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: JTB

Gene summary for JTB

Gene summary.

Gene information	Species	Human
	Gene symbol	JTB
	Gene ID	10899
	Gene name	jumping translocation breakpoint
	Gene Alias	HJTB
	Cytomap	1q21.3
	Gene Type	protein-coding
	GO ID	GO:0000278
	UniProtAcc	O76095

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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
10899	JTB	GSM4909281	Human	Breast	IDC	4.94e-07	3.68e-01	0.21
10899	JTB	GSM4909282	Human	Breast	IDC	8.55e-08	3.16e-01	-0.0288
10899	JTB	GSM4909285	Human	Breast	IDC	3.64e-10	3.94e-01	0.21
10899	JTB	GSM4909286	Human	Breast	IDC	2.63e-03	7.51e-02	0.1081
10899	JTB	GSM4909290	Human	Breast	IDC	2.18e-02	3.25e-01	0.2096
10899	JTB	GSM4909291	Human	Breast	IDC	1.21e-04	3.89e-01	0.1753
10899	JTB	GSM4909294	Human	Breast	IDC	3.04e-04	-1.05e-02	0.2022
10899	JTB	GSM4909295	Human	Breast	IDC	2.52e-07	4.77e-01	0.0898
10899	JTB	GSM4909296	Human	Breast	IDC	1.09e-15	1.55e-01	0.1524
10899	JTB	GSM4909297	Human	Breast	IDC	1.89e-17	-2.20e-01	0.1517
10899	JTB	GSM4909298	Human	Breast	IDC	3.99e-13	3.91e-01	0.1551
10899	JTB	GSM4909302	Human	Breast	IDC	8.36e-07	2.62e-01	0.1545
10899	JTB	GSM4909306	Human	Breast	IDC	1.42e-14	4.65e-01	0.1564
10899	JTB	GSM4909307	Human	Breast	IDC	5.79e-24	5.04e-01	0.1569
10899	JTB	GSM4909308	Human	Breast	IDC	1.16e-58	8.34e-01	0.158
10899	JTB	GSM4909309	Human	Breast	IDC	4.82e-02	1.34e-01	0.0483
10899	JTB	GSM4909311	Human	Breast	IDC	1.31e-43	-4.98e-02	0.1534
10899	JTB	GSM4909312	Human	Breast	IDC	5.72e-28	3.87e-01	0.1552
10899	JTB	GSM4909313	Human	Breast	IDC	1.43e-15	4.30e-01	0.0391
10899	JTB	GSM4909316	Human	Breast	IDC	1.57e-05	2.80e-01	0.21

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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
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
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:00336749	Breast	Precancer	positive regulation of kinase activity	42/1080	467/18723	2.94e-03	2.54e-02	42
GO:003367410	Cervix	CC	positive regulation of kinase activity	101/2311	467/18723	8.66e-09	7.22e-07	101
GO:00458608	Cervix	CC	positive regulation of protein kinase activity	85/2311	386/18723	5.61e-08	3.29e-06	85
GO:00009107	Cervix	CC	cytokinesis	37/2311	173/18723	5.40e-04	5.23e-03	37
GO:004586023	Cervix	N_HPV	positive regulation of protein kinase activity	22/534	386/18723	1.73e-03	1.75e-02	22
GO:003367422	Cervix	N_HPV	positive regulation of kinase activity	25/534	467/18723	2.05e-03	1.98e-02	25
GO:0000910	Colorectum	AD	cytokinesis	59/3918	173/18723	3.74e-05	6.75e-04	59
GO:0033674	Colorectum	AD	positive regulation of kinase activity	131/3918	467/18723	1.28e-04	1.85e-03	131
GO:0061640	Colorectum	AD	cytoskeleton-dependent cytokinesis	37/3918	100/18723	1.58e-04	2.20e-03	37
GO:0045860	Colorectum	AD	positive regulation of protein kinase activity	107/3918	386/18723	8.01e-04	7.92e-03	107
GO:0000281	Colorectum	AD	mitotic cytokinesis	25/3918	71/18723	3.77e-03	2.65e-02	25
GO:00009101	Colorectum	SER	cytokinesis	45/2897	173/18723	2.28e-04	3.93e-03	45
GO:00616401	Colorectum	SER	cytoskeleton-dependent cytokinesis	29/2897	100/18723	4.25e-04	6.25e-03	29
GO:00336741	Colorectum	SER	positive regulation of kinase activity	95/2897	467/18723	2.62e-03	2.41e-02	95
GO:00458601	Colorectum	SER	positive regulation of protein kinase activity	79/2897	386/18723	4.85e-03	3.79e-02	79
GO:00336742	Colorectum	MSS	positive regulation of kinase activity	122/3467	467/18723	2.50e-05	5.21e-04	122
GO:00458602	Colorectum	MSS	positive regulation of protein kinase activity	102/3467	386/18723	6.93e-05	1.20e-03	102
GO:00009102	Colorectum	MSS	cytokinesis	49/3467	173/18723	1.02e-03	1.02e-02	49
GO:00002811	Colorectum	MSS	mitotic cytokinesis	23/3467	71/18723	3.55e-03	2.63e-02	23
GO:00336743	Colorectum	MSI-H	positive regulation of kinase activity	53/1319	467/18723	3.99e-04	8.98e-03	53

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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

JTB

SNV

Missense_Mutation

novel

c.303N>A

p.Met101Ile

p.M101I

O76095

protein_coding

deleterious(0.01)

benign(0.081)

TCGA-AN-A0AM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

JTB

SNV

Missense_Mutation

c.184C>T

p.Pro62Ser

p.P62S

O76095

protein_coding

tolerated(0.14)

benign(0.038)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

JTB

SNV

Missense_Mutation

rs778131192

c.121G>A

p.Ala41Thr

p.A41T

O76095

protein_coding

tolerated(0.63)

benign(0.038)

TCGA-AA-A022-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

JTB

SNV

Missense_Mutation

novel

c.22N>A

p.Pro8Thr

p.P8T

O76095

protein_coding

tolerated_low_confidence(0.21)

benign(0.007)

TCGA-A5-A7WJ-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JTB

SNV

Missense_Mutation

novel

c.79N>T

p.Leu27Phe

p.L27F

O76095

protein_coding

tolerated(0.31)

benign(0.005)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JTB

SNV

Missense_Mutation

c.92A>G

p.Glu31Gly

p.E31G

O76095

protein_coding

tolerated(0.1)

benign(0.006)

TCGA-BK-A0C9-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JTB

SNV

Missense_Mutation

novel

c.413N>T

p.Lys138Met

p.K138M

O76095

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-D1-A175-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

paclitaxel

JTB

SNV

Missense_Mutation

novel

c.134N>C

p.Asn45Thr

p.N45T

O76095

protein_coding

tolerated(0.75)

benign(0.003)

TCGA-EO-A3B0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

JTB

SNV

Missense_Mutation

c.101N>A

p.Val34Glu

p.V34E

O76095

protein_coding

tolerated(0.14)

benign(0.005)

TCGA-35-5375-01

Lung

lung adenocarcinoma

Male

<65

III/IV

Unknown

JTB

SNV

Missense_Mutation

novel

c.430N>A

p.Glu144Lys

p.E144K

O76095

protein_coding

deleterious(0.01)

possibly_damaging(0.823)

TCGA-CV-A45O-01

Oral cavity

head & neck squamous cell carcinoma

Male

<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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