provided. APW gratefully acknowledge MAHE, Manipal, for the Dr. TMA Pai Ph.D. fellowship and the Indian Council of Medical Research, Government of India, for the Senior Research Fellowship (Reference ID: BMI/11(10)/2022).
Funding Information:
Open access funding provided by Manipal Academy of Higher Education, Manipal. This work is supported by the Vision Group on Science and Technology, Government of Karnataka (RGS-F/GRD No. 997/2020–21/144).
Funding Information:
The authors would like to thank DST-FIST, the Government of India, TIFAC-CORE in Pharmacogenomics, and Manipal Academy of Higher Education (MAHE), Manipal, for the support and facilities provided. APW gratefully acknowledge MAHE, Manipal, for the Dr. TMA Pai Ph.D. fellowship and the Indian Council of Medical Research, Government of India, for the Senior Research Fellowship (Reference ID: BMI/11(10)/2022).
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Genomic rearrangements and copy number variations (CNVs) are the major regulators of clustered microRNAs (miRNAs) expression. Several clustered miRNAs are harbored in and around chromosome fragile sites (CFSs) and cancer-associated genomic hotspots. Aberrant expression of such clusters can lead to oncogenic or tumor suppressor activities. Here, we developed CmirC (Clustered miRNAs co-localized with CNVs), a comprehensive database of clustered miRNAs co-localized with CNV regions. The database consists of 481 clustered miRNAs co-localized with CNVs and their expression patterns in 35 cancer types of the TCGA. The portal also provides information on CFSs, miRNA cluster candidates, genomic coordinates, target gene networks, and gene functionality. The web portal is integrated with advanced tools such as JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3 to help the researchers in data analysis, visualization, and browsing. This portal provides a promising avenue for integrated data analytics and offers additional evidence for the complex regulation of clustered miRNAs in cancer. The web portal is freely accessible at http://slsdb.manipal.edu/cmirclust to explore clinically significant miRNAs.
AB - Genomic rearrangements and copy number variations (CNVs) are the major regulators of clustered microRNAs (miRNAs) expression. Several clustered miRNAs are harbored in and around chromosome fragile sites (CFSs) and cancer-associated genomic hotspots. Aberrant expression of such clusters can lead to oncogenic or tumor suppressor activities. Here, we developed CmirC (Clustered miRNAs co-localized with CNVs), a comprehensive database of clustered miRNAs co-localized with CNV regions. The database consists of 481 clustered miRNAs co-localized with CNVs and their expression patterns in 35 cancer types of the TCGA. The portal also provides information on CFSs, miRNA cluster candidates, genomic coordinates, target gene networks, and gene functionality. The web portal is integrated with advanced tools such as JBrowse, NCBI-BLAST, GeneSCF, visNetwork, and NetworkD3 to help the researchers in data analysis, visualization, and browsing. This portal provides a promising avenue for integrated data analytics and offers additional evidence for the complex regulation of clustered miRNAs in cancer. The web portal is freely accessible at http://slsdb.manipal.edu/cmirclust to explore clinically significant miRNAs.
UR - http://www.scopus.com/inward/record.url?scp=85140610874&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85140610874&partnerID=8YFLogxK
U2 - 10.1007/s10142-022-00909-w
DO - 10.1007/s10142-022-00909-w
M3 - Article
C2 - 36287286
AN - SCOPUS:85140610874
SN - 1438-793X
VL - 22
SP - 1229
EP - 1241
JO - Functional and Integrative Genomics
JF - Functional and Integrative Genomics
IS - 6
ER -
