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Future Science OA Volume 7, 2021 - Issue 9
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Research Article

Coexpression Network Analysis Identified lncRNAs-mRNAs With Potential Relevance in African Ancestry Prostate Cancer

Rafael Parra-Medina1 Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia;2 Department of Pathology, Research Institute, Fundación Univeristaria de Ciencias de la Salud, Bogotá, Colombia;3 Deparment of Pathology, Instituto Nacional de Cancerología, Bogotá, ColombiaORCID Iconhttps://orcid.org/0000-0002-8428-5837
ORCID Icon,
Liliana López-Kleine4 Department of Statistics, Faculty of Science, Universidad Nacional de Colombia, Bogotá, ColombiaORCID Iconhttps://orcid.org/0000-0001-9325-9529
ORCID Icon,
Sandra Ramírez-Clavijo1 Faculty of Natural Sciences, Universidad del Rosario, Bogotá, ColombiaORCID Iconhttps://orcid.org/0000-0003-0336-5614
ORCID Icon &
César Payán-Gómez1 Faculty of Natural Sciences, Universidad del Rosario, Bogotá, ColombiaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-0633-1332
ORCID Icon
Article: FSO749 | Received 05 Jun 2021, Accepted 30 Jul 2021, Published online: 24 Sep 2021

Figures & data

Table 1. Number and direction of the change of differentially expressed mRNA and lncRNA in African ancestry and European ancestry.

Figure 1. Venn diagrams show the number of (A) DE mRNAs in AA and EA.

(B) lncRNAs in AA and EA.

AA: African ancestry; EA: European Ancestry.

Figure 1. Venn diagrams show the number of (A) DE mRNAs in AA and EA.(B) lncRNAs in AA and EA.AA: African ancestry; EA: European Ancestry.

Table 2. mRNAs and lncRNAs differentially expressed between prostate cancer samples from patients of African ancestry and European ancestry.

Figure 2. Pathway enrichment analysis for the differentially expressed between genes in patients of African ancestry and European ancestry (p < 0.05).

(A) Enriched KEGG pathways for upregulated genes in AA. (B) Enriched KEGG pathways for upregulated genes in EA. (C) Enriched KEGG pathways for downregulated genes in AA (MAPK and WNT pathways). (D) Enriched KEGG pathways for upregulated genes in EA.

AA: African ancestry; EA: European Ancestry; KEGG: Kyoto Encyclopedia of Genes and Genomes.

Figure 2. Pathway enrichment analysis for the differentially expressed between genes in patients of African ancestry and European ancestry (p < 0.05).(A) Enriched KEGG pathways for upregulated genes in AA. (B) Enriched KEGG pathways for upregulated genes in EA. (C) Enriched KEGG pathways for downregulated genes in AA (MAPK and WNT pathways). (D) Enriched KEGG pathways for upregulated genes in EA.AA: African ancestry; EA: European Ancestry; KEGG: Kyoto Encyclopedia of Genes and Genomes.
Figure 3. Co-expression network of DE mRNA and lncRNA in African ancestry tumor samples.

lncRNA are marked in red and mRNA are marked in blue. Four networks with more than eight nodes of co-expressed genes are shown, one network co-expressed three lncRNA and another network co-expressed two lncRNA. Two tightly connected networks of the same family of genes (Protocadherin Alpha and TBC1 domain family member and 3 [TBC1D3]). In the quintet network one lncRNA was co-expressed. One quartets network was with only lncRNA co-expressed. Among the five trios networks, two had two lncRNA co-expressed and the other only one. Small networks with fewer than two nodes are not shown.

Figure 3. Co-expression network of DE mRNA and lncRNA in African ancestry tumor samples.lncRNA are marked in red and mRNA are marked in blue. Four networks with more than eight nodes of co-expressed genes are shown, one network co-expressed three lncRNA and another network co-expressed two lncRNA. Two tightly connected networks of the same family of genes (Protocadherin Alpha and TBC1 domain family member and 3 [TBC1D3]). In the quintet network one lncRNA was co-expressed. One quartets network was with only lncRNA co-expressed. Among the five trios networks, two had two lncRNA co-expressed and the other only one. Small networks with fewer than two nodes are not shown.
Figure 4. Co-expression network of the differences between African ancestry less European ancestry networks.

lncRNA are marked in red and mRNA are marked in blue. One network co-expressed three lncRNA and three network co-expressed one lncRNA. Most of the small networks with fewer than two nodes are not shown.

Figure 4. Co-expression network of the differences between African ancestry less European ancestry networks.lncRNA are marked in red and mRNA are marked in blue. One network co-expressed three lncRNA and three network co-expressed one lncRNA. Most of the small networks with fewer than two nodes are not shown.

Table 3. lncRNAs and mRNAs coexpressed in African ancestry.

Figure 5. Kaplan–Meier survival plots for overall survival related to DE genes between tumors from patients of African ancestry versus tumors from patients of European ancestry and genes coexpressed with lncRNA in the African ancestry-European ancestry coexpression network.

The X and Y axes represent survival time (months) and disease-free survival, respectively. The analysis was made in GEPIA.

Figure 5. Kaplan–Meier survival plots for overall survival related to DE genes between tumors from patients of African ancestry versus tumors from patients of European ancestry and genes coexpressed with lncRNA in the African ancestry-European ancestry coexpression network.The X and Y axes represent survival time (months) and disease-free survival, respectively. The analysis was made in GEPIA.
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