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: ROCK2

Gene summary for ROCK2

Gene summary.

Gene information	Species	Human
	Gene symbol	ROCK2
	Gene ID	9475
	Gene name	Rho associated coiled-coil containing protein kinase 2
	Gene Alias	ROCK-II
	Cytomap	2p25.1
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	O75116

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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
9475	ROCK2	CCI_2	Human	Cervix	CC	8.74e-08	8.19e-01	0.5249
9475	ROCK2	CCI_3	Human	Cervix	CC	2.99e-03	6.37e-01	0.516
9475	ROCK2	HTA11_3410_2000001011	Human	Colorectum	AD	3.53e-02	-2.80e-01	0.0155
9475	ROCK2	HTA11_1938_2000001011	Human	Colorectum	AD	1.56e-05	6.22e-01	-0.0811
9475	ROCK2	HTA11_347_2000001011	Human	Colorectum	AD	1.96e-09	5.90e-01	-0.1954
9475	ROCK2	HTA11_411_2000001011	Human	Colorectum	SER	1.02e-06	7.49e-01	-0.2602
9475	ROCK2	HTA11_1391_2000001011	Human	Colorectum	AD	8.84e-03	5.18e-01	-0.059
9475	ROCK2	HTA11_866_3004761011	Human	Colorectum	AD	2.59e-02	-3.79e-01	0.096
9475	ROCK2	HTA11_8622_2000001021	Human	Colorectum	SER	4.22e-05	-4.02e-01	0.0528
9475	ROCK2	HTA11_99999965104_69814	Human	Colorectum	MSS	1.07e-04	6.04e-01	0.281
9475	ROCK2	HTA11_99999971662_82457	Human	Colorectum	MSS	9.58e-05	5.75e-01	0.3859
9475	ROCK2	HTA11_99999974143_84620	Human	Colorectum	MSS	6.62e-07	5.58e-01	0.3005
9475	ROCK2	F007	Human	Colorectum	FAP	5.84e-03	1.44e-01	0.1176
9475	ROCK2	A002-C-010	Human	Colorectum	FAP	1.18e-04	1.78e-01	0.242
9475	ROCK2	A001-C-207	Human	Colorectum	FAP	2.09e-05	1.05e-01	0.1278
9475	ROCK2	A015-C-203	Human	Colorectum	FAP	6.50e-30	-1.60e-01	-0.1294
9475	ROCK2	A015-C-204	Human	Colorectum	FAP	1.22e-06	-1.56e-01	-0.0228
9475	ROCK2	A014-C-040	Human	Colorectum	FAP	2.49e-06	-2.39e-01	-0.1184
9475	ROCK2	A002-C-201	Human	Colorectum	FAP	1.25e-15	-3.72e-02	0.0324
9475	ROCK2	A002-C-203	Human	Colorectum	FAP	4.43e-03	1.10e-01	0.2786

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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
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:000166618	Prostate	Tumor	response to hypoxia	90/3246	307/18723	1.27e-07	3.28e-06	90
GO:003465516	Prostate	Tumor	nucleobase-containing compound catabolic process	112/3246	407/18723	1.61e-07	4.02e-06	112
GO:004343418	Prostate	Tumor	response to peptide hormone	113/3246	414/18723	2.24e-07	5.42e-06	113
GO:004348815	Prostate	Tumor	regulation of mRNA stability	54/3246	158/18723	2.26e-07	5.42e-06	54
GO:003103216	Prostate	Tumor	actomyosin structure organization	63/3246	196/18723	2.94e-07	6.72e-06	63
GO:003223118	Prostate	Tumor	regulation of actin filament bundle assembly	40/3246	105/18723	3.34e-07	7.55e-06	40
GO:001063217	Prostate	Tumor	regulation of epithelial cell migration	85/3246	292/18723	3.91e-07	8.63e-06	85
GO:003432915	Prostate	Tumor	cell junction assembly	113/3246	420/18723	4.94e-07	1.07e-05	113
GO:000716015	Prostate	Tumor	cell-matrix adhesion	71/3246	233/18723	5.40e-07	1.16e-05	71
GO:003085614	Prostate	Tumor	regulation of epithelial cell differentiation	52/3246	154/18723	5.76e-07	1.22e-05	52
GO:007266514	Prostate	Tumor	protein localization to vacuole	29/3246	67/18723	6.20e-07	1.30e-05	29
GO:003424912	Prostate	Tumor	negative regulation of cellular amide metabolic process	80/3246	273/18723	6.33e-07	1.32e-05	80
GO:001095018	Prostate	Tumor	positive regulation of endopeptidase activity	58/3246	179/18723	6.35e-07	1.32e-05	58
GO:007155915	Prostate	Tumor	response to transforming growth factor beta	76/3246	256/18723	6.86e-07	1.40e-05	76
GO:011002019	Prostate	Tumor	regulation of actomyosin structure organization	38/3246	100/18723	7.01e-07	1.42e-05	38
GO:000188514	Prostate	Tumor	endothelial cell development	28/3246	64/18723	7.39e-07	1.47e-05	28
GO:004670014	Prostate	Tumor	heterocycle catabolic process	117/3246	445/18723	1.11e-06	2.10e-05	117
GO:007137514	Prostate	Tumor	cellular response to peptide hormone stimulus	83/3246	290/18723	1.14e-06	2.16e-05	83
GO:004427015	Prostate	Tumor	cellular nitrogen compound catabolic process	118/3246	451/18723	1.30e-06	2.39e-05	118
GO:003003818	Prostate	Tumor	contractile actin filament bundle assembly	39/3246	106/18723	1.31e-06	2.39e-05	39

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513020	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa0541720	Cervix	CC	Lipid and atherosclerosis	65/1267	215/8465	6.47e-09	1.10e-07	6.52e-08	65
hsa0516318	Cervix	CC	Human cytomegalovirus infection	65/1267	225/8465	4.59e-08	6.47e-07	3.83e-07	65
hsa0513120	Cervix	CC	Shigellosis	69/1267	247/8465	7.64e-08	1.03e-06	6.10e-07	69
hsa0520516	Cervix	CC	Proteoglycans in cancer	60/1267	205/8465	9.13e-08	1.18e-06	7.00e-07	60
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
hsa0452020	Cervix	CC	Adherens junction	33/1267	93/8465	6.99e-07	7.31e-06	4.32e-06	33
hsa0453020	Cervix	CC	Tight junction	49/1267	169/8465	1.87e-06	1.78e-05	1.05e-05	49
hsa0467020	Cervix	CC	Leukocyte transendothelial migration	36/1267	114/8465	5.22e-06	4.83e-05	2.86e-05	36
hsa0513516	Cervix	CC	Yersinia infection	39/1267	137/8465	3.27e-05	2.41e-04	1.42e-04	39
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
hsa043109	Cervix	CC	Wnt signaling pathway	43/1267	171/8465	3.03e-04	1.64e-03	9.68e-04	43
hsa04062	Cervix	CC	Chemokine signaling pathway	43/1267	192/8465	3.60e-03	1.34e-02	7.91e-03	43
hsa049218	Cervix	CC	Oxytocin signaling pathway	34/1267	154/8465	1.12e-02	3.42e-02	2.02e-02	34
hsa046115	Cervix	CC	Platelet activation	28/1267	124/8465	1.50e-02	4.45e-02	2.63e-02	28
hsa05130110	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa05417110	Cervix	CC	Lipid and atherosclerosis	65/1267	215/8465	6.47e-09	1.10e-07	6.52e-08	65
hsa0516319	Cervix	CC	Human cytomegalovirus infection	65/1267	225/8465	4.59e-08	6.47e-07	3.83e-07	65

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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

ROCK2

SNV

Missense_Mutation

novel

c.3226N>C

p.Lys1076Gln

p.K1076Q

O75116

protein_coding

deleterious(0)

probably_damaging(0.946)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ROCK2

SNV

Missense_Mutation

rs747260728

c.1715N>A

p.Arg572Gln

p.R572Q

O75116

protein_coding

tolerated(0.38)

benign(0.065)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ROCK2

SNV

Missense_Mutation

c.3560N>A

p.Ser1187Asn

p.S1187N

O75116

protein_coding

tolerated(0.16)

benign(0.097)

TCGA-AN-A0FL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ROCK2

SNV

Missense_Mutation

c.4091G>C

p.Arg1364Thr

p.R1364T

O75116

protein_coding

deleterious(0.01)

benign(0.041)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ROCK2

SNV

Missense_Mutation

c.1849N>C

p.Glu617Gln

p.E617Q

O75116

protein_coding

tolerated(0.34)

benign(0.083)

TCGA-BH-A0HP-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

doxorubicin

ROCK2

SNV

Missense_Mutation

novel

c.2329N>C

p.Glu777Gln

p.E777Q

O75116

protein_coding

tolerated(0.67)

benign(0.028)

TCGA-PE-A5DE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

ROCK2

SNV

Missense_Mutation

novel

c.186N>C

p.Leu62Phe

p.L62F

O75116

protein_coding

deleterious(0.02)

probably_damaging(0.95)

TCGA-XX-A89A-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ROCK2

insertion

Nonsense_Mutation

novel

c.2665_2666insCAATTTAACTATAATCCAA

p.Glu889AlafsTer3

p.E889Afs*3

O75116

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ROCK2

SNV

Missense_Mutation

novel

c.712A>C

p.Lys238Gln

p.K238Q

O75116

protein_coding

deleterious(0)

probably_damaging(0.929)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ROCK2

SNV

Missense_Mutation

c.2719N>A

p.Glu907Lys

p.E907K

O75116

protein_coding

deleterious(0)

probably_damaging(0.957)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

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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
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	178102655
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		AR-12286	VEROSUDIL
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		BAY-613606	CHEMBL541400
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		AST-487	AST-487
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		THROMBIN	THROMBIN	16720831
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	178101973
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		KD025
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		VER-49009	CHEMBL365617
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE		Tricyclic compound 4
9475	ROCK2	KINASE, ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	310264692	VEROSUDIL

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