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Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm.

Jiang Y, Zhang P, Li LP, He YC, Gao RJ, Gao YF - Biomed Res Int (2015)

Bottom Line: To this end, it is necessary to uncover the mechanism underlying this disease.In this study, we generalized some previous methods to discover both disease genes and chemicals.It is indicated that the proposed method is effective for the discovery of novel disease genes and chemicals.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China.

ABSTRACT
Thyroid cancer is a typical endocrine malignancy. In the past three decades, the continued growth of its incidence has made it urgent to design effective treatments to treat this disease. To this end, it is necessary to uncover the mechanism underlying this disease. Identification of thyroid cancer-related genes and chemicals is helpful to understand the mechanism of thyroid cancer. In this study, we generalized some previous methods to discover both disease genes and chemicals. The method was based on shortest path algorithm and applied to discover novel thyroid cancer-related genes and chemicals. The analysis of the final obtained genes and chemicals suggests that some of them are crucial to the formation and development of thyroid cancer. It is indicated that the proposed method is effective for the discovery of novel disease genes and chemicals.

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Related in: MedlinePlus

The top twelve KEGG pathways that were enriched by 169 significant candidate genes.
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fig2: The top twelve KEGG pathways that were enriched by 169 significant candidate genes.

Mentions: For the KEGG pathway enrichment analysis results, 169 candidate genes are enriched in 19 KEGG pathways (see Online Supporting Information S4). Among these 19 KEGG pathways, twelve of them were with P value (modified Fisher exact P value) less than 0.05. Figure 2 shows these twelve KEGG pathways and the number of enriched genes among the significant candidate genes (“count”). Hsa05200 (pathways in cancer, “count” = 20) is the most significant pathway, which enriched 20 significant candidate genes, such as FGFR2, FGF6, DVL3, EPAS1, and PPARG. Since all these genes enriched in this pathway were reported related to cancer formation and development, it further revealed the validity of our method. Hsa05211 (renal cell carcinoma, “count” = 7) is the second significant pathway with 7 genes related to renal cell carcinoma. Hsa04722 (neurotrophin signaling pathway, “count” = 7) is the third significant pathway, enriching 7 genes, such as KRAS, PLCG1, and NTF3. Among them, NTF3 in neurotrophin signaling pathway has been reported with the association to cancer [40]. Other pathways, such as hsa05221 (acute myeloid leukemia, “count” = 5) and hsa05215 (prostate cancer, “count” = 6), also revealed that the significant candidate genes are associated with cancer.


Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm.

Jiang Y, Zhang P, Li LP, He YC, Gao RJ, Gao YF - Biomed Res Int (2015)

The top twelve KEGG pathways that were enriched by 169 significant candidate genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385622&req=5

fig2: The top twelve KEGG pathways that were enriched by 169 significant candidate genes.
Mentions: For the KEGG pathway enrichment analysis results, 169 candidate genes are enriched in 19 KEGG pathways (see Online Supporting Information S4). Among these 19 KEGG pathways, twelve of them were with P value (modified Fisher exact P value) less than 0.05. Figure 2 shows these twelve KEGG pathways and the number of enriched genes among the significant candidate genes (“count”). Hsa05200 (pathways in cancer, “count” = 20) is the most significant pathway, which enriched 20 significant candidate genes, such as FGFR2, FGF6, DVL3, EPAS1, and PPARG. Since all these genes enriched in this pathway were reported related to cancer formation and development, it further revealed the validity of our method. Hsa05211 (renal cell carcinoma, “count” = 7) is the second significant pathway with 7 genes related to renal cell carcinoma. Hsa04722 (neurotrophin signaling pathway, “count” = 7) is the third significant pathway, enriching 7 genes, such as KRAS, PLCG1, and NTF3. Among them, NTF3 in neurotrophin signaling pathway has been reported with the association to cancer [40]. Other pathways, such as hsa05221 (acute myeloid leukemia, “count” = 5) and hsa05215 (prostate cancer, “count” = 6), also revealed that the significant candidate genes are associated with cancer.

Bottom Line: To this end, it is necessary to uncover the mechanism underlying this disease.In this study, we generalized some previous methods to discover both disease genes and chemicals.It is indicated that the proposed method is effective for the discovery of novel disease genes and chemicals.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China.

ABSTRACT
Thyroid cancer is a typical endocrine malignancy. In the past three decades, the continued growth of its incidence has made it urgent to design effective treatments to treat this disease. To this end, it is necessary to uncover the mechanism underlying this disease. Identification of thyroid cancer-related genes and chemicals is helpful to understand the mechanism of thyroid cancer. In this study, we generalized some previous methods to discover both disease genes and chemicals. The method was based on shortest path algorithm and applied to discover novel thyroid cancer-related genes and chemicals. The analysis of the final obtained genes and chemicals suggests that some of them are crucial to the formation and development of thyroid cancer. It is indicated that the proposed method is effective for the discovery of novel disease genes and chemicals.

Show MeSH
Related in: MedlinePlus