Predicting the effect of LncRNAs on different types of cancers in bipartite networks using link prediction

Document Type : Original Article

Authors

1 Department of Genetics, Faculty of Basic Science, Shahrekord University, Shahrekord, Iran,

2 Department of Biology, Faculty of Basic Science, Islamic Republic Azad University, Tehran, Iran.

3 Department of Biological Science, University of Kurdistan, Sanandaj, Iran

Abstract

Many complex systems such as the Internet, the World Wide Web, the brain, and the causes of diseases can be described by networks with nodes representing agents and links representing relationships or interactions between nodes. Despite these systems seeming utterly different at first glance, they are all made up of interacting parts. Individual objects in this type of system are not isolated but connected through links or relationships. Long non-coding RNAs (LncRNAs), one of the factors related to many diseases, are specific genes in the human genome that control many different biological processes. lncRNAs have been shown to regulate cancer development and occurrence. We used link prediction bioinformatics tools to identify lncRNAs affecting various types of cancers. To achieve this goal, two-part networks were used using CN (Common Neighbors), AA (Adamic/Adar), PA (Preferential Attachment), and JC (Jaccard's Coefficient) algorithms. The results indicated that all the obtained lncRNAs with a high score had been reviewed in other research articles, which was a sign of the correctness of our algorithms. 4.5% of the obtained results lacked scientific and research studies, all with a high score for future studies and included lncRNA H19 and SPRY4-IT1. In addition, in one case with a high score and first position in the Excel file obtained using the Jaccard coefficient algorithm, lncRNA with the symbol AC09510.3 was associated with adenocarcinoma. Still, this possible link has not been investigated in any article yet.
Conclusion: The current study may identify novel lncRNAs implicated in Adenocarcinoma, vulva squamous cell carcinoma, basal cell carcinoma, gestational choriocarcinoma, chromophobe renal cell carcinoma, brain cancer, pancreatic cancer, hepatocellular carcinoma, prostate cancer, embryonal cancer, germ cell cancer, and choriocarcinoma; however, further research is required to determine the potential functions of this lncRNAs in cancers mentioned above.

Keywords

Main Subjects

References

Ahmad, I., M. U. Akhtar, S. Noor and A. Shahnaz (2020). "Missing link prediction using common neighbor and centrality based parameterized algorithm." Scientific reports 10(1): 1-9.
Albert, R. and A.-L. Barabási (2002). "Statistical mechanics of complex networks." Reviews of modern physics 74(1): 47.
 
Ali, T. and P. Grote (2020). "Beyond the RNA-dependent function of LncRNA genes." Elife 9: e60583.
 
Bhan, A. and S. S. Mandal (2015). "LncRNA HOTAIR: A master regulator of chromatin dynamics and cancer." Biochimica et Biophysica Acta (BBA)-Reviews on Cancer 1856(1): 151-164.
 
Boccaletti, S., V. Latora, Y. Moreno, M. Chavez and D.-U. Hwang (2006). "Complex networks: Structure and dynamics." Physics reports 424(4-5): 175-308.
 
Bridges, M. C., A. C. Daulagala and A. Kourtidis (2021). "LNCcation: lncRNA localization and function." Journal of Cell Biology 220(2).
 
Cheng, C., J. Chen, X. Cao and H. Guo (2016). "Comparison of local information indices applied in resting state functional brain network connectivity prediction." Frontiers in neuroscience 10: 585.
 
Coşkun, M. and M. Koyutürk (2021). "Node similarity-based graph convolution for link prediction in biological networks." Bioinformatics 37(23): 4501-4508.
 
Costa, L. d. F., F. A. Rodrigues, G. Travieso and P. R. Villas Boas (2007). "Characterization of complex networks: A survey of measurements." Advances in physics 56(1): 167-242.
 
Dorogovtsev, S. N., A. V. Goltsev and J. F. F. Mendes (2002). "Pseudofractal scale-free web." Physical review E 65(6): 066122.
 
Gao, Q., X. Fang, Y. Chen, Z. Li and M. Wang (2021). "Exosomal lncRNA UCA1 from cancer‐associated fibroblasts enhances chemoresistance in vulvar squamous cell carcinoma cells." Journal of Obstetrics and Gynaecology Research 47(1): 73-87.
 
Ghasemian, A., H. Hosseinmardi, A. Galstyan, E. M. Airoldi and A. Clauset (2020). "Stacking models for nearly optimal link prediction in complex networks." Proceedings of the National Academy of Sciences 117(38): 23393-23400.
 
Guo, X., N. Liu and M. Liu (2019). "Long non-coding RNA LINC00336 as an independent prognostic indicator and an oncogenic lncRNA in bladder cancer." Archives of Medical Science 15(1).
 
He, Y., F. Yang, Y. Yu and C. Grebogi (2018). "Link prediction investigation of dynamic information flow in epilepsy." Journal of Healthcare Engineering 2018.
 
Hua, Q., X. Lv, X. Gu, Y. Chen, H. Chu, M. Du, W. Gong, M. Wang and Z. Zhang (2016). "Genetic variants in lncRNA H19 are associated with the risk of bladder cancer in a Chinese population." Mutagenesis 31(5): 531-538.
 
Jaccard, P. (1901). "Étude comparative de la distribution florale dans une portion des Alpes et des Jura." Bull Soc Vaudoise Sci Nat 37: 547-579.
 
Jafari, S. H., A. M. Abdolhosseini-Qomi, M. Asadpour, M. Rahgozar and N. Yazdani (2021). "An information theoretic approach to link prediction in multiplex networks." Scientific Reports 11(1): 1-21.
 
Kerrache, S., R. Alharbi and H. Benhidour (2020). "A scalable similarity-popularity link prediction method." Scientific reports 10(1): 1-14.
 
Li, S., J. Huang, Z. Zhang, J. Liu, T. Huang and H. Chen (2018). "Similarity-based future common neighbors model for link prediction in complex networks." Scientific reports 8(1): 1-11.
 
Lü, L. and T. Zhou (2010). "Link prediction in weighted networks: The role of weak ties." EPL (Europhysics Letters) 89(1): 18001.
 
Naz, F., I. Tariq, S. Ali, A. Somaida, E. Preis and U. Bakowsky (2021). "The role of long non-coding RNAs (lncRNAs) in female oriented cancers." Cancers 13(23): 6102.
 
Newman, M. E. (2001). "Clustering and preferential attachment in growing networks." Physical review E 64(2): 025102.
 
Newman, M. E. (2003). "The structure and function of complex networks." SIAM review 45(2): 167-256.
 
Peng, W.-X., P. Koirala and Y.-Y. Mo (2017). "LncRNA-mediated regulation of cell signaling in cancer." Oncogene 36(41): 5661-5667.
 
Pournoor, E., Z. Mousavian, A. N. Dalini and A. Masoudi-Nejad (2020). "Identification of key components in colon adenocarcinoma using transcriptome to interactome multilayer framework." Scientific reports 10(1): 1-14.
 
Qiu, X., X. Zhong and H. Zhang (2021). "Applied research on the combination of weighted network and supervised learning in acupoints compatibility." Journal of Healthcare Engineering 2021.
 
Shang, K.-k. and M. Small (2022). "Link prediction for long-circle-like networks." Physical Review E 105(2): 024311.
 
Wang, G.-Y., Y.-Y. Zhu and Y.-Q. Zhang (2014). "The functional role of long non-coding RNA in digestive system carcinomas." Bulletin du Cancer 101(9): E27-E31.
 
Wang, H. and Z. Le (2020). "Seven-layer model in complex networks link prediction: A survey." Sensors 20(22): 6560.
 
Wang, J., Z. Su, S. Lu, W. Fu, Z. Liu, X. Jiang and S. Tai (2018). "LncRNA HOXA-AS2 and its molecular mechanisms in human cancer." Clinica chimica acta 485: 229-233.
 
Xing, C., S.-g. Sun, Z.-Q. Yue and F. Bai (2021). "Role of lncRNA LUCAT1 in cancer." Biomedicine & Pharmacotherapy 134: 111158.
 
Zhang, G., X. An, H. Zhao, Q. Zhang and H. Zhao (2018). "Long non-coding RNA HNF1A-AS1 promotes cell proliferation and invasion via regulating miR-17-5p in non-small cell lung cancer." Biomedicine & pharmacotherapy 98: 594-599.
 
Zhang, L., D. Wang and P. Yu (2018). "LncRNA H19 regulates the expression of its target gene HOXA10 in endometrial carcinoma through competing with miR-612." Eur Rev Med Pharmacol Sci 22(15): 4820-4827.
 
Zhang, Z., W. Qian, S. Wang, D. Ji, Q. Wang, J. Li, W. Peng, J. Gu, T. Hu and B. Ji (2018). "Analysis of lncRNA-associated ceRNA network reveals potential lncRNA biomarkers in human colon adenocarcinoma." Cellular Physiology and Biochemistry 49(5): 1778-1791.
Journal of Epigenetics
Volume 4, Issue 1 - Serial Number 1
September 2023
Pages 45-40

Files

History

  • Receive Date: 16 April 2023
  • Revise Date: 18 September 2023
  • Accept Date: 07 October 2023

Share

How to cite

Statistics