Table 4 Diet-induced differential expression of lncRNA genes.

From: Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver

Gene symbol

edgeR FC (H/S)

edgeR FDR

nCounter FC (H/S)

nCounter p-Value

nCounter targeted transcript isoforms

A330076H08Rik

0.02

1.9E-03

0.74

3.29E-01

ENSMUST00000181804

0.45

1.17E-02

ENSMUST00000181187

A530040E14Rik

0.06

6.0E-02

0.39

1.95E-02

ENSMUST00000161666

ENSMUST00000162453

0.29

3.47E-03

ENSMUST00000162353

ENSMUST00000093501

ENSMUST00000161150

AY512915

0.01

2.2E-03

0.39

1.81E-02

ENSMUST00000089303

0.67

1.78E-01

ENSMUST00000159751

0.54

3.85E-02

ENSMUST00000162315

0.55

9.59E-02

all transcript isoforms

Dlx6os1

0.01

1.8E-04

0.39

2.42E-02

ENSMUST00000159827

Gm12002

0.003

3.8E-03

0.38

4.16E-03

ENSMUST00000153794

0.72

7.83E-03

ENSMUST00000174550

Gm13582

0.02

2.1E-04

0.50

5.06E-02

all transcript isoforms

Gm16025

0.06

3.95E-02

0.56

1.67E-02

ENSMUST00000161282

0.81

2.11E-02

all transcript isoforms

Gm16028

0.06

1.5E-02

0.20

7.95E-03

all transcript isoforms

Gm20631

0.06

9.1E-03

0.40

7.51E-03

ENSMUST00000177239

0.39

2.00E-02

ENSMUST00000177268

0.48

1.34E-02

all transcript isoforms

Gm21846

0.04

1.7E-02

0.52

6.53E-03

All transcript isoforms

Wt1os

0.003

3.1E-05

0.67

1.96E-01

ENSMUST00000172701

ENSMUST00000174870

0.42

1.97E-02

ENSMUST00000135153

Gm26870

0.19

1.5E-08

n.d.

n.d.

n.d.

Gm11399

0.07

6.4E-03

n.d.

n.d.

n.d.

D230017M19Rik

0.1

2.7E-03

n.d.

n.d.

n.d.

  1. Differential expression of lncRNA genes was validated by nCounter® technology in individual livers (n = 6/diet). nCounter® probes targeted all or specific transcript isoforms of a lncRNA gene. Specifically targeted transcript isoforms are denoted by their Ensembl transcript IDs. nCounter® fold-change values were not determined (n.d.) for Gm26870, Gm11399, D230017M19Rik due to lack of specific nCounter® probes. FC (H/S) refers to the fold-change (FC) in expression in HFD livers (H) relative to STD livers (S). nCounter® p-values were calculated by two-sided t test. edgeR FDR refers to the False Discovery Rate-adjusted p-value calculated by edgeR.
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