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Functional and protein‑protein interaction network analysis of colorectal cancer induced by ulcerative colitis.

Dai Y, Jiang JB, Wang YL, Jin ZT, Hu SY - Mol Med Rep (2015)

Bottom Line: Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness.PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes.The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.

View Article: PubMed Central - PubMed

Affiliation: Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.

ABSTRACT
Colorectal cancer (CRC) is a well‑recognized complication of ulcerative colitis (UC), and patients with UC have a higher incidence of CRC, compared with the general population. However, the properties of CRC induced by UC have not been clarified using an interaction network to analyze and compare gene sets. In the present study, six microarray datasets of CRC and UC were extracted from the Array Express database, and gene signatures were identified using the genome‑wide relative significance (GWRS) method. Functional analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Prediction of the genes and microRNA were performed using a hypergeometric method. A protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins, and clusters were obtained through the Molecular Complex Detection algorithm. Topological centrality and a novel analyzing method, based on the rank value of GWGS, were used to characterize the biological importance of the clusters. A total of 217 differentially expressed (DE) genes of CRC were identified, 341 DE genes were identified in UC, and 62 common genes existed in the two. Several KEGG pathways were the same in CRC and UC. Collagenase, progesterone, heparin, urokinase, nadh and adenosine drugs demonstrated potential for use in treatment of CRC and UC. In the PPI network of CRC, 210 nodes and 752 edges were observed, wheras 314 nodes and 882 edges were identified in UC. Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness. PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes. The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.

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Related in: MedlinePlus

Centralities analysis based on the degree of the clusters. (A) Cluster 1 of CRC; (B) cluster 2 of CRC; (C) cluster 3 of CRC; (D) cluster 1 of UC; (E) cluster 2 of UC; (F) cluster 3 of UC. No significant differences were observed between the degrees of the clusters in CRC. Cluster 2 of UC had the highest degree (29), while Cluster 3 of UC had the lowest degree (13). CRC, colorectal cancer; UC, ulcerative colitis.
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f5-mmr-12-04-4947: Centralities analysis based on the degree of the clusters. (A) Cluster 1 of CRC; (B) cluster 2 of CRC; (C) cluster 3 of CRC; (D) cluster 1 of UC; (E) cluster 2 of UC; (F) cluster 3 of UC. No significant differences were observed between the degrees of the clusters in CRC. Cluster 2 of UC had the highest degree (29), while Cluster 3 of UC had the lowest degree (13). CRC, colorectal cancer; UC, ulcerative colitis.

Mentions: The degree and betweenness centralities for the clusters in CRC and UC were calculated. As shown in Fig. 5, the topological centrality-based degree among the clusters revealed that Cluster 2 of UC had the highest degree at 29), while Cluster 3 of UC had the lowest degree at 13. As shown in Fig. 6, the betweenness of Cluster 3 also had the lowest betweenness (0.02). GWGS is closely associated with log2FC and indicates the corresponding degree of the DE genes, with DE genes of a higher degree exhibiting higher ranking values. As shown in Fig. 7, no significant difference was observed in the rank values between CRC and UC. On comparison of the clusters in CRC, Cluster 1 had the highest rank value (5.02), while cluster 3 of UC had the highest rank value (5.91).


Functional and protein‑protein interaction network analysis of colorectal cancer induced by ulcerative colitis.

Dai Y, Jiang JB, Wang YL, Jin ZT, Hu SY - Mol Med Rep (2015)

Centralities analysis based on the degree of the clusters. (A) Cluster 1 of CRC; (B) cluster 2 of CRC; (C) cluster 3 of CRC; (D) cluster 1 of UC; (E) cluster 2 of UC; (F) cluster 3 of UC. No significant differences were observed between the degrees of the clusters in CRC. Cluster 2 of UC had the highest degree (29), while Cluster 3 of UC had the lowest degree (13). CRC, colorectal cancer; UC, ulcerative colitis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581825&req=5

f5-mmr-12-04-4947: Centralities analysis based on the degree of the clusters. (A) Cluster 1 of CRC; (B) cluster 2 of CRC; (C) cluster 3 of CRC; (D) cluster 1 of UC; (E) cluster 2 of UC; (F) cluster 3 of UC. No significant differences were observed between the degrees of the clusters in CRC. Cluster 2 of UC had the highest degree (29), while Cluster 3 of UC had the lowest degree (13). CRC, colorectal cancer; UC, ulcerative colitis.
Mentions: The degree and betweenness centralities for the clusters in CRC and UC were calculated. As shown in Fig. 5, the topological centrality-based degree among the clusters revealed that Cluster 2 of UC had the highest degree at 29), while Cluster 3 of UC had the lowest degree at 13. As shown in Fig. 6, the betweenness of Cluster 3 also had the lowest betweenness (0.02). GWGS is closely associated with log2FC and indicates the corresponding degree of the DE genes, with DE genes of a higher degree exhibiting higher ranking values. As shown in Fig. 7, no significant difference was observed in the rank values between CRC and UC. On comparison of the clusters in CRC, Cluster 1 had the highest rank value (5.02), while cluster 3 of UC had the highest rank value (5.91).

Bottom Line: Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness.PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes.The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.

View Article: PubMed Central - PubMed

Affiliation: Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.

ABSTRACT
Colorectal cancer (CRC) is a well‑recognized complication of ulcerative colitis (UC), and patients with UC have a higher incidence of CRC, compared with the general population. However, the properties of CRC induced by UC have not been clarified using an interaction network to analyze and compare gene sets. In the present study, six microarray datasets of CRC and UC were extracted from the Array Express database, and gene signatures were identified using the genome‑wide relative significance (GWRS) method. Functional analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Prediction of the genes and microRNA were performed using a hypergeometric method. A protein‑protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/proteins, and clusters were obtained through the Molecular Complex Detection algorithm. Topological centrality and a novel analyzing method, based on the rank value of GWGS, were used to characterize the biological importance of the clusters. A total of 217 differentially expressed (DE) genes of CRC were identified, 341 DE genes were identified in UC, and 62 common genes existed in the two. Several KEGG pathways were the same in CRC and UC. Collagenase, progesterone, heparin, urokinase, nadh and adenosine drugs demonstrated potential for use in treatment of CRC and UC. In the PPI network of CRC, 210 nodes and 752 edges were observed, wheras 314 nodes and 882 edges were identified in UC. Cluster 3 in UC had the highest GWGS, while the topological centrality of Cluster 3 in UC had the lowest degree and betweenness. PPI network analysis provided an effective way to estimate and understand the likelihood of the potential connections between proteins/genes. The results obtained following the use of GWGS to analyze differences between clusters did not agree with the topological degree and betweenness centrality, which indicated that gene fold change based GWGS was controversial with degree here in CRC and UC.

Show MeSH
Related in: MedlinePlus