Table 4 Significant results for known breast cancer-related lncRNAs in our data.

From: Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer

lncRNA ID

lncRNA/Reference

Position

lncRNA-DE analysis

mRNA-DE Analysis

Dose-response Co-expression Analysis

Differential Co-expression Analysis

Log2FC a

FDR adjusted P value

mRNA

position

Log2FCa

FDR adjusted P value

β b , c

P valueb,d

β in Tumorb,e

β in Normalb,e

P value Interactionb,f

ENSG00000251562.3

MALAT129

11

0.70

3.80E-02

ALG14

1p21.3

−0.12

8.18E-01

—

—

1.24

−0.65

2.86E-10

     

TOX4

14q11.2

0.39

4.60E-01

—

—

−4.05

−7.27

1.46E-10

ENSG00000229807.5

XIST60

Xq13.2

−0.04

8.90E-01

C12orf32

12p13.33

1.5

1.88E-05

—

—

2.30

−0.16

1.29E-10

ENSG00000228630.1

HOTAIR29

12q13.13

3.64

4.02E-08

—

—

—

—

—

—

—

—

—

ENSG00000233429.5

HOTAIRM160

7p15.2

−1.19

5.64E-06

—

—

—

—

—

—

—

—

—

  1. aFC refers to the fold change of expression level in breast tumor versus normal tissue for mRNAs and lncRNAs, respectively.
  2. b“-” refers to non-significant in our study.
  3. cβ refers to the change of mRNA expression level corresponding to each unit increase of lncRNA expression level in tumor and normal breast tissue, which was estimated from generalized linear model 3.
  4. dP value was estimated from generalized linear model 3.
  5. eβ refers to the change of mRNA expression level corresponding to each unit increase of lncRNA expression level in tumor and normal breast tissue, respectively, which was estimated from generalized linear model 2.
  6. fP value for interaction term (lncRNA· tissue type) was estimated from generalized linear model 2.
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