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: RPS14

Gene summary for RPS14

Gene summary.

Gene information	Species	Human
	Gene symbol	RPS14
	Gene ID	6208
	Gene name	ribosomal protein S14
	Gene Alias	EMTB
	Cytomap	5q33.1
	Gene Type	protein-coding
	GO ID	GO:0000028
	UniProtAcc	P62263

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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
6208	RPS14	GSM4909281	Human	Breast	IDC	2.00e-39	-2.55e-01	0.21
6208	RPS14	GSM4909282	Human	Breast	IDC	1.68e-55	-2.83e-01	-0.0288
6208	RPS14	GSM4909286	Human	Breast	IDC	4.06e-02	-4.03e-02	0.1081
6208	RPS14	GSM4909287	Human	Breast	IDC	4.59e-22	-2.97e-01	0.2057
6208	RPS14	GSM4909290	Human	Breast	IDC	5.38e-25	-2.79e-01	0.2096
6208	RPS14	GSM4909293	Human	Breast	IDC	3.14e-07	-7.30e-02	0.1581
6208	RPS14	GSM4909297	Human	Breast	IDC	1.29e-11	-1.84e-01	0.1517
6208	RPS14	GSM4909304	Human	Breast	IDC	6.06e-38	-2.03e-01	0.1636
6208	RPS14	GSM4909305	Human	Breast	IDC	9.51e-03	6.66e-02	0.0436
6208	RPS14	GSM4909315	Human	Breast	IDC	2.33e-08	-1.52e-01	0.21
6208	RPS14	GSM4909316	Human	Breast	IDC	5.29e-11	-4.30e-01	0.21
6208	RPS14	GSM4909317	Human	Breast	IDC	2.74e-06	-1.79e-01	0.1355
6208	RPS14	GSM4909319	Human	Breast	IDC	5.32e-24	-3.58e-01	0.1563
6208	RPS14	brca2	Human	Breast	Precancer	4.28e-14	-1.18e-01	-0.024
6208	RPS14	brca3	Human	Breast	Precancer	7.78e-05	-6.17e-02	-0.0263
6208	RPS14	brca10	Human	Breast	Precancer	5.22e-12	-2.18e-01	-0.0029
6208	RPS14	M2	Human	Breast	IDC	1.32e-11	-4.99e-01	0.21
6208	RPS14	M5	Human	Breast	IDC	1.15e-03	-3.77e-01	0.1598
6208	RPS14	NCCBC14	Human	Breast	DCIS	7.07e-38	-5.68e-01	0.2021
6208	RPS14	NCCBC3	Human	Breast	DCIS	9.48e-04	-6.44e-02	0.1198

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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:00302188	Lung	IAC	erythrocyte differentiation	32/2061	120/18723	1.39e-06	7.05e-05	32
GO:00422558	Lung	IAC	ribosome assembly	20/2061	61/18723	4.46e-06	1.81e-04	20
GO:00022628	Lung	IAC	myeloid cell homeostasis	37/2061	157/18723	5.42e-06	2.09e-04	37
GO:00000288	Lung	IAC	ribosomal small subunit assembly	10/2061	19/18723	9.24e-06	3.06e-04	10
GO:00300998	Lung	IAC	myeloid cell differentiation	70/2061	381/18723	1.12e-05	3.45e-04	70
GO:00488728	Lung	IAC	homeostasis of number of cells	54/2061	272/18723	1.20e-05	3.64e-04	54
GO:00718268	Lung	IAC	ribonucleoprotein complex subunit organization	46/2061	227/18723	3.02e-05	7.79e-04	46
GO:00226188	Lung	IAC	ribonucleoprotein complex assembly	44/2061	220/18723	6.16e-05	1.34e-03	44
GO:00422748	Lung	IAC	ribosomal small subunit biogenesis	20/2061	73/18723	8.40e-05	1.71e-03	20
GO:000218113	Lung	AIS	cytoplasmic translation	85/1849	148/18723	5.48e-47	3.19e-43	85
GO:004225513	Lung	AIS	ribosome assembly	20/1849	61/18723	8.18e-07	5.96e-05	20
GO:000641713	Lung	AIS	regulation of translation	78/1849	468/18723	2.68e-06	1.49e-04	78
GO:000002813	Lung	AIS	ribosomal small subunit assembly	10/1849	19/18723	3.44e-06	1.81e-04	10
GO:003410113	Lung	AIS	erythrocyte homeostasis	30/1849	129/18723	6.51e-06	2.92e-04	30
GO:003021813	Lung	AIS	erythrocyte differentiation	28/1849	120/18723	1.22e-05	4.71e-04	28
GO:004227413	Lung	AIS	ribosomal small subunit biogenesis	20/1849	73/18723	1.77e-05	6.17e-04	20
GO:003009913	Lung	AIS	myeloid cell differentiation	63/1849	381/18723	3.05e-05	9.70e-04	63
GO:000226213	Lung	AIS	myeloid cell homeostasis	32/1849	157/18723	5.57e-05	1.57e-03	32
GO:004887213	Lung	AIS	homeostasis of number of cells	47/1849	272/18723	1.03e-04	2.50e-03	47
GO:007182613	Lung	AIS	ribonucleoprotein complex subunit organization	41/1849	227/18723	1.03e-04	2.50e-03	41

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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

RPS14

SNV

Missense_Mutation

rs137915903

c.221N>G

p.Ala74Gly

p.A74G

P62263

protein_coding

deleterious(0.01)

probably_damaging(0.928)

TCGA-BH-A0BG-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPS14

insertion

Frame_Shift_Ins

novel

c.364_365insTAAAAGATTTTTTCAGACTTTTTTTCAGTGTCTTTTTACTTAATGAA

p.Ser122LeufsTer19

p.S122Lfs*19

P62263

protein_coding

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

RPS14

SNV

Missense_Mutation

novel

c.382N>T

p.Arg128Trp

p.R128W

P62263

protein_coding

deleterious(0.04)

benign(0.056)

TCGA-VS-A9UJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPS14

SNV

Missense_Mutation

c.221N>A

p.Ala74Asp

p.A74D

P62263

protein_coding

deleterious(0)

benign(0.443)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

RPS14

SNV

Missense_Mutation

novel

c.293G>A

p.Arg98Gln

p.R98Q

P62263

protein_coding

tolerated(0.14)

benign(0.168)

TCGA-AJ-A3EK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

RPS14

SNV

Missense_Mutation

c.64N>A

p.Ala22Thr

p.A22T

P62263

protein_coding

tolerated(0.12)

benign(0.009)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPS14

SNV

Missense_Mutation

c.292C>T

p.Arg98Trp

p.R98W

P62263

protein_coding

tolerated(0.06)

benign(0.159)

TCGA-AX-A2HD-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Unknown

RPS14

SNV

Missense_Mutation

novel

c.421C>T

p.Arg141Cys

p.R141C

P62263

protein_coding

tolerated(0.13)

possibly_damaging(0.898)

TCGA-EO-A22U-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPS14

SNV

Missense_Mutation

novel

c.55N>T

p.Pro19Ser

p.P19S

P62263

protein_coding

deleterious(0.02)

benign(0.139)

TCGA-EY-A215-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPS14

SNV

Missense_Mutation

novel

c.446N>A

p.Arg149His

p.R149H

P62263

protein_coding

tolerated(0.34)

possibly_damaging(0.522)

TCGA-FI-A2D0-01

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

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