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: SELENOP

Gene summary for SELENOP

Gene summary.

Gene information	Species	Human
	Gene symbol	SELENOP
	Gene ID	6414
	Gene name	selenoprotein P
	Gene Alias	SELP
	Cytomap	5p12
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P49908

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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
6414	SELENOP	GSM4909281	Human	Breast	IDC	8.58e-09	-3.67e-01	0.21
6414	SELENOP	GSM4909282	Human	Breast	IDC	5.04e-24	-5.45e-01	-0.0288
6414	SELENOP	GSM4909285	Human	Breast	IDC	4.73e-10	7.37e-02	0.21
6414	SELENOP	GSM4909286	Human	Breast	IDC	1.22e-18	-4.58e-01	0.1081
6414	SELENOP	GSM4909290	Human	Breast	IDC	1.20e-08	4.09e-01	0.2096
6414	SELENOP	GSM4909293	Human	Breast	IDC	3.22e-19	2.76e-01	0.1581
6414	SELENOP	GSM4909297	Human	Breast	IDC	1.25e-04	-1.07e-01	0.1517
6414	SELENOP	GSM4909298	Human	Breast	IDC	4.18e-32	7.69e-01	0.1551
6414	SELENOP	GSM4909299	Human	Breast	IDC	2.12e-04	2.89e-01	0.035
6414	SELENOP	GSM4909304	Human	Breast	IDC	2.78e-07	2.69e-01	0.1636
6414	SELENOP	GSM4909305	Human	Breast	IDC	1.20e-03	3.29e-02	0.0436
6414	SELENOP	GSM4909306	Human	Breast	IDC	2.24e-06	-7.67e-02	0.1564
6414	SELENOP	GSM4909308	Human	Breast	IDC	3.13e-12	1.02e-01	0.158
6414	SELENOP	GSM4909311	Human	Breast	IDC	4.50e-16	-1.92e-01	0.1534
6414	SELENOP	GSM4909315	Human	Breast	IDC	2.16e-35	9.02e-01	0.21
6414	SELENOP	GSM4909316	Human	Breast	IDC	1.91e-09	6.95e-01	0.21
6414	SELENOP	GSM4909319	Human	Breast	IDC	5.59e-26	-3.75e-01	0.1563
6414	SELENOP	GSM4909321	Human	Breast	IDC	4.85e-02	-9.21e-02	0.1559
6414	SELENOP	brca1	Human	Breast	Precancer	1.19e-30	-5.67e-01	-0.0338
6414	SELENOP	brca2	Human	Breast	Precancer	1.83e-29	-5.67e-01	-0.024

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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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:00069799	Breast	Precancer	response to oxidative stress	70/1080	446/18723	1.59e-14	4.26e-12	70
GO:000697914	Breast	IDC	response to oxidative stress	83/1434	446/18723	2.36e-14	7.06e-12	83
GO:000697924	Breast	DCIS	response to oxidative stress	82/1390	446/18723	1.22e-14	3.85e-12	82
GO:000697910	Cervix	CC	response to oxidative stress	102/2311	446/18723	2.99e-10	4.36e-08	102
GO:00097915	Cervix	CC	post-embryonic development	20/2311	80/18723	1.40e-03	1.10e-02	20
GO:000697915	Cervix	HSIL_HPV	response to oxidative stress	48/737	446/18723	2.76e-10	7.02e-08	48
GO:000697916	Endometrium	AEH	response to oxidative stress	93/2100	446/18723	1.94e-09	1.64e-07	93
GO:000697917	Endometrium	EEC	response to oxidative stress	99/2168	446/18723	9.02e-11	1.13e-08	99
GO:00097916	Endometrium	EEC	post-embryonic development	17/2168	80/18723	9.23e-03	4.95e-02	17
GO:000697927	Esophagus	HGIN	response to oxidative stress	107/2587	446/18723	3.91e-09	2.76e-07	107
GO:0006979111	Esophagus	ESCC	response to oxidative stress	303/8552	446/18723	7.15e-22	1.30e-19	303
GO:00097919	Esophagus	ESCC	post-embryonic development	56/8552	80/18723	9.08e-06	8.71e-05	56
GO:00069797	Liver	NAFLD	response to oxidative stress	78/1882	446/18723	7.85e-07	4.29e-05	78
GO:000697912	Liver	Cirrhotic	response to oxidative stress	196/4634	446/18723	2.80e-19	5.86e-17	196
GO:000697922	Liver	HCC	response to oxidative stress	281/7958	446/18723	9.75e-19	1.24e-16	281
GO:00069798	Lung	IAC	response to oxidative stress	82/2061	446/18723	1.99e-06	9.18e-05	82
GO:000697913	Lung	AIS	response to oxidative stress	75/1849	446/18723	2.97e-06	1.60e-04	75
GO:0007626	Lung	AIS	locomotory behavior	31/1849	179/18723	1.39e-03	1.70e-02	31
GO:000697923	Lung	MIAC	response to oxidative stress	43/967	446/18723	6.39e-05	3.12e-03	43
GO:000697918	Prostate	BPH	response to oxidative stress	142/3107	446/18723	8.11e-16	1.36e-13	142

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗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

SELENOP

SNV

Missense_Mutation

novel

c.163C>G

p.Leu55Val

p.L55V

P49908

protein_coding

deleterious(0)

probably_damaging(0.955)

TCGA-A7-A4SF-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

SELENOP

SNV

Missense_Mutation

c.366N>G

p.Asp122Glu

p.D122E

P49908

protein_coding

deleterious(0.01)

probably_damaging(0.976)

TCGA-AR-A1AO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SELENOP

SNV

Missense_Mutation

c.1036N>G

p.Arg346Gly

p.R346G

P49908

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.997)

TCGA-D8-A27F-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin+cyclophosphamide

SELENOP

SNV

Missense_Mutation

rs769801038

c.481N>A

p.Glu161Lys

p.E161K

P49908

protein_coding

tolerated(0.1)

benign(0.344)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SELENOP

SNV

Missense_Mutation

rs769801038

c.481N>A

p.Glu161Lys

p.E161K

P49908

protein_coding

tolerated(0.1)

benign(0.344)

TCGA-D8-A27M-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

methotrexate+5

SELENOP

insertion

Nonsense_Mutation

novel

c.625_626insTTTTGTAAATCTTGTAA

p.His209LeufsTer?

p.H209Lfs*?

P49908

protein_coding

TCGA-AC-A3QQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SELENOP

SNV

Missense_Mutation

rs759863312

c.580G>A

p.Val194Met

p.V194M

P49908

protein_coding

tolerated(0.09)

possibly_damaging(0.778)

TCGA-5M-AAT6-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Unknown

SELENOP

SNV

Missense_Mutation

novel

c.550N>T

p.Asp184Tyr

p.D184Y

P49908

protein_coding

deleterious(0)

probably_damaging(0.909)

TCGA-AA-3510-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SELENOP

SNV

Missense_Mutation

rs761519480

c.599C>T

p.Thr200Ile

p.T200I

P49908

protein_coding

tolerated(0.2)

benign(0.003)

TCGA-AA-A02J-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

SELENOP

SNV

Missense_Mutation

rs570817380

c.840A>T

p.Arg280Ser

p.R280S

P49908

protein_coding

tolerated_low_confidence(0.16)

benign(0.007)

TCGA-CK-4951-01

Colorectum

colon adenocarcinoma

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

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