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: RPL23

Gene summary for RPL23

Gene summary.

Gene information	Species	Human
	Gene symbol	RPL23
	Gene ID	9349
	Gene name	ribosomal protein L23
	Gene Alias	L23
	Cytomap	17q12
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	A0A024R1Q8

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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
9349	RPL23	GSM4909281	Human	Breast	IDC	1.80e-20	-2.70e-01	0.21
9349	RPL23	GSM4909282	Human	Breast	IDC	5.55e-29	-3.92e-01	-0.0288
9349	RPL23	GSM4909286	Human	Breast	IDC	1.73e-54	3.58e-01	0.1081
9349	RPL23	GSM4909287	Human	Breast	IDC	4.03e-30	-5.41e-01	0.2057
9349	RPL23	GSM4909288	Human	Breast	IDC	1.16e-08	-3.95e-01	0.0988
9349	RPL23	GSM4909290	Human	Breast	IDC	1.04e-165	7.82e-01	0.2096
9349	RPL23	GSM4909292	Human	Breast	IDC	2.39e-47	7.31e-01	0.1236
9349	RPL23	GSM4909293	Human	Breast	IDC	9.17e-169	8.63e-01	0.1581
9349	RPL23	GSM4909294	Human	Breast	IDC	3.36e-41	3.46e-01	0.2022
9349	RPL23	GSM4909296	Human	Breast	IDC	7.60e-12	-2.97e-01	0.1524
9349	RPL23	GSM4909297	Human	Breast	IDC	1.43e-22	1.88e-02	0.1517
9349	RPL23	GSM4909299	Human	Breast	IDC	5.08e-03	1.77e-01	0.035
9349	RPL23	GSM4909302	Human	Breast	IDC	1.09e-09	5.24e-02	0.1545
9349	RPL23	GSM4909304	Human	Breast	IDC	6.67e-24	-2.95e-01	0.1636
9349	RPL23	GSM4909307	Human	Breast	IDC	2.47e-04	1.61e-01	0.1569
9349	RPL23	GSM4909308	Human	Breast	IDC	2.68e-12	2.26e-01	0.158
9349	RPL23	GSM4909309	Human	Breast	IDC	1.18e-07	-6.88e-02	0.0483
9349	RPL23	GSM4909311	Human	Breast	IDC	1.90e-37	-2.36e-01	0.1534
9349	RPL23	GSM4909316	Human	Breast	IDC	3.90e-10	-5.01e-01	0.21
9349	RPL23	GSM4909317	Human	Breast	IDC	5.22e-05	-1.74e-01	0.1355

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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:1904666113	Thyroid	PTC	regulation of ubiquitin protein ligase activity	16/5968	23/18723	2.31e-04	1.67e-03	16
GO:003298618	Thyroid	PTC	protein-DNA complex disassembly	14/5968	20/18723	5.24e-04	3.37e-03	14
GO:01400536	Thyroid	PTC	mitochondrial gene expression	51/5968	108/18723	6.04e-04	3.83e-03	51
GO:00466776	Thyroid	PTC	response to antibiotic	26/5968	47/18723	7.38e-04	4.59e-03	26
GO:00325437	Thyroid	PTC	mitochondrial translation	38/5968	76/18723	7.52e-04	4.67e-03	38
GO:0045861113	Thyroid	PTC	negative regulation of proteolysis	136/5968	351/18723	3.54e-03	1.71e-02	136
GO:0002181210	Thyroid	goiters	cytoplasmic translation	73/497	148/18723	1.65e-75	6.83e-72	73
GO:0042255210	Thyroid	goiters	ribosome assembly	19/497	61/18723	8.57e-16	3.23e-13	19
GO:0042254210	Thyroid	goiters	ribosome biogenesis	38/497	299/18723	1.07e-15	3.69e-13	38
GO:0022613210	Thyroid	goiters	ribonucleoprotein complex biogenesis	47/497	463/18723	2.79e-15	8.90e-13	47
GO:0042273210	Thyroid	goiters	ribosomal large subunit biogenesis	18/497	72/18723	3.48e-13	8.48e-11	18
GO:0022618210	Thyroid	goiters	ribonucleoprotein complex assembly	26/497	220/18723	1.99e-10	2.85e-08	26
GO:0071826210	Thyroid	goiters	ribonucleoprotein complex subunit organization	26/497	227/18723	3.98e-10	5.50e-08	26
GO:0000027210	Thyroid	goiters	ribosomal large subunit assembly	10/497	27/18723	8.93e-10	1.12e-07	10
GO:002261334	Thyroid	ATC	ribonucleoprotein complex biogenesis	292/6293	463/18723	3.05e-39	9.63e-36	292
GO:004225434	Thyroid	ATC	ribosome biogenesis	203/6293	299/18723	3.63e-34	4.59e-31	203
GO:000218135	Thyroid	ATC	cytoplasmic translation	121/6293	148/18723	1.41e-33	1.49e-30	121
GO:004217635	Thyroid	ATC	regulation of protein catabolic process	239/6293	391/18723	2.63e-29	1.85e-26	239
GO:007259429	Thyroid	ATC	establishment of protein localization to organelle	247/6293	422/18723	2.88e-26	1.40e-23	247
GO:190336235	Thyroid	ATC	regulation of cellular protein catabolic process	168/6293	255/18723	3.50e-26	1.58e-23	168

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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

RPL23

SNV

Missense_Mutation

c.295N>C

p.Glu99Gln

p.E99Q

P62829

protein_coding

deleterious(0.01)

possibly_damaging(0.794)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPL23

SNV

Missense_Mutation

novel

c.119T>G

p.Ile40Ser

p.I40S

P62829

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0HK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

RPL23

SNV

Missense_Mutation

c.11N>A

p.Arg4Gln

p.R4Q

P62829

protein_coding

tolerated(0.19)

benign(0.328)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPL23

insertion

Nonsense_Mutation

novel

c.149_150insGTTCCTGGCCATCCCTTGATTTACAAATGTGATGTTGATTTGT

p.Asn50LysfsTer7

p.N50Kfs*7

P62829

protein_coding

TCGA-A7-A0D9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

RPL23

insertion

Frame_Shift_Ins

novel

c.116_117insGAAAGGTAGGAAATCAGTC

p.Ile39MetfsTer27

p.I39Mfs*27

P62829

protein_coding

TCGA-BH-A0HK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

RPL23

SNV

Missense_Mutation

novel

c.254N>A

p.Arg85Gln

p.R85Q

P62829

protein_coding

tolerated(0.07)

benign(0.046)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RPL23

SNV

Missense_Mutation

novel

c.397G>A

p.Ala133Thr

p.A133T

P62829

protein_coding

deleterious(0.01)

benign(0.367)

TCGA-F4-6856-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Ancillary

leucovorin

RPL23

SNV

Missense_Mutation

novel

c.107N>G

p.Asn36Ser

p.N36S

P62829

protein_coding

tolerated(0.24)

benign(0.262)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPL23

SNV

Missense_Mutation

c.213N>T

p.Glu71Asp

p.E71D

P62829

protein_coding

tolerated(0.32)

benign(0.248)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPL23

SNV

Missense_Mutation

c.172G>T

p.Gly58Cys

p.G58C

P62829

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-D1-A17R-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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