Identification of Differentially Expressed Genes Between Preadipocytes and Adipocytes Using Affymetrix Bovine Genome Array

Yu, Seong Lan; Lee, Sang Mi; Kang, Man‐Jong; Jeong, Hang Jin; Sang, B. C.; Jeon, J. T.; Lee, Jun Heon

doi:10.5187/jast.2009.51.6.443

Cited by 8 publications

(7 citation statements)

References 28 publications

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“…The RNF220 gene is involved in calving performance and milk yield ( Abdel-Shafy et al, 2020 ; Purfield et al, 2020 ). In addition, the HECTD3 in this region is associated with cell cycle regulation and fat deposition, while PLK3 is related to gain and feed intake in cattle ( Yu et al, 2009 ; Bahbahani et al, 2015 ; Zarek et al, 2017 ). We also detected in this region the PTCH2 and SLC6A9 which are involved in reproduction and Porphyria disease, respectively ( Nezamzadeh et al, 2005 ; Basavaraja et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

et al. 2021

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The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Section: Discussionmentioning

confidence: 99%

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

et al. 2021

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“…These findings support our suggestion that K1 is significant in terms of CWT. K2 and K4, associated with fat-related traits (BF and IMF) in DEM analysis, include eight ( ACSL3 [30], NFKB1 [31], CYP2R1 [32], HSF2 [33], TMEM135 [34], PDCD4 [35], HERPUD2 [36], and NMRAL1 [37]) and seven ( SPNS1 [31], MYOD1 [38], PDXK [39], TMUB1 [34], ARHGAP26 [40], RAB15 [31], and TP73 [41]) fat-related hub genes, respectively. Thus, future research should identify the relationships between fat metabolism and modules K2 and K4.…”

Section: Resultsmentioning

confidence: 99%

“…NFKB1 [31], CYP2R1 [32], HSF2 [33], TMEM135 [34], PDCD4 [35], HERPUD2 [36], and NMRAL1 [37]) and seven (SPNS1 [31], MYOD1 [38], PDXK [39], TMUB1 [34],…”

Section: Hub Gene Searches For Modules Of Interestmentioning

confidence: 99%

Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle

Lee

Chung

Chung³

et al. 2021

Preprint

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In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar. Here, a novel gene module clustering algorithm for WGCNA is proposed. We develop a gene module clustering network (gmcNet), which simultaneously addresses single-level expression and topological overlap measure. The proposed gmcNet includes a "co-expression pattern recognizer" (CEPR) and "module classifier". The CEPR incorporates expression features of single genes into the topological features of co-expressed ones. Given this CEPR-embedded feature, the module classifier computes module assignment probabilities. We validated gmcNet performance using 4,976 genes from 20 native Korean cattle. We observed that the CEPR generates more robust features than single-level expression or topological overlap measure. Given the CEPR-embedded feature, gmcNet achieved the best performance in terms of modularity (0.261) and the differentially expressed signal (27.739) compared with other clustering methods tested. Furthermore, gmcNet detected some interesting biological functionalities for carcass weight, backfat thickness, intramuscular fat, and beef tenderness of Korean native cattle. Therefore, gmcNet is a useful framework for WGCNA module clustering.

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“…These findings support our suggestion that K1 is significant in terms of CWT. K2 and K4, associated with fat-related traits (BF and IMF) in DEM analysis, include eight (ACSL3 31 , NFKB1 32 , CYP2R1 33 , HSF2 34 , TMEM135 35 , PDCD4 36 , HERPUD2 37 ,…”

Section: Hub Gene Searches For Modules Of Interestmentioning

confidence: 99%

Use of a Graph Neural Network to the Weighted Gene Co-expression Network Analysis of Korean Native Cattle

Lee

Chung

Chung³

et al. 2021

Preprint

View full text Add to dashboard Cite

In the general framework of the weighted gene co-expression network analysis (WGCNA), a hierarchical clustering algorithm is commonly used to module definition. However, hierarchical clustering depends strongly on the topological overlap measure. In other words, this algorithm may assign two genes with low topological overlap to different modules even though their expression patterns are similar. Here, a novel gene module clustering algorithm for WGCNA is proposed. We develop a gene module clustering network (gmcNet), which simultaneously addresses single-level expression and topological overlap measure. The proposed gmcNet includes a “co-expression pattern recognizer" (CEPR) and “module classifier". The CEPR incorporates expression features of single genes into the topological features of co-expressed ones. Given this CEPR-embedded feature, the module classifier computes module assignment probabilities. We validated gmcNet performance using 4,976 genes from 20 native Korean cattle. We observed that the CEPR generates more robust features than single-level expression or topological overlap measure. Given the CEPR-embedded feature, gmcNet achieved the best performance in terms of modularity (0.261) and the differentially expressed signal (27.739) compared with other clustering methods tested. Furthermore, gmcNet detected some interesting biological functionalities for carcass weight, backfat thickness, intramuscular fat, and beef tenderness of Korean native cattle. Therefore, gmcNet is a useful framework for WGCNA module clustering.

show abstract

Identification of Differentially Expressed Genes Between Preadipocytes and Adipocytes Using Affymetrix Bovine Genome Array

Cited by 8 publications

References 28 publications

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Use of a graph neural network to the weighted gene co-expression network analysis of Korean native cattle

Use of a Graph Neural Network to the Weighted Gene Co-expression Network Analysis of Korean Native Cattle

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