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: MRPL51

Gene summary for MRPL51

Gene summary.

Gene information	Species	Human
	Gene symbol	MRPL51
	Gene ID	51258
	Gene name	mitochondrial ribosomal protein L51
	Gene Alias	CDA09
	Cytomap	12p13.31
	Gene Type	protein-coding
	GO ID	GO:0006412
	UniProtAcc	Q4U2R6

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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
51258	MRPL51	cirrhotic1	Human	Liver	Cirrhotic	9.60e-37	3.77e-01	0.0202
51258	MRPL51	cirrhotic2	Human	Liver	Cirrhotic	3.92e-33	2.79e-01	0.0201
51258	MRPL51	cirrhotic3	Human	Liver	Cirrhotic	1.35e-34	3.54e-01	0.0215
51258	MRPL51	HCC1	Human	Liver	HCC	8.16e-12	5.22e+00	0.5336
51258	MRPL51	HCC2	Human	Liver	HCC	7.78e-08	4.22e+00	0.5341
51258	MRPL51	Pt13.a	Human	Liver	HCC	1.61e-05	1.57e-01	0.021
51258	MRPL51	Pt13.b	Human	Liver	HCC	1.56e-41	3.21e-01	0.0251
51258	MRPL51	Pt14.a	Human	Liver	HCC	4.66e-08	3.50e-01	0.0169
51258	MRPL51	Pt14.b	Human	Liver	HCC	2.98e-13	5.13e-01	0.018
51258	MRPL51	Pt14.d	Human	Liver	HCC	2.20e-03	1.37e-01	0.0143
51258	MRPL51	S014	Human	Liver	HCC	6.71e-40	2.17e+00	0.2254
51258	MRPL51	S015	Human	Liver	HCC	1.23e-33	2.51e+00	0.2375
51258	MRPL51	S016	Human	Liver	HCC	7.64e-40	2.16e+00	0.2243
51258	MRPL51	S027	Human	Liver	HCC	1.56e-15	2.06e+00	0.2446
51258	MRPL51	S028	Human	Liver	HCC	2.89e-28	2.34e+00	0.2503
51258	MRPL51	S029	Human	Liver	HCC	8.64e-28	2.44e+00	0.2581
51258	MRPL51	C04	Human	Oral cavity	OSCC	1.60e-37	3.41e+00	0.2633
51258	MRPL51	C21	Human	Oral cavity	OSCC	1.42e-65	3.46e+00	0.2678
51258	MRPL51	C30	Human	Oral cavity	OSCC	4.78e-60	4.39e+00	0.3055
51258	MRPL51	C38	Human	Oral cavity	OSCC	2.23e-26	3.65e+00	0.172

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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
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
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:00325432	Breast	IDC	mitochondrial translation	13/1434	76/18723	4.81e-03	3.67e-02	13
GO:003254311	Breast	DCIS	mitochondrial translation	13/1390	76/18723	3.70e-03	2.99e-02	13
GO:00325435	Esophagus	HGIN	mitochondrial translation	23/2587	76/18723	1.61e-04	3.16e-03	23
GO:01400534	Esophagus	HGIN	mitochondrial gene expression	27/2587	108/18723	1.34e-03	1.57e-02	27
GO:014005313	Esophagus	ESCC	mitochondrial gene expression	93/8552	108/18723	1.96e-18	2.03e-16	93
GO:003254314	Esophagus	ESCC	mitochondrial translation	68/8552	76/18723	1.02e-15	6.86e-14	68
GO:0032543	Liver	Cirrhotic	mitochondrial translation	40/4634	76/18723	1.61e-07	4.29e-06	40
GO:0140053	Liver	Cirrhotic	mitochondrial gene expression	49/4634	108/18723	2.35e-06	4.31e-05	49
GO:01400531	Liver	HCC	mitochondrial gene expression	82/7958	108/18723	1.49e-12	7.20e-11	82
GO:00325431	Liver	HCC	mitochondrial translation	62/7958	76/18723	2.95e-12	1.34e-10	62
GO:01400533	Oral cavity	OSCC	mitochondrial gene expression	78/7305	108/18723	2.37e-12	9.86e-11	78
GO:00325434	Oral cavity	OSCC	mitochondrial translation	59/7305	76/18723	7.21e-12	2.70e-10	59
GO:003254313	Oral cavity	LP	mitochondrial translation	43/4623	76/18723	2.85e-09	1.26e-07	43
GO:014005312	Oral cavity	LP	mitochondrial gene expression	53/4623	108/18723	3.54e-08	1.27e-06	53
GO:00325433	Prostate	BPH	mitochondrial translation	23/3107	76/18723	2.21e-03	1.22e-02	23
GO:01400532	Prostate	BPH	mitochondrial gene expression	29/3107	108/18723	4.68e-03	2.25e-02	29
GO:003254312	Prostate	Tumor	mitochondrial translation	24/3246	76/18723	1.73e-03	1.03e-02	24
GO:014005311	Prostate	Tumor	mitochondrial gene expression	31/3246	108/18723	2.31e-03	1.30e-02	31
GO:00325436	Skin	cSCC	mitochondrial translation	47/4864	76/18723	4.70e-11	2.22e-09	47
GO:01400535	Skin	cSCC	mitochondrial gene expression	56/4864	108/18723	8.06e-09	2.56e-07	56

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

MRPL51

SNV

Missense_Mutation

c.209N>T

p.Pro70Leu

p.P70L

Q4U2R6

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-A8-A097-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

MRPL51

SNV

Missense_Mutation

rs776718738

c.383G>A

p.Arg128Gln

p.R128Q

Q4U2R6

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

MRPL51

SNV

Missense_Mutation

rs191438555

c.338G>A

p.Arg113His

p.R113H

Q4U2R6

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

c.238N>A

p.Leu80Ile

p.L80I

Q4U2R6

protein_coding

deleterious(0.01)

probably_damaging(0.912)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

rs191438555

c.338N>A

p.Arg113His

p.R113H

Q4U2R6

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AX-A0J1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

rs377340253

c.269N>A

p.Arg90His

p.R90H

Q4U2R6

protein_coding

deleterious(0.03)

probably_damaging(0.999)

TCGA-AX-A0J1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

novel

c.193N>C

p.Asn65His

p.N65H

Q4U2R6

protein_coding

deleterious(0.03)

possibly_damaging(0.771)

TCGA-D1-A16X-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

c.100A>G

p.Ile34Val

p.I34V

Q4U2R6

protein_coding

tolerated(1)

benign(0)

TCGA-MI-A75G-01

Liver

liver hepatocellular carcinoma

Male

<65

I/II

Unknown

MRPL51

SNV

Missense_Mutation

c.147N>C

p.Glu49Asp

p.E49D

Q4U2R6

protein_coding

deleterious(0.01)

possibly_damaging(0.492)

TCGA-75-5126-01

Lung

lung adenocarcinoma

Female

Unknown

III/IV

Unknown

MRPL51

SNV

Missense_Mutation

novel

c.188N>A

p.Leu63Gln

p.L63Q

Q4U2R6

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-21-1083-01

Lung

lung squamous cell carcinoma

Male

>=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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