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: RPS24

Gene summary for RPS24

Gene summary.

Gene information	Species	Human
	Gene symbol	RPS24
	Gene ID	6229
	Gene name	ribosomal protein S24
	Gene Alias	DBA3
	Cytomap	10q22.3
	Gene Type	protein-coding
	GO ID	GO:0002181
	UniProtAcc	P62847

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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
6229	RPS24	GSM4909281	Human	Breast	IDC	8.35e-30	-2.71e-01	0.21
6229	RPS24	GSM4909282	Human	Breast	IDC	5.67e-25	-2.18e-01	-0.0288
6229	RPS24	GSM4909285	Human	Breast	IDC	7.61e-09	1.35e-01	0.21
6229	RPS24	GSM4909286	Human	Breast	IDC	1.23e-47	2.61e-01	0.1081
6229	RPS24	GSM4909287	Human	Breast	IDC	3.10e-10	-2.13e-01	0.2057
6229	RPS24	GSM4909291	Human	Breast	IDC	5.10e-04	-1.41e-01	0.1753
6229	RPS24	GSM4909295	Human	Breast	IDC	1.16e-12	-2.92e-01	0.0898
6229	RPS24	GSM4909297	Human	Breast	IDC	2.09e-07	-1.45e-01	0.1517
6229	RPS24	GSM4909300	Human	Breast	IDC	1.68e-06	-2.28e-01	0.0334
6229	RPS24	GSM4909301	Human	Breast	IDC	3.57e-16	-2.25e-01	0.1577
6229	RPS24	GSM4909302	Human	Breast	IDC	1.48e-02	-1.39e-01	0.1545
6229	RPS24	GSM4909306	Human	Breast	IDC	3.93e-13	-1.64e-01	0.1564
6229	RPS24	GSM4909307	Human	Breast	IDC	7.28e-06	-1.39e-01	0.1569
6229	RPS24	GSM4909308	Human	Breast	IDC	3.73e-06	-1.19e-01	0.158
6229	RPS24	GSM4909309	Human	Breast	IDC	3.05e-09	-2.21e-01	0.0483
6229	RPS24	GSM4909311	Human	Breast	IDC	1.76e-02	-5.29e-02	0.1534
6229	RPS24	GSM4909313	Human	Breast	IDC	7.08e-15	-2.22e-01	0.0391
6229	RPS24	GSM4909317	Human	Breast	IDC	3.14e-16	-2.10e-01	0.1355
6229	RPS24	GSM4909319	Human	Breast	IDC	3.28e-45	-8.07e-01	0.1563
6229	RPS24	GSM4909320	Human	Breast	IDC	1.23e-14	-4.60e-01	0.1575

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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:003410127	Esophagus	HGIN	erythrocyte homeostasis	34/2587	129/18723	1.16e-04	2.43e-03	34
GO:00325435	Esophagus	HGIN	mitochondrial translation	23/2587	76/18723	1.61e-04	3.16e-03	23
GO:000226227	Esophagus	HGIN	myeloid cell homeostasis	37/2587	157/18723	6.63e-04	9.04e-03	37
GO:01400534	Esophagus	HGIN	mitochondrial gene expression	27/2587	108/18723	1.34e-03	1.57e-02	27
GO:004887227	Esophagus	HGIN	homeostasis of number of cells	54/2587	272/18723	3.50e-03	3.23e-02	54
GO:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:0042254111	Esophagus	ESCC	ribosome biogenesis	252/8552	299/18723	3.27e-44	1.04e-40	252
GO:003447015	Esophagus	ESCC	ncRNA processing	300/8552	395/18723	3.09e-35	3.26e-32	300
GO:0016072110	Esophagus	ESCC	rRNA metabolic process	197/8552	236/18723	1.31e-33	1.18e-30	197
GO:0006364110	Esophagus	ESCC	rRNA processing	189/8552	225/18723	4.88e-33	3.87e-30	189
GO:0002181111	Esophagus	ESCC	cytoplasmic translation	135/8552	148/18723	4.17e-32	2.65e-29	135
GO:003466012	Esophagus	ESCC	ncRNA metabolic process	346/8552	485/18723	4.35e-31	2.51e-28	346
GO:014005313	Esophagus	ESCC	mitochondrial gene expression	93/8552	108/18723	1.96e-18	2.03e-16	93
GO:0042274111	Esophagus	ESCC	ribosomal small subunit biogenesis	67/8552	73/18723	6.62e-17	5.38e-15	67
GO:003254314	Esophagus	ESCC	mitochondrial translation	68/8552	76/18723	1.02e-15	6.86e-14	68
GO:0002262111	Esophagus	ESCC	myeloid cell homeostasis	104/8552	157/18723	1.49e-07	2.36e-06	104
GO:0034101111	Esophagus	ESCC	erythrocyte homeostasis	88/8552	129/18723	1.81e-07	2.84e-06	88
GO:0048872111	Esophagus	ESCC	homeostasis of number of cells	163/8552	272/18723	1.40e-06	1.69e-05	163
GO:00021817	Liver	NAFLD	cytoplasmic translation	93/1882	148/18723	1.44e-55	8.41e-52	93
GO:00226137	Liver	NAFLD	ribonucleoprotein complex biogenesis	76/1882	463/18723	1.19e-05	3.67e-04	76

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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

RPS24

SNV

Missense_Mutation

novel

c.526G>T

p.Val176Leu

p.V176L

P62847

protein_coding

deleterious_low_confidence(0)

benign(0.003)

TCGA-AR-A5QM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

RPS24

SNV

Missense_Mutation

c.454G>C

p.Asp152His

p.D152H

P62847

protein_coding

deleterious_low_confidence(0)

benign(0.154)

TCGA-MU-A51Y-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPS24

SNV

Missense_Mutation

novel

c.320N>A

p.Arg107Gln

p.R107Q

P62847

protein_coding

tolerated_low_confidence(0.12)

benign(0.195)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

RPS24

SNV

Missense_Mutation

novel

c.462N>T

p.Lys154Asn

p.K154N

P62847

protein_coding

deleterious_low_confidence(0.01)

benign(0.339)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

RPS24

SNV

Missense_Mutation

c.142T>A

p.Tyr48Asn

p.Y48N

P62847

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.995)

TCGA-CK-5916-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

RPS24

SNV

Missense_Mutation

c.535T>C

p.Cys179Arg

p.C179R

P62847

protein_coding

deleterious_low_confidence(0)

benign(0)

TCGA-CK-5916-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

RPS24

SNV

Missense_Mutation

c.428G>T

p.Arg143Ile

p.R143I

P62847

protein_coding

deleterious_low_confidence(0)

benign(0)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

RPS24

SNV

Missense_Mutation

novel

c.418N>A

p.Ala140Thr

p.A140T

P62847

protein_coding

deleterious_low_confidence(0.02)

benign(0.003)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPS24

SNV

Missense_Mutation

novel

c.104N>C

p.Val35Ala

p.V35A

P62847

protein_coding

deleterious_low_confidence(0.03)

possibly_damaging(0.838)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

RPS24

SNV

Missense_Mutation

novel

c.462N>T

p.Lys154Asn

p.K154N

P62847

protein_coding

deleterious_low_confidence(0.01)

benign(0.339)

TCGA-A5-A2K5-01

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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