LYVE1 and PROX1 in the reconstruction of hepatic sinusoids after partial hepatectomy in mice

Meng, Fanwei

doi:10.5603/fm.a2016.0074

Cited by 8 publications

(9 citation statements)

References 28 publications

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“…• Cluster 0: Endothelial cells Markers: Pecam1,Ushbp1,Oit3,F8, Bmp2, C1qtnf1, Mmrn2, Pcdh12, Dpp4, Tek, S100a1, Tie1, Egfl7, Scarf1, Stab2, Lyve1, Icam2, Sox18, Flt4, Nr2f2 [59,22,26,53,57,62,28,43,54,30,18,17,15].…”

Section: -Samplementioning

confidence: 99%

Bayesian Correlation is a robust similarity measure for single cell RNA-seq data

Sánchez-Taltavull

Perkins

Dommann

et al. 2019

Preprint

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AbstractAssessing similarity is highly important for bioinformatics algorithms to determine correlations between biological information. A common problem is that similarity can appear by chance, particularly for low expressed entities. This is especially relevant in single cell RNA-seq (scRNA-seq) data because read counts are much lower compared to bulk RNA-seq.Recently, a Bayesian correlation scheme, that assigns low similarity to genes that have low confidence expression estimates, has been proposed to assess similarity for bulk RNA-seq. Our goal is to extend the properties of the Bayesian correlation in scRNA-seq data by considering 3 ways to compute similarity. First, we compute the similarity of pairs of genes over all cells. Second, we identify specific cell populations and compute the correlation in those populations. Third, we compute the similarity of pairs of genes over all clusters, by considering the total mRNA expression.We demonstrate that Bayesian correlations are more reproducible than Pearson correlations. Compared to Pearson correlations, Bayesian correlations have a smaller dependence on the number of input cells. We show that the Bayesian correlation algorithm assigns high similarity values to genes with a biological relevance in a specific population.We conclude that Bayesian correlation is a robust similarity measure in scRNA-seq data.

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Section: -Samplementioning

confidence: 99%

Bayesian Correlation is a robust similarity measure for single cell RNA-seq data

Sánchez-Taltavull

Perkins

Dommann

et al. 2019

Preprint

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“…Meng (2017) 12 found that PROX1 and LYVE1 correlate with liver regeneration and can be used as biomarkers to identify formation of new liver sinusoidal endothelial cells. However, Meng (2017) 12 did not indicate how the endothelial cells constitute sinusoidal final shape. The abovementioned studies found factors correlated with organogenesis (see orange highlight in Table 3).…”

Section: Factors Associated With Regeneration Process Pacementioning

confidence: 99%

Organogenesis: A New Theme to Study Genetic Expression in Adult Liver Regeneration After Partial Hepatectomy

Witwit¹

2019

Preprint

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Researchers in different disciplines studied liver’s genetic expression of organogenesis in embryogenesis; however, organogenesis has not been studied as an independent and a complementary process during adult liver regeneration. This paper reviewed studies and extracted information related to organogenesis in adult liver regeneration because of organogenesis’ important role in cancer and tissue regeneration.

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“…While many studies investigated different factors involved in liver regeneration, only a few researched factors involved in organogenesis (Table 3) investigated hepatocyte nuclear factor (vHnf1) gene and its effect on regeneration process and concluded that a lack of vHNF1 leads to formation of a defective hepatic bud and an abnormal gut regionalization. Meng (2017) 9 found that PROX1 and LYVE1 correlate with liver regeneration and can be used as biomarkers to identify formation of new liver sinusoidal endothelial cells. However, Meng (2017) 9 did not indicate how the endothelial cells constitute sinusoidal final shape.…”

Section: Factors Associated With Regeneration Process Pacementioning

confidence: 99%

“…Meng (2017) 9 found that PROX1 and LYVE1 correlate with liver regeneration and can be used as biomarkers to identify formation of new liver sinusoidal endothelial cells. However, Meng (2017) 9 did not indicate how the endothelial cells constitute sinusoidal final shape. The abovementioned studies found factors correlated with organogenesis (see orange highlight in Table 3).…”

Section: Factors Associated With Regeneration Process Pacementioning

confidence: 99%

Organogenesis: A New Theme to Study Genetic Expression in Adult Liver Regeneration After Partial Hepatectomy

Witwit¹

2018

Preprint

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Researchers in different disciplines studied liver's genetic expression of organogenesis in embryogenesis; however, organogenesis has not been studied as an independent and a complementary process during adult liver regeneration. This paper reviewed studies and extracted information related to organogenesis in adult liver regeneration because of organogenesis' important role in cancer and tissue regeneration.

show abstract

LYVE1 and PROX1 in the reconstruction of hepatic sinusoids after partial hepatectomy in mice

Cited by 8 publications

References 28 publications

Bayesian Correlation is a robust similarity measure for single cell RNA-seq data

Bayesian Correlation is a robust similarity measure for single cell RNA-seq data

Organogenesis: A New Theme to Study Genetic Expression in Adult Liver Regeneration After Partial Hepatectomy

Organogenesis: A New Theme to Study Genetic Expression in Adult Liver Regeneration After Partial Hepatectomy

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