A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis)

Young, Rachel; Lefèvre, Lucas; Bush, Stephen J.; Joshi, Akshay; Singh, Shailesh Kumar; Jadhav, Santosh Kumar; Velu, Dhanikachalam; Lisowski, Zofia M.; Iamartino, Daniela; Summers, Kim M.; Williams, J. L.; Archibald, Alan; Gokhale, S. B.; Kumar, Satish; Hume, David

doi:10.3389/fgene.2019.00668

Cited by 38 publications

(25 citation statements)

References 54 publications

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“…As observed in other atlas projects (Hume et al, 2010;Freeman et al, 2012;FANTOM Consortium et al, 2014;Clark et al, 2017;Bush et al, 2018;Young et al, 2019) tissue-specific coregulated clusters contained the transcription factors that likely drive coexpression. For example, the thymus/T cell cluster (cluster 17) contains the transcription factors LEF1 and TCF7 which are known T lymphocyte regulators and the inner cell mass cluster (cluster 21) contains NANOG and PRDM14 which are involved in cell pluripotency.…”

Section: Network Analysis Of the Pig Transcriptomesupporting

confidence: 59%

“…For each library, expression was quantified using Kallisto v0.44.0 (Bray et al, 2016) as described in detail in previous studies on other species (Clark et al, 2017;Bush et al, 2018;Young et al, 2019). Kallisto quantifies expression at the transcript level, as transcripts per million (TPM), by building an index of k-mers from a set of reference transcripts and then "pseudo-aligning" reads to it, matching k-mers in the reads to k-mers in the index.…”

Section: Quantifying Gene Expression For the Atlasmentioning

confidence: 99%

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Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Summers

Bush

et al. 2020

Front. Genet.

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The domestic pig (Sus scrofa) is both an economically important livestock species and a model for biomedical research. Two highly contiguous pig reference genomes have recently been released. To support functional annotation of the pig genomes and comparative analysis with large human transcriptomic data sets, we aimed to create a pig gene expression atlas. To achieve this objective, we extended a previous approach developed for the chicken. We downloaded RNAseq data sets from public repositories, down-sampled to a common depth, and quantified expression against a reference transcriptome using the mRNA quantitation tool, Kallisto. We then used the network analysis tool Graphia to identify clusters of transcripts that were coexpressed across the merged data set. Consistent with the principle of guilt-by-association, we identified coexpression clusters that were highly tissue or cell-type restricted and contained transcription factors that have previously been implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes, such as the cell cycle and oxidative phosphorylation. The same approach was used to identify coexpression clusters within RNAseq data from multiple individual liver and brain samples, highlighting cell type, process, and region-specific gene expression. Evidence of conserved expression can add confidence to assignment of orthology between pig and human genes. Many transcripts currently identified as novel genes with ENSSSCG or LOC IDs were found to be coexpressed with annotated neighbouring transcripts in the same orientation, indicating they may be products of the same transcriptional unit. The metaanalytic approach to utilising public RNAseq data is extendable to include new data sets and new species and provides a framework to support the Functional Annotation of Animals Genomes (FAANG) initiative.

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Section: Network Analysis Of the Pig Transcriptomesupporting

confidence: 59%

Section: Quantifying Gene Expression For the Atlasmentioning

confidence: 99%

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Summers

Bush

et al. 2020

Front. Genet.

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“…In this analysis we reviewed all clusters with at least 5 nodes (probesets with expression patterns correlated at r ≥ 0.9). As we have seen in other studies [ 29 , 30 ] there was considerable individual dog-specific variation and many clusters were driven by high expression of a subset of genes in a single or small number of individuals, independent of disease status. These clusters were not analysed further.…”

Section: Resultssupporting

confidence: 72%

Comparative transcriptomic profiling of myxomatous mitral valve disease in the cavalier King Charles spaniel

et al. 2020

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Background Almost all elderly dogs develop myxomatous mitral valve disease by the end of their life, but the cavalier King Charles spaniel (CKCS) has a heightened susceptibility, frequently resulting in death at a young age and suggesting that there is a genetic component to the condition in this breed. Transcriptional profiling can reveal the impact of genetic variation through differences in gene expression levels. The aim of this study was to determine whether expression patterns were different in mitral valves showing myxomatous degeneration from CKCS dogs compared to valves from non-CKCS dogs. Results Gene expression patterns in three groups of canine valves resulted in distinct separation of normal valves, diseased valves from CKCS and diseased valves from other breeds; the latter were more similar to the normal valves than were the valves from CKCS. Gene expression patterns in diseased valves from CKCS dogs were quite different from those in the valves from other dogs, both affected and normal. Patterns in all diseased valves (from CKCS and other breeds) were also somewhat different from normal non-diseased samples. Analysis of differentially expressed genes showed enrichment in GO terms relating to cardiac development and function and to calcium signalling canonical pathway in the genes down-regulated in the diseased valves from CKCS, compared to normal valves and to diseased valves from other breeds. F2 (prothrombin) (CKCS diseased valves compared to normal) and MEF2C pathway activation (CKCS diseased valves compared to non-CKCS diseased valves) had the strongest association with the gene changes. A large number of genes that were differentially expressed in the CKCS diseased valves compared with normal valves and diseased valves from other breeds were associated with cardiomyocytes including CASQ2, TNNI3 and RYR2. Conclusion Transcriptomic profiling identified gene expression changes in CKCS diseased valves that were not present in age and disease severity-matched non-CKCS valves. These genes are associated with cardiomyocytes, coagulation and extra-cellular matrix remodelling. Identification of genes that vary in the CKCS will allow exploration of genetic variation to understand the aetiology of the disease in this breed, and ultimately development of breeding strategies to eliminate this disease from the breed.

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“…In this analysis we reviewed all clusters with at least 5 nodes (probesets with expression patterns correlated at r ≥ 0.9). As we have seen in other studies [29,30] there was considerable individual dog-speci c variation and many clusters were driven by high expression of a subset of genes in a single or small number of individuals, independent of disease status. These clusters were not analysed further.…”

Section: Network Analysis Of Samplessupporting

confidence: 71%

Comparative transcriptomic profiling of myxomatous mitral valve disease in the Cavalier King Charles Spaniel

Markby

MacRae

Corcoran

et al. 2020

Preprint

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Background. Almost all elderly dogs develop myxomatous mitral valve disease by the end of their life, but the Cavalier King Charles Spaniel (CKCS) has a heightened susceptibility, frequently resulting in death at a young age and suggesting that there is a genetic component to the condition in this breed. Transcriptional profiling can reveal the impact of genetic variation through differences in gene expression levels. The aim of this study was to determine whether expression patterns were different in mitral valves showing myxomatous degeneration from CKCS dogs compared to valves from non-CKCS dogs. Results. Gene expression patterns in three groups of canine valves resulted in distinct separation of normal valves, diseased valves from CKCS and diseased valves from other breeds; the latter were more similar to the normal valves than were the valves from CKCS. Gene expression patterns in diseased valves from CKCS dogs were quite different from those in the valves from other dogs, both affected and normal. Patterns in all diseased valves (from CKCS and other breeds) were also somewhat different from normal non-diseased samples. Analysis of differentially expressed genes showed enrichment in GO terms relating to cardiac development and function and to calcium signalling canonical pathway in the genes down-regulated in the diseased valves from CKCS, compared to normal valves and to diseased valves from other breeds. F2 (prothrombin) (CKCS diseased valves compared to normal) and MEF2C pathway activation (CKCS diseased valves compared to non-CKCS diseased valves) had the strongest association with the gene changes. A large number of genes that were differentially expressed in the CKCS diseased valves compared with normal valves and diseased valves from other breeds were associated with cardiomyocytes including CASQ2, TNNI3 and RYR2. Conclusion. Transcriptomic profiling identified gene expression changes in CKCS diseased valves that were not present in age and disease severity-matched non-CKCS valves. These genes are associated with cardiomyocytes, coagulation and extra-cellular matrix remodelling. Identification of genes that vary in the CKCS will allow exploration of genetic variation to understand the aetiology of the disease in this breed, and ultimately development of breeding strategies to eliminate this disease from the breed.

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A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis)

Cited by 38 publications

References 54 publications

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

Comparative transcriptomic profiling of myxomatous mitral valve disease in the cavalier King Charles spaniel

Comparative transcriptomic profiling of myxomatous mitral valve disease in the Cavalier King Charles Spaniel

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