Hypoxia-inducible factor stabilisation-related lncRNAs in retinopathy of prematurity

Figures & data

Table 1. RNA-seq data summary.

#Library	Total reads	Mapped reads	Mapping rate
Liver_PBS	98,526,919	91,335,829	92.74%
Liver_DMOG	95,106,800	89,609,117	94.25%
Liver_RXD	87,799,495	82,661,434	94.10%
Retina_PBS	83,426,826	76,767,316	92.08%
Retina_DMOG	99,742,039	93,549,367	93.90%
Retina_RXD	93,244,413	87,898,398	94.14%
Average	92,974,415	86,970,244	93.54%

Figure 1. (A–D) Volcano plots showing the differentially expressed lncRNAs. (F) Venn diagram of the overlap number of DElncRNAs. (E, G) Histogram of differentially expressed known lncRNAs. DElncRNAs were defined as the lncRNAs with significant (q≤ 0.05) differential expression upon Roxadustat (RXD) and dimethyloxalylglycine (DMOG) treatment, when compared with the control groups (Liver_PBS group or Retina_PBS group).

Table 2. The numbers of known differentially expressed lncRNAs.

Organ	DElncRNAs	Total	Upregulated	Downregulated
Liver	Common	17	4	13
	Unique to DMOG	62	43	19
	Unique to RXD	25	13	12
Retina	Common	2	0	2
	Unique to DMOG	19	19	0
	Unique to RXD	13	6	7

DElncRNAs: differentially expressed lncRNAs.

Figure 2. Function enrichment results of the target genes of DElncRNAs. (A) Top 10 enrichment KEGG pathways of target genes of DElncRNAs between liver DMOG treatment samples and liver PBS treatment samples. (B) Top 10 enrichment KEGG pathways of target genes of DElncRNAs between liver RXD treatment samples and liver PBS treatment samples. (C) Heatmap of enrichment q-value value of GO terms (biological processes). (D) Heatmap of enrichment FDR value of GO terms (cellular component GO terms).

Table 3. The numbers of GO terms and KEGG pathways of the target genes of differentially expressed lncRNAs.

Group	KEGG	GO
		BP	CC	MF
Liver_DMOG	76	439	89	72
Liver_RXD	37	334	53	62
Retinal_DMOG	3	0	5	1
Retinal_RXD	1	0	27	0

BP: biological processes; CC: cellular components; MF: molecular functions.

Figure 3. The interaction network of DElncRNAs and the target genes in the HIF-1 pathway. (A) In the liver; (B) in the retina. Genes involved in the HIF-1 signalling pathway of Mus musculus (mmu04066) were downloaded from the KEGG PATHWAY Database. The cis-acting regulatory genes or the trans-acting regulatory genes of DElncRNAs were defined as the target genes.

Data availability statement

The data were downloaded from the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE74170; NCBI tracking system no. 17567121).