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: PAK2

Gene summary for PAK2

Gene summary.

Gene information	Species	Human
	Gene symbol	PAK2
	Gene ID	5062
	Gene name	p21 (RAC1) activated kinase 2
	Gene Alias	PAK65
	Cytomap	3q29
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A8K5M4

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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
5062	PAK2	GSM4909285	Human	Breast	IDC	2.94e-11	3.97e-01	0.21
5062	PAK2	GSM4909286	Human	Breast	IDC	2.73e-04	1.65e-01	0.1081
5062	PAK2	GSM4909293	Human	Breast	IDC	9.24e-10	4.02e-01	0.1581
5062	PAK2	GSM4909296	Human	Breast	IDC	2.82e-05	-1.08e-01	0.1524
5062	PAK2	GSM4909297	Human	Breast	IDC	4.87e-06	-1.45e-01	0.1517
5062	PAK2	GSM4909311	Human	Breast	IDC	2.04e-15	-2.16e-01	0.1534
5062	PAK2	GSM4909312	Human	Breast	IDC	4.54e-04	-9.35e-02	0.1552
5062	PAK2	GSM4909315	Human	Breast	IDC	4.28e-06	4.13e-01	0.21
5062	PAK2	GSM4909319	Human	Breast	IDC	4.01e-25	-1.76e-01	0.1563
5062	PAK2	GSM4909320	Human	Breast	IDC	1.54e-03	-7.88e-02	0.1575
5062	PAK2	GSM4909321	Human	Breast	IDC	6.22e-10	-1.56e-01	0.1559
5062	PAK2	M2	Human	Breast	IDC	4.15e-12	7.43e-01	0.21
5062	PAK2	NCCBC14	Human	Breast	DCIS	2.18e-08	3.85e-01	0.2021
5062	PAK2	NCCBC5	Human	Breast	DCIS	1.42e-07	7.13e-02	0.2046
5062	PAK2	P1	Human	Breast	IDC	3.19e-06	-6.83e-02	0.1527
5062	PAK2	P2	Human	Breast	IDC	1.34e-14	6.89e-01	0.21
5062	PAK2	DCIS2	Human	Breast	DCIS	1.11e-58	3.67e-01	0.0085
5062	PAK2	CA_HPV_1	Human	Cervix	CC	1.37e-09	-2.39e-03	0.0264
5062	PAK2	CCI_2	Human	Cervix	CC	8.39e-18	1.18e+00	0.5249
5062	PAK2	CCII_1	Human	Cervix	CC	1.46e-09	-5.16e-01	0.3249

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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
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
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:006156422	Skin	cSCC	axon development	146/4864	467/18723	5.50e-03	2.73e-02	146
GO:0032231111	Skin	cSCC	regulation of actin filament bundle assembly	39/4864	105/18723	7.56e-03	3.53e-02	39
GO:001820923	Skin	cSCC	peptidyl-serine modification	108/4864	338/18723	7.73e-03	3.60e-02	108
GO:2001233113	Thyroid	PTC	regulation of apoptotic signaling pathway	197/5968	356/18723	2.58e-20	3.69e-18	197
GO:1902903113	Thyroid	PTC	regulation of supramolecular fiber organization	202/5968	383/18723	1.16e-17	1.15e-15	202
GO:0007015112	Thyroid	PTC	actin filament organization	225/5968	442/18723	3.76e-17	3.44e-15	225
GO:0010563113	Thyroid	PTC	negative regulation of phosphorus metabolic process	219/5968	442/18723	4.47e-15	3.07e-13	219
GO:0045936113	Thyroid	PTC	negative regulation of phosphate metabolic process	218/5968	441/18723	7.08e-15	4.75e-13	218
GO:0032956113	Thyroid	PTC	regulation of actin cytoskeleton organization	182/5968	358/18723	4.64e-14	2.79e-12	182
GO:0032970113	Thyroid	PTC	regulation of actin filament-based process	197/5968	397/18723	8.91e-14	4.89e-12	197
GO:0001933113	Thyroid	PTC	negative regulation of protein phosphorylation	173/5968	342/18723	3.46e-13	1.75e-11	173
GO:0110053112	Thyroid	PTC	regulation of actin filament organization	146/5968	278/18723	5.87e-13	2.85e-11	146
GO:0042326113	Thyroid	PTC	negative regulation of phosphorylation	189/5968	385/18723	1.00e-12	4.64e-11	189
GO:0097191113	Thyroid	PTC	extrinsic apoptotic signaling pathway	117/5968	219/18723	2.73e-11	1.03e-09	117
GO:0051348113	Thyroid	PTC	negative regulation of transferase activity	137/5968	268/18723	3.78e-11	1.36e-09	137
GO:0010639112	Thyroid	PTC	negative regulation of organelle organization	163/5968	348/18723	3.04e-09	8.39e-08	163
GO:0045860111	Thyroid	PTC	positive regulation of protein kinase activity	176/5968	386/18723	8.89e-09	2.17e-07	176
GO:2001236113	Thyroid	PTC	regulation of extrinsic apoptotic signaling pathway	82/5968	151/18723	9.01e-09	2.18e-07	82
GO:006099616	Thyroid	PTC	dendritic spine development	59/5968	99/18723	1.18e-08	2.83e-07	59
GO:0006469111	Thyroid	PTC	negative regulation of protein kinase activity	107/5968	212/18723	1.24e-08	2.96e-07	107

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513024	Breast	IDC	Pathogenic Escherichia coli infection	42/867	197/8465	2.66e-06	3.92e-05	2.94e-05	42
hsa0481014	Breast	IDC	Regulation of actin cytoskeleton	36/867	229/8465	5.79e-03	3.13e-02	2.34e-02	36
hsa045109	Breast	IDC	Focal adhesion	32/867	203/8465	8.60e-03	4.23e-02	3.17e-02	32
hsa052118	Breast	IDC	Renal cell carcinoma	14/867	69/8465	9.16e-03	4.37e-02	3.27e-02	14
hsa0517014	Breast	IDC	Human immunodeficiency virus 1 infection	33/867	212/8465	9.28e-03	4.37e-02	3.27e-02	33
hsa0513034	Breast	IDC	Pathogenic Escherichia coli infection	42/867	197/8465	2.66e-06	3.92e-05	2.94e-05	42
hsa0481015	Breast	IDC	Regulation of actin cytoskeleton	36/867	229/8465	5.79e-03	3.13e-02	2.34e-02	36
hsa0451013	Breast	IDC	Focal adhesion	32/867	203/8465	8.60e-03	4.23e-02	3.17e-02	32
hsa0521113	Breast	IDC	Renal cell carcinoma	14/867	69/8465	9.16e-03	4.37e-02	3.27e-02	14
hsa0517015	Breast	IDC	Human immunodeficiency virus 1 infection	33/867	212/8465	9.28e-03	4.37e-02	3.27e-02	33
hsa0513043	Breast	DCIS	Pathogenic Escherichia coli infection	42/846	197/8465	1.40e-06	2.15e-05	1.59e-05	42
hsa0517024	Breast	DCIS	Human immunodeficiency virus 1 infection	33/846	212/8465	6.49e-03	3.22e-02	2.37e-02	33
hsa0481023	Breast	DCIS	Regulation of actin cytoskeleton	35/846	229/8465	6.89e-03	3.37e-02	2.48e-02	35
hsa0521123	Breast	DCIS	Renal cell carcinoma	14/846	69/8465	7.42e-03	3.48e-02	2.56e-02	14
hsa0513053	Breast	DCIS	Pathogenic Escherichia coli infection	42/846	197/8465	1.40e-06	2.15e-05	1.59e-05	42
hsa0517034	Breast	DCIS	Human immunodeficiency virus 1 infection	33/846	212/8465	6.49e-03	3.22e-02	2.37e-02	33
hsa0481033	Breast	DCIS	Regulation of actin cytoskeleton	35/846	229/8465	6.89e-03	3.37e-02	2.48e-02	35
hsa0521133	Breast	DCIS	Renal cell carcinoma	14/846	69/8465	7.42e-03	3.48e-02	2.56e-02	14
hsa0513020	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa0451010	Cervix	CC	Focal adhesion	59/1267	203/8465	1.53e-07	1.84e-06	1.09e-06	59

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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

PAK2

SNV

Missense_Mutation

c.1312G>A

p.Glu438Lys

p.E438K

Q13177

protein_coding

deleterious(0.02)

probably_damaging(0.995)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PAK2

SNV

Missense_Mutation

c.1336N>A

p.Glu446Lys

p.E446K

Q13177

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

PAK2

SNV

Missense_Mutation

c.103N>G

p.His35Asp

p.H35D

Q13177

protein_coding

tolerated(0.19)

benign(0.003)

TCGA-AN-A0XN-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

PAK2

SNV

Missense_Mutation

c.419N>C

p.Leu140Pro

p.L140P

Q13177

protein_coding

tolerated(0.08)

possibly_damaging(0.62)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PAK2

SNV

Missense_Mutation

novel

c.241G>A

p.Glu81Lys

p.E81K

Q13177

protein_coding

tolerated(0.35)

possibly_damaging(0.734)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PAK2

SNV

Missense_Mutation

rs774110601

c.1250N>A

p.Arg417Gln

p.R417Q

Q13177

protein_coding

tolerated(0.11)

probably_damaging(0.993)

TCGA-E9-A295-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

PAK2

insertion

In_Frame_Ins

novel

c.627_628insTCTCGCTCTGTCGCC

p.Ser209_His210insSerArgSerValAla

p.S209_H210insSRSVA

Q13177

protein_coding

TCGA-A8-A08F-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

5-fluorouracil

PAK2

insertion

Frame_Shift_Ins

novel

c.566_567insAAGAAGCAAACTTTTTGAAG

p.His189GlnfsTer17

p.H189Qfs*17

Q13177

protein_coding

TCGA-A8-A09D-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PAK2

insertion

Frame_Shift_Ins

novel

c.570_571insTTCATAAAGGGCGATAGTCG

p.Lys191PhefsTer15

p.K191Ffs*15

Q13177

protein_coding

TCGA-A8-A09D-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PAK2

insertion

Nonsense_Mutation

novel

c.746_747insATGATACACAGTCATTGCTAACAACTAGTACAGTT

p.Tyr249Ter

p.Y249*

Q13177

protein_coding

TCGA-AN-A03X-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
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	310264720
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	249565812
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	310264719
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	329968394
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	allosteric modulator	310264717
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	310264722
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	310264718	PF-03758309
5062	PAK2	ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME	inhibitor	135652717	STAUROSPORINE

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