Construction of an oesophageal cancer-specific ceRNA network based on miRNA, lncRNA, and mRNA expression data

Table 1 mRNA GO analysis in oesophageal squamous cell carcinoma

Goid	GO name	GO diffgene count	GO gene count	Enrichment	P value	FDR
GO:0030198	Extracellular matrix organization	20	210	25.11013216	1.54276E-21	1.68623E-18
GO:0030574	Collagen catabolic process	12	72	43.94273128	3.32314E-16	1.8161E-13
GO:0022617	Extracellular matrix disassembly	11	79	36.71164892	5.27621E-14	1.9223E-11
GO:0045944	Positive regulation of transcription	18	708	6.7031285	1.3435E-09	3.6711E-07
GO:0007155	Cell adhesion	14	454	8.130373188	1.16162E-08	2.30356E-06
GO:0044281	Small molecule metabolic process	23	1363	4.449080643	1.26454E-08	2.30356E-06
GO:0008285	Negative regulation of cell prolifer	12	358	8.837644279	6.42989E-08	1.00398E-05
GO:0001501	Skeletal system development	8	127	16.60827639	1.37682E-07	1.88108E-05
GO:0048699	Generation of neurons	4	11	95.87505006	2.60527E-07	3.16396E-05
GO:0008284	Positive regulation of cell prolifera	12	411	7.69799672	2.89703E-07	3.16645E-05
GO:0007165	Signal transduction	18	1030	4.607587357	4.19668E-07	4.16997E-05
GO:0055085	Transmembrane transport transmembrane transport	13	538	6.370879256	7.27191E-07	6.6235E-05
GO:0007566	Embryo implantation	5	37	35.62924158	1.18601E-06	9.97159E-05
GO:0048704	Embryonic skeletal system morph	5	40	32.95704846	1.77383E-06	0.000131776
GO:0006508	Proteolysis	12	488	6.483353795	1.80845E-06	0.000131776
GO:0008544	Epidermis development	6	76	20.81497797	1.95203E-06	0.000133348
GO:0048015	Phosphatidylinositol-mediated sign	7	129	14.30693576	2.77867E-06	0.000178652
GO:0043065	Positive regulation of apoptotic pr	8	197	10.70685838	3.9876E-06	0.000242136
GO:0019369	Arachidonic acid metabolic process	5	50	26.36563877	5.53803E-06	0.000318583
GO:0006979	Response to oxidative stress	6	101	15.6627557	1.04573E-05	0.000571494

Table 2 mRNA pathway analysis in oesophageal squamous cell carcinoma

Path_id	Path_name	Path_diffgene_count	Path_gene_count	Enrichment	P value	FDR
05202	Transcriptional misregulation in cancer	12	179	17.67528856	2.34961E-11	3.94734E-09
04512	ECM-receptor interaction	9	87	27.27479872	2.19839E-10	1.84664E-08
04510	Focal adhesion	10	207	12.73702356	3.3619E-08	1.79605E-06
04151	PI3K-Akt signalling pathway	12	345	9.170656962	4.27632E-08	1.79605E-06
05146	Amoebiasis	7	108	17.08883994	8.29201E-07	2.78612E-05
01100	Metabolic pathways	19	1234	4.059539194	1.27125E-06	3.5595E-05
05200	Pathways in cancer	11	397	7.305340716	1.71545E-06	4.11707E-05
04810	Regulation of actin cytoskeleton	8	214	9.856313558	7.4028E-06	0.000155459
00590	Arachidonic acid metabolism	5	62	21.26261191	1.62994E-05	0.000304255
04115	p53 signalling pathway	5	68	19.38649909	2.57756E-05	0.00043303
04060	Cytokine-cytokine receptor interaction	8	265	7.959438118	3.5607E-05	0.000543816
04974	Protein digestion and absorption	5	90	14.64757709	0.000101556	0.001421784
04666	Fc gamma R-mediated phagocytosis	5	92	14.3291515	0.000112939	0.001459525
05205	Proteoglycans in cancer	6	203	7.792799635	0.000540094	0.006142299
04610	Complement and coagulationcasc	4	69	15.28442827	0.000574387	0.006142299
04611	Platelet activation	5	130	10.14063029	0.000584981	0.006142299
05132	Salmonella infection	4	86	12.2630878	0.001341668	0.01252223
05222	Small cell lung cancer	4	86	12.2630878	0.001341668	0.01252223
05323	Rheumatoid arthritis	4	89	11.84972529	0.001529001	0.01351959
00564	Glycerophospholipid metabolism	4	95	11.10132159	0.001958567	0.016451962