Table 2 A summarized list of results of Kaplan–Meier plot tool for 53 potential genes categorized based on their stages and literature screening references.

From: Systems biology comprehensive analysis on breast cancer for identification of key gene modules and genes associated with TNM-based clinical stages

Stages	Rank	Gene symbol	Expression	Overall P value	Related cancers	References
Stage I	1	SMC4	Downregulated	1.7e−14	ER-positive and ER-negative breast cancer	³⁸
	2	IRF7	Downregulated	0.1861	Suppressor of an innate immune pathway in breast cancer	^38,39
	3	POSTN	Downregulated	0.3289	A factor in preventing and treating breast cancer	^38,40
	4	ABAT	Downregulated	8.9e−16	ER-positive and ER-negative breast cancer	⁴¹
	5	LMOD1	Upregulated	0.1821	Involved in the development of breast cancer	⁴²
	6	TRIM2	Upregulated	0.7228	Invasive and basal-like breast cancer	^43,44
	7	CHRDL1	Upregulated	2.4e−8	Malignant breast cancer	⁴⁵
	8	MFGE8	Upregulated	0.1294	Triple-negative and ER + breast cancers	^46,47
	9	GLRX5	Downregulated	0.0001	Breast cancer Neurological disorders such as Parkinson’s disease and those associated with ageing	⁴⁸
	10	ELF5	Upregulated	0.1522	TNM staging system for all types of breast cancer and metastasis in breast cancer	^49,50
	11	CSN2	Upregulated	1.0e−8	Invasive breast cancer triple-negative breast cancer	^51,52
	12	PRLR	Downregulated	7.7e−5	Progression of breast carcinoma	^53,54,55
	13	PPAP2B	Upregulated	9.4e−10	Coronary artery disease Breast cancer Tumor growth in breast cancer	^56,57,58,59
	14	FZD2	Downregulated	3.3e−11	Breast cancer	^60,61,62
	15	FZD7	Upregulated	0.6871	Breast cancer	^60,61,62
	16	GPC4	Downregulated	0.0004	In both MCF-7 (human breast adenocarcinoma) and MCF-10F (normal-like breast cancer)	^63,64,65
	17	CERS2	Downregulated	0.2238	Less invasive breast cancer	^66,67,68
	18	UGCG	Downregulated	1.1e−10	Triple-negative BC ER-negative BC tumors Lung metastases	^{69,70,71,72,73}
	19	LIPE	Upregulated	0.0051	Prognostic cofactor in BC Cancer lipolysis	^74,75,76
	20	PLIN1	Upregulated	2.6e−5	HER2 tumors Breast cancer Triple-negative breast cancer	^77,77,78,79
Stage II	1	CCNB2	Downregulated	< 1e−16	Basal-like, HER2, and luminal breast cancers	^80,81,82,83
	2	OAS3	Downregulated	0.697	Mutated gene in breast cancer	^84,85,86
	3	IRF7	Downregulated	0.1861	Suppressor of an innate immune pathway in breast cancer	^38,39
	4	OAS1	Downregulated	0.5676	Development of various cancer types like breast cancer	^85,86,87
	5	CDKN1C	Upregulated	1.9e−5	Breast tumors	^88,89
	6	PEG3	Upregulated	0.0029	Several cancers such as breast and ovary cancers	^90,91
	7	PHLDA2	Downregulated	4.0e−10	PRL treatment Tumor progression	^92,93
	8	PLAGL1	Upregulated	0.3823	Breast cancer patients under radiotherapy treatment	⁹⁴
	9	SGCE	Upregulated	0.0293	Progression of breast cancer invasion in terms of stromal changes	⁹⁵
	10	SLC22A18	Downregulated	3.2e−8	Breast cancer	⁹⁶
	11	SERPING1	Upregulated	1.3e−8	Breast carcinoma cells	⁹⁷
	12	ACTA2	Upregulated	0.6126	Metastasis of breast cancer cells Dimerization of epidermal growth factor receptor (EGFR) and HER2	^98,99,100
	13	LCP2	Downregulated	0.7828	Predicting the development of secondary lymphedema followed by breast cancer surgery	^101,102
	14	ABCG1	Downregulated	0.2418	High expression level of ABCG1 transporters in MCF-7 cells	^103,104
	15	ZFP36L1	Upregulated	0.0507	In all types of breast cancer	¹⁰⁵
	16	BICC1	Upregulated	1.0e−10	Cystic renal dysplasia embryonic node, kidney, liver, and pancreas in the mouse Basal-like breast tumors	^106,107
	17	SSPN	Upregulated	0.0007	Several types of cancer, including breast invasive cancer	^108,109,110
Stage III	1	FEN1	Downregulated	< 1e−16	High stages of breast cancer Inhibition of the tumor growth	^111,112,113
	2	ADH1B	Upregulated	0.0068	Risk factors for breast cancer	^114,115,116
	3	IRF7	Downregulated	0.1861	Suppressor of an innate immune pathway in breast cancer	^38,39
	4	ACTA2	Upregulated	0.6126	Metastasis of breast cancer cells Dimerization of epidermal growth factor receptor (EGFR) and HER2	^98,99,100
	5	CLDN5	Upregulated	9.4e−6	In both breast tumor stromal (BTS) and prostate tumor stromal (PTS)	^117,118
	6	SLC31A1	Downregulated	0.4854	Progression of breast cancer	^119,120
	7	FBLN1	Upregulated	3.6e−5	In several types of cancer, including breast cancer	^121,122
	8	MFAP4	Upregulated	5.8e−9	In cell adhesion, motility, invasion, and metastasis of BC	^95,123,124
	9	COL1A2	Downregulated	0.4121	High expression level at higher stages of breast cancer	^125,126,127
	10	ASPN	Downregulated	0.2608	Upregulated expression in breast cancer	^128,129
Stage IV	1	NUSAP1	Upregulated	< 1e−16	A potential biomarker clinically correlated with breast cancer	^130,131
	2	COL6A2	Downregulated	0.0038	Important role in breast cancer development	^132,133
	3	HIST1H2BD	Upregulated	0.2745	ER-positive breast cancer In breast cancer development	^42,134
	4	HIST1H2BH	Upregulated	0.0006	ER-positive breast cancer In breast cancer development	^42,134
	5	HIST1H2BK	Upregulated	8.6e−8	ER-positive breast cancer In breast cancer development	^42,134
	6	HIST2H2BE	Upregulated	0.1077	ER-positive breast cancer In breast cancer development	^42,134
Integrated group	1	KIF11	Upregulated	< 1e−16	Triple-negative breast cancer	^135,136
	2	IRF7	Upregulated	0.1861	Suppressor of an innate immune pathway in breast cancer	^38,39
	3	OAS1	Downregulated	0.5676	Development of various cancer types like breast cancer	^85,86,87
	4	OAS3	Downregulated	0.697	Mutated gene in breast cancer	^84,85,86
	5	SGCE	Upregulated	0.0293	Progression of breast cancer invasion in terms of stromal changes	⁹⁵
	6	ALDH7A1	Downregulated	0.0208	Breast cancer Potent marker in different types of cancer like prostate cancer	^137,138,139
	7	ABCG1	Downregulated	0.2418	Breast cancer	¹⁴⁰
	8	C1S	Downregulated	1.2e−6	HER2-positive and basal-like breast cancer	¹⁴⁰

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Table 2 A summarized list of results of Kaplan–Meier plot tool for 53 potential genes categorized based on their stages and literature screening references.

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