Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: SOD1

Gene summary for SOD1

Gene summary.

Gene information	Species	Human
	Gene symbol	SOD1
	Gene ID	6647
	Gene name	superoxide dismutase 1
	Gene Alias	ALS
	Cytomap	21q22.11
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P00441

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
6647	SOD1	GSM4909282	Human	Breast	IDC	2.20e-06	2.87e-01	-0.0288
6647	SOD1	GSM4909285	Human	Breast	IDC	1.19e-63	7.52e-01	0.21
6647	SOD1	GSM4909287	Human	Breast	IDC	1.45e-11	3.18e-01	0.2057
6647	SOD1	GSM4909290	Human	Breast	IDC	5.90e-04	3.09e-01	0.2096
6647	SOD1	GSM4909294	Human	Breast	IDC	7.03e-34	3.97e-01	0.2022
6647	SOD1	GSM4909296	Human	Breast	IDC	4.07e-20	1.09e-01	0.1524
6647	SOD1	GSM4909297	Human	Breast	IDC	3.55e-29	1.15e-01	0.1517
6647	SOD1	GSM4909298	Human	Breast	IDC	6.37e-06	3.83e-01	0.1551
6647	SOD1	GSM4909301	Human	Breast	IDC	7.44e-08	2.35e-01	0.1577
6647	SOD1	GSM4909306	Human	Breast	IDC	1.00e-02	2.62e-01	0.1564
6647	SOD1	GSM4909307	Human	Breast	IDC	4.70e-14	3.94e-01	0.1569
6647	SOD1	GSM4909308	Human	Breast	IDC	2.79e-29	5.52e-01	0.158
6647	SOD1	GSM4909309	Human	Breast	IDC	7.60e-06	1.68e-01	0.0483
6647	SOD1	GSM4909311	Human	Breast	IDC	5.48e-68	1.19e-01	0.1534
6647	SOD1	GSM4909312	Human	Breast	IDC	4.33e-23	3.06e-01	0.1552
6647	SOD1	GSM4909316	Human	Breast	IDC	1.56e-03	4.47e-02	0.21
6647	SOD1	GSM4909317	Human	Breast	IDC	1.27e-05	-3.63e-01	0.1355
6647	SOD1	GSM4909319	Human	Breast	IDC	5.22e-81	1.50e-01	0.1563
6647	SOD1	GSM4909320	Human	Breast	IDC	1.46e-15	2.86e-01	0.1575
6647	SOD1	GSM4909321	Human	Breast	IDC	1.57e-40	4.38e-01	0.1559

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0090075	Colorectum	SER	relaxation of muscle	12/2897	34/18723	3.60e-03	3.03e-02	12
GO:00435231	Colorectum	SER	regulation of neuron apoptotic process	48/2897	212/18723	3.63e-03	3.04e-02	48
GO:00353151	Colorectum	SER	hair cell differentiation	15/2897	47/18723	3.68e-03	3.07e-02	15
GO:00614581	Colorectum	SER	reproductive system development	87/2897	427/18723	3.69e-03	3.07e-02	87
GO:0042743	Colorectum	SER	hydrogen peroxide metabolic process	17/2897	58/18723	5.50e-03	4.07e-02	17
GO:00307051	Colorectum	SER	cytoskeleton-dependent intracellular transport	44/2897	195/18723	5.53e-03	4.09e-02	44
GO:00486081	Colorectum	SER	reproductive structure development	85/2897	424/18723	6.33e-03	4.56e-02	85
GO:0014044	Colorectum	SER	Schwann cell development	11/2897	32/18723	6.58e-03	4.68e-02	11
GO:0002093	Colorectum	SER	auditory receptor cell morphogenesis	7/2897	16/18723	6.63e-03	4.69e-02	7
GO:00487322	Colorectum	MSS	gland development	143/3467	436/18723	3.85e-13	8.01e-11	143
GO:00971932	Colorectum	MSS	intrinsic apoptotic signaling pathway	102/3467	288/18723	6.06e-12	9.82e-10	102
GO:20012422	Colorectum	MSS	regulation of intrinsic apoptotic signaling pathway	66/3467	164/18723	6.70e-11	7.47e-09	66
GO:00020642	Colorectum	MSS	epithelial cell development	81/3467	220/18723	1.02e-10	1.06e-08	81
GO:20012332	Colorectum	MSS	regulation of apoptotic signaling pathway	116/3467	356/18723	1.02e-10	1.06e-08	116
GO:00069792	Colorectum	MSS	response to oxidative stress	128/3467	446/18723	7.65e-08	3.81e-06	128
GO:00621972	Colorectum	MSS	cellular response to chemical stress	102/3467	337/18723	9.73e-08	4.71e-06	102
GO:00345992	Colorectum	MSS	cellular response to oxidative stress	88/3467	288/18723	4.58e-07	1.77e-05	88
GO:00022622	Colorectum	MSS	myeloid cell homeostasis	55/3467	157/18723	6.35e-07	2.34e-05	55
GO:00086312	Colorectum	MSS	intrinsic apoptotic signaling pathway in response to oxidative stress	23/3467	45/18723	7.86e-07	2.77e-05	23
GO:00430872	Colorectum	MSS	regulation of GTPase activity	101/3467	348/18723	1.00e-06	3.46e-05	101

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501218	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502016	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501616	Breast	Precancer	Huntington disease	98/684	306/8465	2.85e-35	2.25e-33	1.72e-33	98
hsa0501416	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502216	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0520818	Breast	Precancer	Chemical carcinogenesis - reactive oxygen species	68/684	223/8465	3.61e-23	1.14e-21	8.73e-22	68
hsa0501219	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502017	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501617	Breast	Precancer	Huntington disease	98/684	306/8465	2.85e-35	2.25e-33	1.72e-33	98
hsa0501417	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502217	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0520819	Breast	Precancer	Chemical carcinogenesis - reactive oxygen species	68/684	223/8465	3.61e-23	1.14e-21	8.73e-22	68
hsa0501224	Breast	IDC	Parkinson disease	107/867	266/8465	2.57e-39	8.36e-37	6.26e-37	107
hsa0502023	Breast	IDC	Prion disease	102/867	273/8465	3.70e-34	4.01e-32	3.00e-32	102
hsa0501623	Breast	IDC	Huntington disease	103/867	306/8465	5.14e-30	4.17e-28	3.12e-28	103
hsa0501423	Breast	IDC	Amyotrophic lateral sclerosis	102/867	364/8465	1.29e-22	5.22e-21	3.91e-21	102
hsa0502223	Breast	IDC	Pathways of neurodegeneration - multiple diseases	116/867	476/8465	3.63e-20	1.18e-18	8.82e-19	116
hsa0520824	Breast	IDC	Chemical carcinogenesis - reactive oxygen species	71/867	223/8465	2.55e-19	7.53e-18	5.63e-18	71
hsa0501234	Breast	IDC	Parkinson disease	107/867	266/8465	2.57e-39	8.36e-37	6.26e-37	107
hsa0502033	Breast	IDC	Prion disease	102/867	273/8465	3.70e-34	4.01e-32	3.00e-32	102

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
SOD1	LYMEND	Pancreas	ADJ	IGFBP7,NDUFA4,PEBP1, etc.	2.43e-01

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

SOD1

SNV

Missense_Mutation

c.315N>G

p.Ile105Met

p.I105M

P00441

protein_coding

deleterious(0.02)

probably_damaging(0.969)

TCGA-A2-A04W-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

SOD1

SNV

Missense_Mutation

c.224N>T

p.Pro75Leu

p.P75L

P00441

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A18J-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SOD1

SNV

Missense_Mutation

novel

c.109N>C

p.Lys37Gln

p.K37Q

P00441

protein_coding

tolerated(0.08)

benign(0)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

SOD1

SNV

Missense_Mutation

c.32N>T

p.Gly11Val

p.G11V

P00441

protein_coding

deleterious(0)

probably_damaging(0.982)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SOD1

SNV

Missense_Mutation

c.446N>C

p.Val149Ala

p.V149A

P00441

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SOD1

SNV

Missense_Mutation

c.331N>A

p.His111Asn

p.H111N

P00441

protein_coding

tolerated(0.7)

benign(0.005)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SOD1

SNV

Missense_Mutation

rs121912459

c.289N>A

p.Asp97Asn

p.D97N

P00441

protein_coding

tolerated(0.29)

benign(0)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SOD1

SNV

Missense_Mutation

novel

c.239G>T

p.Arg80Met

p.R80M

P00441

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AX-A1CE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

SOD1

SNV

Missense_Mutation

novel

c.8C>T

p.Thr3Met

p.T3M

P00441

protein_coding

tolerated(0.31)

benign(0)

TCGA-AX-A3FX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

SOD1

SNV

Missense_Mutation

c.268N>A

p.Ala90Thr

p.A90T

P00441

protein_coding

tolerated(0.17)

probably_damaging(0.976)

TCGA-BG-A0MG-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID	Symbol	Category	Interaction Types	Drug Claim Name	Drug Name	PMIDs
6647	SOD1	ENZYME, DRUGGABLE GENOME		OXYTETRACYCLINE	OXYTETRACYCLINE
6647	SOD1	ENZYME, DRUGGABLE GENOME		TETRACYCLINE	TETRACYCLINE
6647	SOD1	ENZYME, DRUGGABLE GENOME		DOXYCYCLINE	DOXYCYCLINE
6647	SOD1	ENZYME, DRUGGABLE GENOME		ISIS-SOD1RX	TOFERSEN

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