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: RPS20

Gene summary for RPS20

Gene summary.

Gene information	Species	Human
	Gene symbol	RPS20
	Gene ID	6224
	Gene name	ribosomal protein S20
	Gene Alias	S20
	Cytomap	8q12.1
	Gene Type	protein-coding
	GO ID	GO:0002181
	UniProtAcc	P60866

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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
6224	RPS20	GSM4909281	Human	Breast	IDC	3.64e-31	3.11e-01	0.21
6224	RPS20	GSM4909282	Human	Breast	IDC	3.76e-82	4.98e-01	-0.0288
6224	RPS20	GSM4909285	Human	Breast	IDC	1.94e-17	2.80e-01	0.21
6224	RPS20	GSM4909286	Human	Breast	IDC	8.68e-130	5.90e-01	0.1081
6224	RPS20	GSM4909287	Human	Breast	IDC	1.08e-09	-3.52e-01	0.2057
6224	RPS20	GSM4909290	Human	Breast	IDC	3.46e-25	-4.35e-01	0.2096
6224	RPS20	GSM4909291	Human	Breast	IDC	7.10e-33	4.20e-01	0.1753
6224	RPS20	GSM4909292	Human	Breast	IDC	3.49e-06	-6.73e-01	0.1236
6224	RPS20	GSM4909294	Human	Breast	IDC	8.12e-09	1.77e-01	0.2022
6224	RPS20	GSM4909295	Human	Breast	IDC	8.27e-18	3.58e-01	0.0898
6224	RPS20	GSM4909296	Human	Breast	IDC	6.02e-23	2.56e-01	0.1524
6224	RPS20	GSM4909297	Human	Breast	IDC	3.28e-06	2.91e-02	0.1517
6224	RPS20	GSM4909299	Human	Breast	IDC	1.11e-24	3.23e-01	0.035
6224	RPS20	GSM4909301	Human	Breast	IDC	5.42e-09	2.03e-01	0.1577
6224	RPS20	GSM4909302	Human	Breast	IDC	6.83e-12	2.30e-01	0.1545
6224	RPS20	GSM4909304	Human	Breast	IDC	1.83e-53	-4.94e-01	0.1636
6224	RPS20	GSM4909305	Human	Breast	IDC	5.15e-21	3.30e-01	0.0436
6224	RPS20	GSM4909306	Human	Breast	IDC	3.34e-36	3.61e-01	0.1564
6224	RPS20	GSM4909307	Human	Breast	IDC	1.18e-13	2.37e-01	0.1569
6224	RPS20	GSM4909308	Human	Breast	IDC	1.65e-08	2.30e-01	0.158

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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
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
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:190332010	Cervix	CC	regulation of protein modification by small protein conjugation or removal	66/2311	242/18723	2.31e-10	3.46e-08	66
GO:003139610	Cervix	CC	regulation of protein ubiquitination	59/2311	210/18723	5.90e-10	7.51e-08	59
GO:003139710	Cervix	CC	negative regulation of protein ubiquitination	28/2311	83/18723	3.32e-07	1.35e-05	28
GO:190179810	Cervix	CC	positive regulation of signal transduction by p53 class mediator	13/2311	25/18723	1.83e-06	5.89e-05	13
GO:190332110	Cervix	CC	negative regulation of protein modification by small protein conjugation or removal	29/2311	95/18723	2.15e-06	6.55e-05	29
GO:005134810	Cervix	CC	negative regulation of transferase activity	60/2311	268/18723	2.77e-06	8.02e-05	60
GO:19046669	Cervix	CC	regulation of ubiquitin protein ligase activity	12/2311	23/18723	4.41e-06	1.12e-04	12
GO:005144410	Cervix	CC	negative regulation of ubiquitin-protein transferase activity	10/2311	19/18723	2.58e-05	4.34e-04	10
GO:00514387	Cervix	CC	regulation of ubiquitin-protein transferase activity	18/2311	53/18723	3.69e-05	5.84e-04	18
GO:007233110	Cervix	CC	signal transduction by p53 class mediator	38/2311	163/18723	7.06e-05	9.85e-04	38
GO:190466710	Cervix	CC	negative regulation of ubiquitin protein ligase activity	7/2311	12/18723	1.94e-04	2.24e-03	7
GO:190179610	Cervix	CC	regulation of signal transduction by p53 class mediator	23/2311	93/18723	7.52e-04	6.72e-03	23
GO:000218115	Cervix	HSIL_HPV	cytoplasmic translation	86/737	148/18723	3.97e-82	1.91e-78	86
GO:003139615	Cervix	HSIL_HPV	regulation of protein ubiquitination	33/737	210/18723	1.02e-11	6.81e-09	33
GO:190332015	Cervix	HSIL_HPV	regulation of protein modification by small protein conjugation or removal	34/737	242/18723	1.16e-10	4.31e-08	34
GO:003139715	Cervix	HSIL_HPV	negative regulation of protein ubiquitination	17/737	83/18723	1.95e-08	1.92e-06	17
GO:005134815	Cervix	HSIL_HPV	negative regulation of transferase activity	31/737	268/18723	8.21e-08	5.50e-06	31
GO:190466715	Cervix	HSIL_HPV	negative regulation of ubiquitin protein ligase activity	7/737	12/18723	9.49e-08	6.26e-06	7
GO:190332115	Cervix	HSIL_HPV	negative regulation of protein modification by small protein conjugation or removal	17/737	95/18723	1.58e-07	9.99e-06	17
GO:190179815	Cervix	HSIL_HPV	positive regulation of signal transduction by p53 class mediator	9/737	25/18723	2.50e-07	1.47e-05	9

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0301018	Breast	Precancer	Ribosome	80/684	167/8465	7.33e-44	2.32e-41	1.77e-41	80
hsa0517118	Breast	Precancer	Coronavirus disease - COVID-19	81/684	232/8465	3.74e-32	2.36e-30	1.81e-30	81
hsa0301019	Breast	Precancer	Ribosome	80/684	167/8465	7.33e-44	2.32e-41	1.77e-41	80
hsa0517119	Breast	Precancer	Coronavirus disease - COVID-19	81/684	232/8465	3.74e-32	2.36e-30	1.81e-30	81
hsa0301024	Breast	IDC	Ribosome	83/867	167/8465	6.07e-39	9.87e-37	7.38e-37	83
hsa0517124	Breast	IDC	Coronavirus disease - COVID-19	86/867	232/8465	1.50e-28	9.72e-27	7.27e-27	86
hsa0301034	Breast	IDC	Ribosome	83/867	167/8465	6.07e-39	9.87e-37	7.38e-37	83
hsa0517134	Breast	IDC	Coronavirus disease - COVID-19	86/867	232/8465	1.50e-28	9.72e-27	7.27e-27	86
hsa0301044	Breast	DCIS	Ribosome	82/846	167/8465	8.69e-39	1.40e-36	1.03e-36	82
hsa0517144	Breast	DCIS	Coronavirus disease - COVID-19	86/846	232/8465	2.42e-29	1.56e-27	1.15e-27	86
hsa0301054	Breast	DCIS	Ribosome	82/846	167/8465	8.69e-39	1.40e-36	1.03e-36	82
hsa0517154	Breast	DCIS	Coronavirus disease - COVID-19	86/846	232/8465	2.42e-29	1.56e-27	1.15e-27	86
hsa0517120	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa0301020	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa05171110	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa03010110	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa0301025	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517125	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91
hsa0301035	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517135	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91

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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

RPS20

SNV

Missense_Mutation

c.40N>A

p.Glu14Lys

p.E14K

P60866

protein_coding

tolerated(0.08)

benign(0.101)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPS20

SNV

Missense_Mutation

c.235C>T

p.Arg79Cys

p.R79C

P60866

protein_coding

deleterious(0.04)

benign(0.168)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

RPS20

SNV

Missense_Mutation

c.254N>G

p.His85Arg

p.H85R

P60866

protein_coding

deleterious(0.01)

probably_damaging(0.991)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

RPS20

SNV

Missense_Mutation

novel

c.325G>A

p.Gly109Arg

p.G109R

P60866

protein_coding

deleterious(0.01)

probably_damaging(0.958)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPS20

SNV

Missense_Mutation

rs371598524

c.403N>A

p.Glu135Lys

p.E135K

P60866

protein_coding

deleterious_low_confidence(0.04)

possibly_damaging(0.905)

TCGA-AX-A2HC-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

RPS20

SNV

Missense_Mutation

c.340G>A

p.Glu114Lys

p.E114K

P60866

protein_coding

tolerated(0.08)

benign(0.185)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

RPS20

SNV

Missense_Mutation

c.197G>T

p.Arg66Ile

p.R66I

P60866

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

RPS20

SNV

Missense_Mutation

novel

c.304A>G

p.Thr102Ala

p.T102A

P60866

protein_coding

deleterious(0.04)

possibly_damaging(0.852)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

RPS20

SNV

Missense_Mutation

novel

c.190N>G

p.Thr64Ala

p.T64A

P60866

protein_coding

deleterious(0.02)

possibly_damaging(0.896)

TCGA-FI-A2F4-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPS20

SNV

Missense_Mutation

c.232N>A

p.Asp78Asn

p.D78N

P60866

protein_coding

deleterious(0.02)

probably_damaging(0.984)

TCGA-49-AARN-01

Lung

lung 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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