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: RNF213

Gene summary for RNF213

Gene summary.

Gene information	Species	Human
	Gene symbol	RNF213
	Gene ID	57674
	Gene name	ring finger protein 213
	Gene Alias	ALO17
	Cytomap	17q25.3
	Gene Type	protein-coding
	GO ID	GO:0001525
	UniProtAcc	A0A0A0MTR7

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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
57674	RNF213	GSM4909287	Human	Breast	IDC	4.93e-03	2.95e-01	0.2057
57674	RNF213	GSM4909290	Human	Breast	IDC	1.66e-04	3.56e-01	0.2096
57674	RNF213	GSM4909296	Human	Breast	IDC	5.89e-06	-1.75e-01	0.1524
57674	RNF213	GSM4909297	Human	Breast	IDC	9.09e-04	-1.08e-01	0.1517
57674	RNF213	GSM4909301	Human	Breast	IDC	6.83e-07	3.71e-01	0.1577
57674	RNF213	GSM4909302	Human	Breast	IDC	2.07e-06	3.48e-01	0.1545
57674	RNF213	GSM4909307	Human	Breast	IDC	1.34e-19	5.87e-01	0.1569
57674	RNF213	GSM4909308	Human	Breast	IDC	2.78e-06	3.48e-01	0.158
57674	RNF213	GSM4909309	Human	Breast	IDC	1.92e-02	1.36e-01	0.0483
57674	RNF213	GSM4909311	Human	Breast	IDC	1.15e-13	-2.06e-01	0.1534
57674	RNF213	GSM4909312	Human	Breast	IDC	3.77e-09	-1.80e-01	0.1552
57674	RNF213	GSM4909317	Human	Breast	IDC	2.06e-21	6.33e-01	0.1355
57674	RNF213	GSM4909319	Human	Breast	IDC	9.99e-30	-6.25e-02	0.1563
57674	RNF213	GSM4909320	Human	Breast	IDC	1.59e-12	5.49e-01	0.1575
57674	RNF213	GSM4909321	Human	Breast	IDC	2.09e-20	3.84e-01	0.1559
57674	RNF213	M1	Human	Breast	IDC	4.87e-17	6.28e-01	0.1577
57674	RNF213	M2	Human	Breast	IDC	3.77e-02	2.20e-01	0.21
57674	RNF213	NCCBC14	Human	Breast	DCIS	2.72e-02	9.08e-04	0.2021
57674	RNF213	NCCBC5	Human	Breast	DCIS	8.11e-11	1.31e-01	0.2046
57674	RNF213	P1	Human	Breast	IDC	8.10e-30	8.05e-01	0.1527

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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
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:00160557	Cervix	CC	Wnt signaling pathway	98/2311	444/18723	4.82e-09	4.65e-07	98
GO:01987387	Cervix	CC	cell-cell signaling by wnt	98/2311	446/18723	6.16e-09	5.58e-07	98
GO:00301117	Cervix	CC	regulation of Wnt signaling pathway	76/2311	328/18723	3.05e-08	2.08e-06	76
GO:00301784	Cervix	CC	negative regulation of Wnt signaling pathway	35/2311	170/18723	1.52e-03	1.17e-02	35
GO:00518656	Cervix	CC	protein autoubiquitination	17/2311	73/18723	6.71e-03	3.70e-02	17
GO:00301118	Endometrium	AEH	regulation of Wnt signaling pathway	71/2100	328/18723	3.31e-08	1.87e-06	71
GO:00160558	Endometrium	AEH	Wnt signaling pathway	85/2100	444/18723	4.99e-07	1.97e-05	85
GO:01987388	Endometrium	AEH	cell-cell signaling by wnt	85/2100	446/18723	6.07e-07	2.29e-05	85
GO:00301785	Endometrium	AEH	negative regulation of Wnt signaling pathway	34/2100	170/18723	5.63e-04	5.62e-03	34
GO:003011113	Endometrium	EEC	regulation of Wnt signaling pathway	74/2168	328/18723	1.03e-08	6.47e-07	74
GO:001605513	Endometrium	EEC	Wnt signaling pathway	90/2168	444/18723	6.65e-08	3.50e-06	90
GO:019873813	Endometrium	EEC	cell-cell signaling by wnt	90/2168	446/18723	8.25e-08	4.23e-06	90
GO:003017812	Endometrium	EEC	negative regulation of Wnt signaling pathway	35/2168	170/18723	4.84e-04	4.96e-03	35
GO:003011116	Esophagus	HGIN	regulation of Wnt signaling pathway	65/2587	328/18723	1.53e-03	1.77e-02	65
GO:001605516	Esophagus	HGIN	Wnt signaling pathway	83/2587	444/18723	2.27e-03	2.33e-02	83
GO:019873816	Esophagus	HGIN	cell-cell signaling by wnt	83/2587	446/18723	2.58e-03	2.55e-02	83
GO:001605517	Esophagus	ESCC	Wnt signaling pathway	268/8552	444/18723	2.32e-10	6.58e-09	268
GO:019873817	Esophagus	ESCC	cell-cell signaling by wnt	269/8552	446/18723	2.41e-10	6.79e-09	269
GO:003011117	Esophagus	ESCC	regulation of Wnt signaling pathway	194/8552	328/18723	5.39e-07	7.14e-06	194
GO:00518658	Esophagus	ESCC	protein autoubiquitination	47/8552	73/18723	9.72e-04	4.93e-03	47

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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

RNF213

SNV

Missense_Mutation

novel

c.11465N>A

p.Arg3822Lys

p.R3822K

protein_coding

tolerated(0.7)

benign(0.049)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

RNF213

SNV

Missense_Mutation

novel

c.1146N>A

p.Phe382Leu

p.F382L

protein_coding

deleterious(0.01)

benign(0.063)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

RNF213

SNV

Missense_Mutation

rs776579145

c.14665N>T

p.Arg4889Cys

p.R4889C

protein_coding

deleterious(0.01)

possibly_damaging(0.781)

TCGA-A2-A0CW-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

RNF213

SNV

Missense_Mutation

novel

c.15172N>T

p.Asp5058Tyr

p.D5058Y

protein_coding

deleterious(0)

probably_damaging(0.917)

TCGA-A2-A0CX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

RNF213

SNV

Missense_Mutation

c.9712N>A

p.Gly3238Ser

p.G3238S

protein_coding

tolerated(0.19)

benign(0.253)

TCGA-A8-A095-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

RNF213

SNV

Missense_Mutation

rs769984642

c.7425N>C

p.Lys2475Asn

p.K2475N

protein_coding

deleterious(0.01)

possibly_damaging(0.894)

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

RNF213

SNV

Missense_Mutation

c.15067N>A

p.Glu5023Lys

p.E5023K

protein_coding

deleterious(0.01)

benign(0.249)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RNF213

SNV

Missense_Mutation

novel

c.8727N>T

p.Glu2909Asp

p.E2909D

protein_coding

deleterious(0)

possibly_damaging(0.781)

TCGA-AC-A5EH-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RNF213

SNV

Missense_Mutation

c.14951A>G

p.Asp4984Gly

p.D4984G

protein_coding

deleterious(0.04)

probably_damaging(0.913)

TCGA-B6-A0I6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RNF213

SNV

Missense_Mutation

novel

c.7678N>G

p.Pro2560Ala

p.P2560A

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0B6-01

Breast

breast invasive 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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