Identification of Genes Associated with Breast Cancer Metastasis to Bone on a Protein–Protein Interaction Network with a Shortest Path Algorithm

2017 ◽  
Vol 16 (2) ◽  
pp. 1027-1038 ◽  
Author(s):  
Yu-Dong Cai ◽  
Qing Zhang ◽  
Yu-Hang Zhang ◽  
Lei Chen ◽  
Tao Huang
Keyword(s):  
Breast Cancer ◽  
Shortest Path ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Cancer Metastasis ◽  
Interaction Network ◽  
Breast Cancer Metastasis ◽  
Shortest Path Algorithm ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

scholarly journals Identifying Gastric Cancer Related Genes Using the Shortest Path Algorithm and Protein-Protein Interaction Network

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Yang Jiang ◽  
Yang Shu ◽  
Ying Shi ◽  
Li-Peng Li ◽  
Fei Yuan ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Shortest Path ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
High Probability ◽  
Biological Process ◽  
Interaction Network ◽  
Shortest Path Algorithm ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Gastric cancer, as one of the leading causes of cancer related deaths worldwide, causes about 800,000 deaths per year. Up to now, the mechanism underlying this disease is still not totally uncovered. Identification of related genes of this disease is an important step which can help to understand the mechanism underlying this disease, thereby designing effective treatments. In this study, some novel gastric cancer related genes were discovered based on the knowledge of known gastric cancer related ones. These genes were searched by applying the shortest path algorithm in protein-protein interaction network. The analysis results suggest that some of them are indeed involved in the biological process of gastric cancer, which indicates that they are the actual gastric cancer related genes with high probability. It is hopeful that the findings in this study may help promote the study of this disease and the methods can provide new insights to study various diseases.

scholarly journals Identification of Age-Related Macular Degeneration Related Genes by Applying Shortest Path Algorithm in Protein-Protein Interaction Network

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Jian Zhang ◽  
Min Jiang ◽  
Fei Yuan ◽  
Kai-Yan Feng ◽  
Yu-Dong Cai ◽  
...  
Keyword(s):  
Macular Degeneration ◽  
Shortest Path ◽  
Protein Interaction ◽  
Permutation Test ◽  
Interaction Network ◽  
Age Related Macular Degeneration ◽  
Shortest Path Algorithm ◽  
Protein Protein Interaction ◽  
Age Related ◽  
Protein Protein Interaction Network

This study attempted to find novel age-related macular degeneration (AMD) related genes based on 36 known AMD genes. The well-known shortest path algorithm, Dijkstra’s algorithm, was applied to find the shortest path connecting each pair of known AMD related genes in protein-protein interaction (PPI) network. The genes occurring in any shortest path were considered as candidate AMD related genes. As a result, 125 novel AMD genes were predicted. The further analysis based on betweenness and permutation test indicates that there are 10 genes involved in the formation or development of AMD and may be the actual AMD related genes with high probability. We hope that this contribution would promote the study of age-related macular degeneration and discovery of novel effective treatments.

A taxonomy of organ-specific breast cancer metastases based on a protein–protein interaction network

2012 ◽  
Vol 8 (8) ◽  
pp. 2085 ◽  
Author(s):  
Rebeca Sanz-Pamplona ◽  
Javier García-García ◽  
Sergi Franco ◽  
Xavier Messeguer ◽  
Keltouma Driouch ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Breast Cancer Metastases ◽  
Cancer Metastases ◽  
Organ Specific ◽  
Protein Protein Interaction Network

Topology of protein–protein interaction network and edge reduction co-efficiency in VEGF signaling of breast cancer

2017 ◽  
Vol 6 (1) ◽  
Author(s):  
Sharath Belenahalli Shekarappa ◽  
Shivananda Kandagalla ◽  
Pavan Gollapalli ◽  
Bharath Basavapattana Rudresh ◽  
Thriveni Hanumanthappa ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Vegf Signaling ◽  
Edge Reduction ◽  
Protein Protein Interaction Network

scholarly journals Circular RNA hsa_circ_0000376 Participates in Tumorigenesis of Breast Cancer by Targeting miR-1285-3p

2020 ◽  
Vol 19 ◽  
pp. 153303382092847
Author(s):  
Ziqi Peng ◽  
Boyang Xu ◽  
Feng Jin
Keyword(s):  
Breast Cancer ◽  
Protein Interaction ◽  
Protein Interaction Network ◽  
Interaction Network ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Messenger Rnas ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

This study was designed to identify novel circular RNAs and the related regulatory axis to provide research targets for the diagnosis and treatment of breast cancer. The circular RNA expression microarray “GSE101123” related to breast cancer was downloaded from the Gene Expression Omnibus database. The differentially expressed circular RNAs between tumor and normal samples were screened using Limma package. The targeted microRNAs of the differentially expressed circular RNAs and the targeted messenger RNAs of the microRNAs were predicted using miRanda and miRWalk, respectively, and a circular RNAs–microRNAs–messenger RNAs network was constructed. Then, functional enrichment analysis, protein–protein interaction network construction, and drug–gene interaction analysis were conducted for the messenger RNAs. A total of 11 differentially expressed circular RNAs were identified between the breast cancer and normal samples, of which 3 were upregulated, while 8 were downregulated. The circular RNA–microRNA–messenger RNA network contained 1 circular RNA (hsa_circ_0000376), 2 microRNAs (miR-1285-3p and miR-1286), and 353 messenger RNAs. The protein–protein interaction network contained 150 nodes and 240 interactions. The hub genes in the protein–protein interaction network were all targeted messenger RNAs of miR-1285-3p that were significantly enriched in the ubiquitin–proteasome system, apoptosis, cell cycle arrest–related pathways, and cancer-related pathways involving SMAD specific E3 ubiquitin protein ligase 1, β-transducin repeat containing E3 ubiquitin protein ligase, tumor protein P53 among others. Twenty-two drugs were predicted to target 4 messenger RNAs, including tumor protein P53. A novel circular RNA, hsa_circ_0000376, was identified in breast cancer that may act as a sponge targeting miR-1285-3p expression which through its target genes, SMURF1, BTRC, and TP53, may further regulate tumorigenesis.

Sign in / Sign up

Export Citation Format

Share Document