Table 2 Significant differential expression and co-expression results for lncRNAs co-localized with known breast cancer risk SNPs in our data.

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

SNP

Position

Near Gene(s)

LncRNA

lncRNA-DE analysis

mRNA

Dose-response Co-expression analysis

Differential Co-expression analysis

Log2 Fold Change

FDR P-value

β a

P value b

β_ Tumorc

β_ Normalc

Interaction P valued

rs9832625

3p24.1

RBMS3

ENSG00000235904.1|RBMS3-AS3

−2.66

2.61E-04

—

—

—

—

—

—

rs11836164

12p12.1

SSPN - ITPR2

ENSG00000255750.1|RP11-283G6.5

−1.2

1.53E-03

—

—

—

—

—

—

rs2823779

21q21.1

LINC00478, MIR99AHG

ENSG00000215386.6|LINC00478

−1.69

2.88E-04

      
      

TOX4

—

—

1.48

4.26

2.73E-11

      

CETN1

—

—

−0.08

−1.82

8.67E-11

      

KIAA1253

—

—

5.16

3.02

1.25E-10

      

CETN2

—

—

0.98

3.19

2.80E-10

  1. aβ 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.
  2. bP value was estimated from generalized linear model 3.
  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, respectively, which was estimated from generalized linear model 2.
  4. dP value for interaction term (lncRNA· tissue type) was estimated from generalized linear model 2.
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