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: RPL23A

Gene summary for RPL23A

Gene summary.

Gene information	Species	Human
	Gene symbol	RPL23A
	Gene ID	6147
	Gene name	ribosomal protein L23a
	Gene Alias	L23A
	Cytomap	17q11.2
	Gene Type	protein-coding
	GO ID	GO:0000027
	UniProtAcc	P62750

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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
6147	RPL23A	GSM4909281	Human	Breast	IDC	4.15e-04	-9.39e-02	0.21
6147	RPL23A	GSM4909282	Human	Breast	IDC	3.15e-36	-2.18e-01	-0.0288
6147	RPL23A	GSM4909286	Human	Breast	IDC	2.03e-128	4.27e-01	0.1081
6147	RPL23A	GSM4909287	Human	Breast	IDC	7.73e-73	-7.51e-01	0.2057
6147	RPL23A	GSM4909288	Human	Breast	IDC	1.38e-16	-6.07e-01	0.0988
6147	RPL23A	GSM4909289	Human	Breast	IDC	8.29e-21	3.81e-01	0.1064
6147	RPL23A	GSM4909292	Human	Breast	IDC	8.06e-23	4.19e-01	0.1236
6147	RPL23A	GSM4909293	Human	Breast	IDC	1.17e-21	-1.22e-01	0.1581
6147	RPL23A	GSM4909294	Human	Breast	IDC	2.74e-16	1.98e-01	0.2022
6147	RPL23A	GSM4909295	Human	Breast	IDC	3.19e-02	8.35e-02	0.0898
6147	RPL23A	GSM4909297	Human	Breast	IDC	3.90e-09	1.19e-01	0.1517
6147	RPL23A	GSM4909299	Human	Breast	IDC	3.30e-09	1.56e-01	0.035
6147	RPL23A	GSM4909302	Human	Breast	IDC	5.91e-06	5.84e-02	0.1545
6147	RPL23A	GSM4909303	Human	Breast	IDC	3.55e-03	-2.65e-01	0.0438
6147	RPL23A	GSM4909304	Human	Breast	IDC	1.05e-53	-2.98e-01	0.1636
6147	RPL23A	GSM4909305	Human	Breast	IDC	1.79e-05	1.39e-01	0.0436
6147	RPL23A	GSM4909307	Human	Breast	IDC	1.71e-16	1.86e-01	0.1569
6147	RPL23A	GSM4909308	Human	Breast	IDC	1.66e-07	1.39e-01	0.158
6147	RPL23A	GSM4909309	Human	Breast	IDC	8.52e-10	1.32e-01	0.0483
6147	RPL23A	GSM4909311	Human	Breast	IDC	7.89e-42	2.61e-01	0.1534

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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:00021819	Breast	Precancer	cytoplasmic translation	80/1080	148/18723	1.59e-59	8.54e-56	80
GO:00226139	Breast	Precancer	ribonucleoprotein complex biogenesis	79/1080	463/18723	2.11e-18	1.03e-15	79
GO:00718269	Breast	Precancer	ribonucleoprotein complex subunit organization	48/1080	227/18723	2.68e-15	8.45e-13	48
GO:00226189	Breast	Precancer	ribonucleoprotein complex assembly	47/1080	220/18723	3.47e-15	1.03e-12	47
GO:00422549	Breast	Precancer	ribosome biogenesis	52/1080	299/18723	7.35e-13	1.51e-10	52
GO:00422559	Breast	Precancer	ribosome assembly	21/1080	61/18723	1.06e-11	1.53e-09	21
GO:00422739	Breast	Precancer	ribosomal large subunit biogenesis	22/1080	72/18723	5.03e-11	5.61e-09	22
GO:00000279	Breast	Precancer	ribosomal large subunit assembly	9/1080	27/18723	1.24e-05	3.19e-04	9
GO:000218114	Breast	IDC	cytoplasmic translation	82/1434	148/18723	2.60e-52	1.48e-48	82
GO:002261314	Breast	IDC	ribonucleoprotein complex biogenesis	83/1434	463/18723	2.01e-13	5.20e-11	83
GO:007182614	Breast	IDC	ribonucleoprotein complex subunit organization	52/1434	227/18723	5.18e-13	1.21e-10	52
GO:002261814	Breast	IDC	ribonucleoprotein complex assembly	51/1434	220/18723	5.32e-13	1.21e-10	51
GO:004225514	Breast	IDC	ribosome assembly	21/1434	61/18723	1.98e-09	1.76e-07	21
GO:004227314	Breast	IDC	ribosomal large subunit biogenesis	22/1434	72/18723	1.04e-08	7.67e-07	22
GO:004225414	Breast	IDC	ribosome biogenesis	52/1434	299/18723	1.90e-08	1.32e-06	52
GO:000002714	Breast	IDC	ribosomal large subunit assembly	9/1434	27/18723	1.17e-04	2.17e-03	9
GO:000218124	Breast	DCIS	cytoplasmic translation	82/1390	148/18723	2.21e-53	1.25e-49	82
GO:002261324	Breast	DCIS	ribonucleoprotein complex biogenesis	83/1390	463/18723	3.65e-14	1.09e-11	83
GO:007182624	Breast	DCIS	ribonucleoprotein complex subunit organization	52/1390	227/18723	1.54e-13	3.95e-11	52
GO:002261824	Breast	DCIS	ribonucleoprotein complex assembly	51/1390	220/18723	1.60e-13	3.95e-11	51

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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

RPL23A

SNV

Missense_Mutation

novel

c.131N>T

p.Pro44Leu

p.P44L

P62750

protein_coding

tolerated(0.15)

benign(0.104)

TCGA-PL-A8LV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

RPL23A

insertion

Frame_Shift_Ins

novel

c.173_174insA

p.Lys59GlnfsTer14

p.K59Qfs*14

P62750

protein_coding

TCGA-A8-A08G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

RPL23A

insertion

Frame_Shift_Ins

novel

c.174_175insGCACGAAAAAG

p.Lys59AlafsTer27

p.K59Afs*27

P62750

protein_coding

TCGA-A8-A08G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

RPL23A

SNV

Missense_Mutation

c.121C>T

p.Arg41Cys

p.R41C

P62750

protein_coding

tolerated(0.1)

benign(0.117)

TCGA-A5-A0VQ-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

RPL23A

SNV

Missense_Mutation

rs758296129

c.119N>C

p.Ile40Thr

p.I40T

P62750

protein_coding

tolerated(0.07)

benign(0.219)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPL23A

SNV

Missense_Mutation

c.224N>A

p.Ala75Asp

p.A75D

P62750

protein_coding

deleterious(0.04)

benign(0.364)

TCGA-AX-A0J0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPL23A

SNV

Missense_Mutation

novel

c.75G>T

p.Lys25Asn

p.K25N

P62750

protein_coding

deleterious(0.03)

probably_damaging(0.987)

TCGA-B5-A1MX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Hormone Therapy

megace

RPL23A

SNV

Missense_Mutation

novel

c.239N>T

p.Pro80Leu

p.P80L

P62750

protein_coding

deleterious(0.05)

possibly_damaging(0.537)

TCGA-EC-A24G-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

RPL23A

SNV

Missense_Mutation

novel

c.111G>T

p.Lys37Asn

p.K37N

P62750

protein_coding

deleterious(0.04)

possibly_damaging(0.904)

TCGA-EO-A3AY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPL23A

SNV

Missense_Mutation

rs760295259

c.106A>G

p.Lys36Glu

p.K36E

P62750

protein_coding

tolerated(0.05)

benign(0.16)

TCGA-EO-A3KX-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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