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: RAF1

Gene summary for RAF1

Gene summary.

Gene information	Species	Human
	Gene symbol	RAF1
	Gene ID	5894
	Gene name	Raf-1 proto-oncogene, serine/threonine kinase
	Gene Alias	CMD1NN
	Cytomap	3p25.2
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	L7RRS6

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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
5894	RAF1	CCI_2	Human	Cervix	CC	5.83e-03	5.23e-01	0.5249
5894	RAF1	CCI_3	Human	Cervix	CC	1.45e-11	5.87e-01	0.516
5894	RAF1	LZE4T	Human	Esophagus	ESCC	1.65e-06	1.26e-01	0.0811
5894	RAF1	LZE7T	Human	Esophagus	ESCC	1.47e-09	2.26e-01	0.0667
5894	RAF1	LZE8T	Human	Esophagus	ESCC	2.44e-04	7.10e-02	0.067
5894	RAF1	LZE20T	Human	Esophagus	ESCC	1.39e-02	1.34e-02	0.0662
5894	RAF1	LZE24T	Human	Esophagus	ESCC	8.75e-13	3.06e-01	0.0596
5894	RAF1	P1T-E	Human	Esophagus	ESCC	2.13e-06	1.75e-01	0.0875
5894	RAF1	P2T-E	Human	Esophagus	ESCC	2.58e-21	3.44e-01	0.1177
5894	RAF1	P4T-E	Human	Esophagus	ESCC	1.97e-17	3.45e-01	0.1323
5894	RAF1	P5T-E	Human	Esophagus	ESCC	6.82e-29	6.01e-01	0.1327
5894	RAF1	P8T-E	Human	Esophagus	ESCC	4.09e-26	2.17e-01	0.0889
5894	RAF1	P9T-E	Human	Esophagus	ESCC	6.08e-14	3.11e-01	0.1131
5894	RAF1	P10T-E	Human	Esophagus	ESCC	2.43e-28	3.74e-01	0.116
5894	RAF1	P11T-E	Human	Esophagus	ESCC	1.67e-16	3.54e-01	0.1426
5894	RAF1	P12T-E	Human	Esophagus	ESCC	2.84e-22	4.10e-01	0.1122
5894	RAF1	P15T-E	Human	Esophagus	ESCC	3.45e-17	2.66e-01	0.1149
5894	RAF1	P16T-E	Human	Esophagus	ESCC	8.00e-12	2.31e-01	0.1153
5894	RAF1	P17T-E	Human	Esophagus	ESCC	5.02e-09	2.42e-01	0.1278
5894	RAF1	P19T-E	Human	Esophagus	ESCC	1.34e-08	4.25e-01	0.1662

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
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:004206010	Cervix	CC	wound healing	109/2311	422/18723	1.84e-14	1.57e-11	109
GO:200123310	Cervix	CC	regulation of apoptotic signaling pathway	96/2311	356/18723	4.08e-14	3.05e-11	96
GO:005254710	Cervix	CC	regulation of peptidase activity	112/2311	461/18723	6.70e-13	3.08e-10	112
GO:005254810	Cervix	CC	regulation of endopeptidase activity	103/2311	432/18723	1.89e-11	5.14e-09	103
GO:00510566	Cervix	CC	regulation of small GTPase mediated signal transduction	75/2311	302/18723	1.54e-09	1.74e-07	75
GO:004325410	Cervix	CC	regulation of protein-containing complex assembly	96/2311	428/18723	2.91e-09	3.05e-07	96
GO:200011610	Cervix	CC	regulation of cysteine-type endopeptidase activity	61/2311	235/18723	8.69e-09	7.22e-07	61
GO:00072656	Cervix	CC	Ras protein signal transduction	79/2311	337/18723	9.49e-09	7.77e-07	79
GO:004328110	Cervix	CC	regulation of cysteine-type endopeptidase activity involved in apoptotic process	55/2311	209/18723	2.77e-08	1.95e-06	55
GO:004586110	Cervix	CC	negative regulation of proteolysis	80/2311	351/18723	2.88e-08	1.98e-06	80
GO:200123410	Cervix	CC	negative regulation of apoptotic signaling pathway	56/2311	224/18723	1.39e-07	6.70e-06	56
GO:00513469	Cervix	CC	negative regulation of hydrolase activity	81/2311	379/18723	4.27e-07	1.67e-05	81
GO:00104669	Cervix	CC	negative regulation of peptidase activity	60/2311	262/18723	1.27e-06	4.34e-05	60
GO:009719110	Cervix	CC	extrinsic apoptotic signaling pathway	52/2311	219/18723	2.06e-06	6.34e-05	52
GO:001095110	Cervix	CC	negative regulation of endopeptidase activity	56/2311	252/18723	7.43e-06	1.74e-04	56
GO:00072666	Cervix	CC	Rho protein signal transduction	35/2311	137/18723	1.77e-05	3.33e-04	35
GO:004873210	Cervix	CC	gland development	84/2311	436/18723	1.93e-05	3.54e-04	84
GO:00465785	Cervix	CC	regulation of Ras protein signal transduction	44/2311	189/18723	2.05e-05	3.73e-04	44
GO:200123610	Cervix	CC	regulation of extrinsic apoptotic signaling pathway	37/2311	151/18723	2.80e-05	4.65e-04	37
GO:00434104	Cervix	CC	positive regulation of MAPK cascade	90/2311	480/18723	2.92e-05	4.83e-04	90

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0520820	Cervix	CC	Chemical carcinogenesis - reactive oxygen species	92/1267	223/8465	4.71e-22	5.09e-20	3.01e-20	92
hsa0501018	Cervix	CC	Alzheimer disease	113/1267	384/8465	9.67e-14	3.92e-12	2.32e-12	113
hsa0502218	Cervix	CC	Pathways of neurodegeneration - multiple diseases	128/1267	476/8465	2.87e-12	9.29e-11	5.50e-11	128
hsa0513220	Cervix	CC	Salmonella infection	74/1267	249/8465	1.33e-09	2.54e-08	1.50e-08	74
hsa0516720	Cervix	CC	Kaposi sarcoma-associated herpesvirus infection	60/1267	194/8465	9.74e-09	1.58e-07	9.33e-08	60
hsa0516318	Cervix	CC	Human cytomegalovirus infection	65/1267	225/8465	4.59e-08	6.47e-07	3.83e-07	65
hsa0520516	Cervix	CC	Proteoglycans in cancer	60/1267	205/8465	9.13e-08	1.18e-06	7.00e-07	60
hsa0421810	Cervix	CC	Cellular senescence	49/1267	156/8465	1.30e-07	1.63e-06	9.61e-07	49
hsa0451010	Cervix	CC	Focal adhesion	59/1267	203/8465	1.53e-07	1.84e-06	1.09e-06	59
hsa0481016	Cervix	CC	Regulation of actin cytoskeleton	64/1267	229/8465	2.24e-07	2.59e-06	1.53e-06	64
hsa0491520	Cervix	CC	Estrogen signaling pathway	44/1267	138/8465	3.55e-07	3.97e-06	2.35e-06	44
hsa0401512	Cervix	CC	Rap1 signaling pathway	56/1267	210/8465	6.23e-06	5.61e-05	3.32e-05	56
hsa0466612	Cervix	CC	Fc gamma R-mediated phagocytosis	31/1267	97/8465	1.78e-05	1.42e-04	8.40e-05	31
hsa0517016	Cervix	CC	Human immunodeficiency virus 1 infection	55/1267	212/8465	1.80e-05	1.42e-04	8.40e-05	55
hsa0401210	Cervix	CC	ErbB signaling pathway	28/1267	85/8465	2.40e-05	1.82e-04	1.08e-04	28
hsa0407110	Cervix	CC	Sphingolipid signaling pathway	35/1267	121/8465	5.70e-05	3.93e-04	2.32e-04	35
hsa043609	Cervix	CC	Axon guidance	47/1267	182/8465	8.13e-05	5.38e-04	3.18e-04	47
hsa0521010	Cervix	CC	Colorectal cancer	27/1267	86/8465	8.60e-05	5.57e-04	3.30e-04	27
hsa052197	Cervix	CC	Bladder cancer	16/1267	41/8465	1.45e-04	9.05e-04	5.35e-04	16
hsa052148	Cervix	CC	Glioma	24/1267	75/8465	1.51e-04	9.20e-04	5.44e-04	24

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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

RAF1

SNV

Missense_Mutation

c.677T>A

p.Val226Asp

p.V226D

P04049

protein_coding

tolerated(0.59)

benign(0)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RAF1

SNV

Missense_Mutation

rs730881004

c.1814N>T

p.Ser605Phe

p.S605F

P04049

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-AC-A3W5-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

RAF1

SNV

Missense_Mutation

c.364N>G

p.Ile122Val

p.I122V

P04049

protein_coding

tolerated(0.3)

benign(0.001)

TCGA-BH-A18S-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RAF1

SNV

Missense_Mutation

c.1819N>C

p.Glu607Gln

p.E607Q

P04049

protein_coding

deleterious(0.02)

probably_damaging(0.949)

TCGA-GM-A2DO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

RAF1

SNV

Missense_Mutation

novel

c.1060N>T

p.Arg354Trp

p.R354W

P04049

protein_coding

deleterious(0)

probably_damaging(0.982)

TCGA-OL-A5RW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

RAF1

insertion

Nonsense_Mutation

novel

c.1576_1577insAGGCTCAGGGCTGCTAGAATGTGATTAAAGC

p.Ser526LysfsTer6

p.S526Kfs*6

P04049

protein_coding

TCGA-A2-A0D1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

RAF1

insertion

In_Frame_Ins

novel

c.1724_1725insAAAGCAGGGGCCCAGCCCCAGCTGTTG

p.Lys575_Asn576insLysGlnGlyProSerProSerCysTrp

p.K575_N576insKQGPSPSCW

P04049

protein_coding

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RAF1

insertion

Frame_Shift_Ins

novel

c.296_297insTGTTGAAGTGCAAATCTTTGAAG

p.Arg100ValfsTer21

p.R100Vfs*21

P04049

protein_coding

TCGA-AO-A0JB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

RAF1

insertion

In_Frame_Ins

novel

c.1697_1698insTTTTAAAGTAAT

p.Ala566_Ser567insPheLysValIle

p.A566_S567insFKVI

P04049

protein_coding

TCGA-BH-A0BA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

RAF1

insertion

Frame_Shift_Ins

novel

c.1696_1697insTTACCTC

p.Ala566ValfsTer8

p.A566Vfs*8

P04049

protein_coding

TCGA-BH-A0BA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

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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
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE		SORAFENIB	SORAFENIB
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE		sorafenib	SORAFENIB	20124951,28362716
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	REGORAFENIB	REGORAFENIB
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	404859105
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE		TRAMETINIB	TRAMETINIB	30835257
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	CHEMBL3545296	ARQ-736
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	CHEMBL1200485	SORAFENIB TOSYLATE
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	SORAFENIB	SORAFENIB
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE	inhibitor	328083491	SB590885
5894	RAF1	DRUGGABLE GENOME, KINASE, ENZYME, SERINE THREONINE KINASE, CLINICALLY ACTIONABLE		XL281

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