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: JAK2

Gene summary for JAK2

Gene summary.

Gene information	Species	Human
	Gene symbol	JAK2
	Gene ID	3717
	Gene name	Janus kinase 2
	Gene Alias	JTK10
	Cytomap	9p24.1
	Gene Type	protein-coding
	GO ID	GO:0001659
	UniProtAcc	O60674

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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
3717	JAK2	CA_HPV_1	Human	Cervix	CC	2.49e-03	2.79e-01	0.0264
3717	JAK2	CCI_1	Human	Cervix	CC	4.65e-03	6.89e-01	0.528
3717	JAK2	CCI_2	Human	Cervix	CC	1.01e-15	1.49e+00	0.5249
3717	JAK2	HTA11_3410_2000001011	Human	Colorectum	AD	2.34e-03	2.12e-01	0.0155
3717	JAK2	HTA11_2487_2000001011	Human	Colorectum	SER	2.65e-10	7.90e-01	-0.1808
3717	JAK2	HTA11_2951_2000001011	Human	Colorectum	AD	8.40e-06	9.47e-01	0.0216
3717	JAK2	HTA11_1938_2000001011	Human	Colorectum	AD	1.01e-14	9.60e-01	-0.0811
3717	JAK2	HTA11_78_2000001011	Human	Colorectum	AD	2.36e-14	8.65e-01	-0.1088
3717	JAK2	HTA11_347_2000001011	Human	Colorectum	AD	1.65e-51	1.41e+00	-0.1954
3717	JAK2	HTA11_411_2000001011	Human	Colorectum	SER	1.11e-03	9.74e-01	-0.2602
3717	JAK2	HTA11_2112_2000001011	Human	Colorectum	SER	3.04e-02	8.56e-01	-0.2196
3717	JAK2	HTA11_3361_2000001011	Human	Colorectum	AD	9.19e-11	8.99e-01	-0.1207
3717	JAK2	HTA11_83_2000001011	Human	Colorectum	SER	3.37e-02	5.35e-01	-0.1526
3717	JAK2	HTA11_696_2000001011	Human	Colorectum	AD	4.74e-12	6.46e-01	-0.1464
3717	JAK2	HTA11_1391_2000001011	Human	Colorectum	AD	9.46e-17	1.03e+00	-0.059
3717	JAK2	HTA11_2992_2000001011	Human	Colorectum	SER	1.22e-07	1.00e+00	-0.1706
3717	JAK2	HTA11_5212_2000001011	Human	Colorectum	AD	1.48e-06	9.88e-01	-0.2061
3717	JAK2	HTA11_5216_2000001011	Human	Colorectum	SER	3.00e-10	1.29e+00	-0.1462
3717	JAK2	HTA11_546_2000001011	Human	Colorectum	AD	7.01e-03	5.80e-01	-0.0842
3717	JAK2	HTA11_7696_3000711011	Human	Colorectum	AD	7.77e-03	-2.47e-01	0.0674

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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
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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:0048008	Colorectum	FAP	platelet-derived growth factor receptor signaling pathway	16/2622	56/18723	3.40e-03	2.47e-02	16
GO:0046677	Colorectum	FAP	response to antibiotic	14/2622	47/18723	3.95e-03	2.75e-02	14
GO:00454282	Colorectum	FAP	regulation of nitric oxide biosynthetic process	17/2622	62/18723	4.12e-03	2.84e-02	17
GO:01061061	Colorectum	FAP	cold-induced thermogenesis	32/2622	144/18723	4.85e-03	3.25e-02	32
GO:01201611	Colorectum	FAP	regulation of cold-induced thermogenesis	32/2622	144/18723	4.85e-03	3.25e-02	32
GO:0046883	Colorectum	FAP	regulation of hormone secretion	50/2622	249/18723	4.97e-03	3.32e-02	50
GO:00109524	Colorectum	FAP	positive regulation of peptidase activity	41/2622	197/18723	5.49e-03	3.56e-02	41
GO:00486601	Colorectum	FAP	regulation of smooth muscle cell proliferation	38/2622	180/18723	5.73e-03	3.67e-02	38
GO:19908451	Colorectum	FAP	adaptive thermogenesis	34/2622	157/18723	5.77e-03	3.69e-02	34
GO:00353061	Colorectum	FAP	positive regulation of dephosphorylation	16/2622	59/18723	5.95e-03	3.75e-02	16
GO:0046879	Colorectum	FAP	hormone secretion	57/2622	295/18723	6.67e-03	4.12e-02	57
GO:01201621	Colorectum	FAP	positive regulation of cold-induced thermogenesis	23/2622	97/18723	6.95e-03	4.26e-02	23
GO:00423064	Colorectum	FAP	regulation of protein import into nucleus	16/2622	60/18723	7.08e-03	4.33e-02	16
GO:00525484	Colorectum	FAP	regulation of endopeptidase activity	79/2622	432/18723	7.15e-03	4.36e-02	79
GO:00435233	Colorectum	FAP	regulation of neuron apoptotic process	43/2622	212/18723	7.28e-03	4.38e-02	43
GO:00510901	Colorectum	FAP	regulation of DNA-binding transcription factor activity	80/2622	440/18723	7.90e-03	4.67e-02	80
GO:0060391	Colorectum	FAP	positive regulation of SMAD protein signal transduction	7/2622	18/18723	8.10e-03	4.77e-02	7
GO:00486591	Colorectum	FAP	smooth muscle cell proliferation	38/2622	184/18723	8.29e-03	4.85e-02	38
GO:00423073	Colorectum	FAP	positive regulation of protein import into nucleus	12/2622	41/18723	8.57e-03	4.96e-02	12
GO:00070155	Colorectum	CRC	actin filament organization	104/2078	442/18723	4.75e-14	7.12e-11	104

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0541720	Cervix	CC	Lipid and atherosclerosis	65/1267	215/8465	6.47e-09	1.10e-07	6.52e-08	65
hsa0516720	Cervix	CC	Kaposi sarcoma-associated herpesvirus infection	60/1267	194/8465	9.74e-09	1.58e-07	9.33e-08	60
hsa0514514	Cervix	CC	Toxoplasmosis	34/1267	112/8465	2.42e-05	1.82e-04	1.08e-04	34
hsa0516414	Cervix	CC	Influenza A	43/1267	171/8465	3.03e-04	1.64e-03	9.68e-04	43
hsa05152	Cervix	CC	Tuberculosis	42/1267	180/8465	1.78e-03	7.21e-03	4.26e-03	42
hsa046596	Cervix	CC	Th17 cell differentiation	28/1267	108/8465	1.99e-03	7.98e-03	4.72e-03	28
hsa04062	Cervix	CC	Chemokine signaling pathway	43/1267	192/8465	3.60e-03	1.34e-02	7.91e-03	43
hsa0514014	Cervix	CC	Leishmaniasis	21/1267	77/8465	3.65e-03	1.34e-02	7.91e-03	21
hsa04658	Cervix	CC	Th1 and Th2 cell differentiation	24/1267	92/8465	3.71e-03	1.34e-02	7.91e-03	24
hsa049336	Cervix	CC	AGE-RAGE signaling pathway in diabetic complications	25/1267	100/8465	5.64e-03	1.88e-02	1.11e-02	25
hsa049172	Cervix	CC	Prolactin signaling pathway	18/1267	70/8465	1.29e-02	3.87e-02	2.29e-02	18
hsa05417110	Cervix	CC	Lipid and atherosclerosis	65/1267	215/8465	6.47e-09	1.10e-07	6.52e-08	65
hsa05167110	Cervix	CC	Kaposi sarcoma-associated herpesvirus infection	60/1267	194/8465	9.74e-09	1.58e-07	9.33e-08	60
hsa0514515	Cervix	CC	Toxoplasmosis	34/1267	112/8465	2.42e-05	1.82e-04	1.08e-04	34
hsa0516415	Cervix	CC	Influenza A	43/1267	171/8465	3.03e-04	1.64e-03	9.68e-04	43
hsa051521	Cervix	CC	Tuberculosis	42/1267	180/8465	1.78e-03	7.21e-03	4.26e-03	42
hsa0465911	Cervix	CC	Th17 cell differentiation	28/1267	108/8465	1.99e-03	7.98e-03	4.72e-03	28
hsa040621	Cervix	CC	Chemokine signaling pathway	43/1267	192/8465	3.60e-03	1.34e-02	7.91e-03	43
hsa0514015	Cervix	CC	Leishmaniasis	21/1267	77/8465	3.65e-03	1.34e-02	7.91e-03	21
hsa046581	Cervix	CC	Th1 and Th2 cell differentiation	24/1267	92/8465	3.71e-03	1.34e-02	7.91e-03	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

JAK2

SNV

Missense_Mutation

c.398N>C

p.Arg133Pro

p.R133P

O60674

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

JAK2

SNV

Missense_Mutation

c.164T>C

p.Leu55Pro

p.L55P

O60674

protein_coding

deleterious(0)

probably_damaging(0.936)

TCGA-A8-A07R-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Ancillary

zoledronic

JAK2

SNV

Missense_Mutation

c.344G>T

p.Arg115Ile

p.R115I

O60674

protein_coding

deleterious(0)

possibly_damaging(0.883)

TCGA-BH-A0AW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

JAK2

SNV

Missense_Mutation

rs777208458

c.413G>C

p.Arg138Pro

p.R138P

O60674

protein_coding

deleterious(0)

possibly_damaging(0.615)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

JAK2

SNV

Missense_Mutation

c.224N>T

p.Cys75Phe

p.C75F

O60674

protein_coding

deleterious(0)

possibly_damaging(0.691)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

JAK2

insertion

Frame_Shift_Ins

novel

c.2221_2222insC

p.Thr742HisfsTer11

p.T742Hfs*11

O60674

protein_coding

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

JAK2

deletion

Frame_Shift_Del

novel

c.352delN

p.Tyr119ThrfsTer48

p.Y119Tfs*48

O60674

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

JAK2

SNV

Missense_Mutation

novel

c.3296N>G

p.Tyr1099Cys

p.Y1099C

O60674

protein_coding

deleterious(0.03)

possibly_damaging(0.893)

TCGA-4J-AA1J-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

JAK2

SNV

Missense_Mutation

c.2173G>A

p.Glu725Lys

p.E725K

O60674

protein_coding

tolerated(0.44)

benign(0.006)

TCGA-C5-A1MN-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

JAK2

SNV

Missense_Mutation

c.2653C>A

p.Gln885Lys

p.Q885K

O60674

protein_coding

tolerated(0.35)

possibly_damaging(0.614)

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
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME	inhibitor	RUXOLITINIB	RUXOLITINIB
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		Pembrolizumab	PEMBROLIZUMAB	27433843
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		A-1155463		25787766
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		BMS-911543	BMS-911543
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		TGX-221		24251790
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		Tricyclic compound 11
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME	inhibitor	CHEMBL1944698	ZOTIRACICLIB
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		SB-1578	CT-1578
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME	inhibitor	381118857
3717	JAK2	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, DRUG RESISTANCE, ENZYME		WHI-P154	CHEMBL473773

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