Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer
The identification of human cancer-related microRNAs (miRNAs) is important for cancer biology research. Although several identification methods have achieved remarkable success, they have overlooked the functional information associated with miRNAs. We present a computational framework that can be u...
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| Format: | Online |
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Oxford University Press
2011
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239203/ |
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pubmed-32392032011-12-16 Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer Li, Xia Wang, Qianghu Zheng, Yan Lv, Sali Ning, Shangwei Sun, Jie Huang, Teng Zheng, Qifan Ren, Huan Xu, Jin Wang, Xishan Li, Yixue Methods Online The identification of human cancer-related microRNAs (miRNAs) is important for cancer biology research. Although several identification methods have achieved remarkable success, they have overlooked the functional information associated with miRNAs. We present a computational framework that can be used to prioritize human cancer miRNAs by measuring the association between cancer and miRNAs based on the functional consistency score (FCS) of the miRNA target genes and the cancer-related genes. This approach proved successful in identifying the validated cancer miRNAs for 11 common human cancers with area under ROC curve (AUC) ranging from 71.15% to 96.36%. The FCS method had a significant advantage over miRNA differential expression analysis when identifying cancer-related miRNAs with a fine regulatory mechanism, such as miR-27a in colorectal cancer. Furthermore, a case study examining thyroid cancer showed that the FCS method can uncover novel cancer-related miRNAs such as miR-27a/b, which were showed significantly upregulated in thyroid cancer samples by qRT-PCR analysis. Our method can be used on a web-based server, CMP (cancer miRNA prioritization) and is freely accessible at http://bioinfo.hrbmu.edu.cn/CMP. This time- and cost-effective computational framework can be a valuable complement to experimental studies and can assist with future studies of miRNA involvement in the pathogenesis of cancers. Oxford University Press 2011-12 2011-10-05 /pmc/articles/PMC3239203/ /pubmed/21976726 http://dx.doi.org/10.1093/nar/gkr770 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Li, Xia Wang, Qianghu Zheng, Yan Lv, Sali Ning, Shangwei Sun, Jie Huang, Teng Zheng, Qifan Ren, Huan Xu, Jin Wang, Xishan Li, Yixue |
| spellingShingle |
Li, Xia Wang, Qianghu Zheng, Yan Lv, Sali Ning, Shangwei Sun, Jie Huang, Teng Zheng, Qifan Ren, Huan Xu, Jin Wang, Xishan Li, Yixue Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| author_facet |
Li, Xia Wang, Qianghu Zheng, Yan Lv, Sali Ning, Shangwei Sun, Jie Huang, Teng Zheng, Qifan Ren, Huan Xu, Jin Wang, Xishan Li, Yixue |
| author_sort |
Li, Xia |
| title |
Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| title_short |
Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| title_full |
Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| title_fullStr |
Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| title_full_unstemmed |
Prioritizing human cancer microRNAs based on genes’ functional consistency between microRNA and cancer |
| title_sort |
prioritizing human cancer micrornas based on genes’ functional consistency between microrna and cancer |
| description |
The identification of human cancer-related microRNAs (miRNAs) is important for cancer biology research. Although several identification methods have achieved remarkable success, they have overlooked the functional information associated with miRNAs. We present a computational framework that can be used to prioritize human cancer miRNAs by measuring the association between cancer and miRNAs based on the functional consistency score (FCS) of the miRNA target genes and the cancer-related genes. This approach proved successful in identifying the validated cancer miRNAs for 11 common human cancers with area under ROC curve (AUC) ranging from 71.15% to 96.36%. The FCS method had a significant advantage over miRNA differential expression analysis when identifying cancer-related miRNAs with a fine regulatory mechanism, such as miR-27a in colorectal cancer. Furthermore, a case study examining thyroid cancer showed that the FCS method can uncover novel cancer-related miRNAs such as miR-27a/b, which were showed significantly upregulated in thyroid cancer samples by qRT-PCR analysis. Our method can be used on a web-based server, CMP (cancer miRNA prioritization) and is freely accessible at http://bioinfo.hrbmu.edu.cn/CMP. This time- and cost-effective computational framework can be a valuable complement to experimental studies and can assist with future studies of miRNA involvement in the pathogenesis of cancers. |
| publisher |
Oxford University Press |
| publishDate |
2011 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239203/ |
| _version_ |
1611494562689187840 |