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: PTPRJ

Gene summary for PTPRJ

Gene summary.

Gene information	Species	Human
	Gene symbol	PTPRJ
	Gene ID	5795
	Gene name	protein tyrosine phosphatase receptor type J
	Gene Alias	CD148
	Cytomap	11p11.2
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	Q12913

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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
5795	PTPRJ	HTA11_3410_2000001011	Human	Colorectum	AD	1.21e-03	-4.36e-01	0.0155
5795	PTPRJ	HTA11_347_2000001011	Human	Colorectum	AD	1.25e-02	3.93e-01	-0.1954
5795	PTPRJ	HTA11_696_2000001011	Human	Colorectum	AD	2.25e-05	5.72e-01	-0.1464
5795	PTPRJ	A015-C-203	Human	Colorectum	FAP	2.41e-17	-3.18e-01	-0.1294
5795	PTPRJ	A015-C-204	Human	Colorectum	FAP	8.04e-03	-1.62e-01	-0.0228
5795	PTPRJ	A014-C-040	Human	Colorectum	FAP	1.59e-02	-3.98e-01	-0.1184
5795	PTPRJ	A002-C-201	Human	Colorectum	FAP	8.99e-07	-1.96e-01	0.0324
5795	PTPRJ	A001-C-119	Human	Colorectum	FAP	3.14e-04	1.92e-01	-0.1557
5795	PTPRJ	A001-C-108	Human	Colorectum	FAP	4.63e-07	-1.98e-01	-0.0272
5795	PTPRJ	A002-C-205	Human	Colorectum	FAP	1.56e-14	-3.23e-01	-0.1236
5795	PTPRJ	A015-C-006	Human	Colorectum	FAP	8.28e-09	-2.06e-01	-0.0994
5795	PTPRJ	A015-C-106	Human	Colorectum	FAP	8.32e-07	-1.36e-01	-0.0511
5795	PTPRJ	A002-C-114	Human	Colorectum	FAP	2.31e-10	-1.79e-01	-0.1561
5795	PTPRJ	A015-C-104	Human	Colorectum	FAP	3.52e-17	-3.08e-01	-0.1899
5795	PTPRJ	A001-C-014	Human	Colorectum	FAP	1.95e-05	-8.90e-02	0.0135
5795	PTPRJ	A002-C-016	Human	Colorectum	FAP	4.19e-08	-1.32e-01	0.0521
5795	PTPRJ	A015-C-002	Human	Colorectum	FAP	1.64e-06	1.75e-02	-0.0763
5795	PTPRJ	A001-C-203	Human	Colorectum	FAP	1.20e-04	-1.31e-01	-0.0481
5795	PTPRJ	A002-C-116	Human	Colorectum	FAP	6.87e-19	-2.02e-01	-0.0452
5795	PTPRJ	A014-C-008	Human	Colorectum	FAP	2.79e-08	-2.58e-01	-0.191

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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

∗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:004593613	Lung	AIS	negative regulation of phosphate metabolic process	75/1849	441/18723	1.93e-06	1.12e-04	75
GO:001056313	Lung	AIS	negative regulation of phosphorus metabolic process	75/1849	442/18723	2.11e-06	1.20e-04	75
GO:001081113	Lung	AIS	positive regulation of cell-substrate adhesion	29/1849	123/18723	6.93e-06	3.03e-04	29
GO:190188811	Lung	AIS	regulation of cell junction assembly	41/1849	204/18723	7.76e-06	3.35e-04	41
GO:004232613	Lung	AIS	negative regulation of phosphorylation	65/1849	385/18723	1.17e-05	4.69e-04	65
GO:001631112	Lung	AIS	dephosphorylation	69/1849	417/18723	1.27e-05	4.78e-04	69
GO:007190012	Lung	AIS	regulation of protein serine/threonine kinase activity	61/1849	359/18723	1.76e-05	6.17e-04	61
GO:004205811	Lung	AIS	regulation of epidermal growth factor receptor signaling pathway	20/1849	73/18723	1.77e-05	6.17e-04	20
GO:000193313	Lung	AIS	negative regulation of protein phosphorylation	57/1849	342/18723	5.71e-05	1.60e-03	57
GO:190118411	Lung	AIS	regulation of ERBB signaling pathway	20/1849	79/18723	6.12e-05	1.67e-03	20
GO:004800811	Lung	AIS	platelet-derived growth factor receptor signaling pathway	16/1849	56/18723	6.89e-05	1.84e-03	16
GO:000195412	Lung	AIS	positive regulation of cell-matrix adhesion	16/1849	58/18723	1.09e-04	2.57e-03	16
GO:190118512	Lung	AIS	negative regulation of ERBB signaling pathway	11/1849	32/18723	1.53e-04	3.26e-03	11
GO:00434101	Lung	AIS	positive regulation of MAPK cascade	72/1849	480/18723	2.11e-04	4.32e-03	72
GO:004205913	Lung	AIS	negative regulation of epidermal growth factor receptor signaling pathway	10/1849	28/18723	2.13e-04	4.35e-03	10
GO:00353351	Lung	AIS	peptidyl-tyrosine dephosphorylation	21/1849	97/18723	4.32e-04	7.38e-03	21
GO:005134813	Lung	AIS	negative regulation of transferase activity	44/1849	268/18723	5.28e-04	8.43e-03	44
GO:004340511	Lung	AIS	regulation of MAP kinase activity	32/1849	177/18723	5.53e-04	8.71e-03	32
GO:000155812	Lung	AIS	regulation of cell growth	62/1849	414/18723	5.85e-04	9.03e-03	62
GO:005189411	Lung	AIS	positive regulation of focal adhesion assembly	9/1849	28/18723	1.06e-03	1.38e-02	9

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05208	Colorectum	AD	Chemical carcinogenesis - reactive oxygen species	126/2092	223/8465	1.01e-24	1.68e-22	1.07e-22	126
hsa04520	Colorectum	AD	Adherens junction	50/2092	93/8465	1.52e-09	2.83e-08	1.81e-08	50
hsa052081	Colorectum	AD	Chemical carcinogenesis - reactive oxygen species	126/2092	223/8465	1.01e-24	1.68e-22	1.07e-22	126
hsa045201	Colorectum	AD	Adherens junction	50/2092	93/8465	1.52e-09	2.83e-08	1.81e-08	50
hsa045208	Colorectum	FAP	Adherens junction	45/1404	93/8465	8.66e-13	2.89e-10	1.76e-10	45
hsa052088	Colorectum	FAP	Chemical carcinogenesis - reactive oxygen species	78/1404	223/8465	1.08e-11	1.80e-09	1.09e-09	78
hsa045209	Colorectum	FAP	Adherens junction	45/1404	93/8465	8.66e-13	2.89e-10	1.76e-10	45
hsa052089	Colorectum	FAP	Chemical carcinogenesis - reactive oxygen species	78/1404	223/8465	1.08e-11	1.80e-09	1.09e-09	78
hsa0452010	Colorectum	CRC	Adherens junction	37/1091	93/8465	5.72e-11	6.37e-09	4.32e-09	37
hsa0520810	Colorectum	CRC	Chemical carcinogenesis - reactive oxygen species	43/1091	223/8465	3.96e-03	2.36e-02	1.60e-02	43
hsa0452011	Colorectum	CRC	Adherens junction	37/1091	93/8465	5.72e-11	6.37e-09	4.32e-09	37
hsa0520811	Colorectum	CRC	Chemical carcinogenesis - reactive oxygen species	43/1091	223/8465	3.96e-03	2.36e-02	1.60e-02	43
hsa0520826	Endometrium	AEH	Chemical carcinogenesis - reactive oxygen species	91/1197	223/8465	3.28e-23	1.33e-21	9.76e-22	91
hsa0452025	Endometrium	AEH	Adherens junction	36/1197	93/8465	3.49e-09	5.98e-08	4.37e-08	36
hsa05208112	Endometrium	AEH	Chemical carcinogenesis - reactive oxygen species	91/1197	223/8465	3.28e-23	1.33e-21	9.76e-22	91
hsa04520111	Endometrium	AEH	Adherens junction	36/1197	93/8465	3.49e-09	5.98e-08	4.37e-08	36
hsa0520827	Endometrium	EEC	Chemical carcinogenesis - reactive oxygen species	94/1237	223/8465	4.11e-24	1.93e-22	1.44e-22	94
hsa0452026	Endometrium	EEC	Adherens junction	36/1237	93/8465	8.57e-09	1.48e-07	1.11e-07	36
hsa0520836	Endometrium	EEC	Chemical carcinogenesis - reactive oxygen species	94/1237	223/8465	4.11e-24	1.93e-22	1.44e-22	94
hsa0452035	Endometrium	EEC	Adherens junction	36/1237	93/8465	8.57e-09	1.48e-07	1.11e-07	36

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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

PTPRJ

SNV

Missense_Mutation

c.3227N>T

p.Pro1076Leu

p.P1076L

Q12913

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AQ-A04J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PTPRJ

SNV

Missense_Mutation

novel

c.959C>T

p.Ser320Phe

p.S320F

Q12913

protein_coding

deleterious(0.02)

benign(0.156)

TCGA-BH-A42V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PTPRJ

SNV

Missense_Mutation

c.2453N>G

p.Pro818Arg

p.P818R

Q12913

protein_coding

tolerated(0.08)

benign(0.011)

TCGA-C8-A12M-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PTPRJ

SNV

Missense_Mutation

c.2854N>A

p.Glu952Lys

p.E952K

Q12913

protein_coding

tolerated(0.14)

benign(0.015)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PTPRJ

SNV

Missense_Mutation

novel

c.1204N>T

p.His402Tyr

p.H402Y

Q12913

protein_coding

tolerated(0.16)

benign(0.013)

TCGA-D8-A1XW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin+cyclophosphamide

PTPRJ

SNV

Missense_Mutation

c.3209G>A

p.Arg1070His

p.R1070H

Q12913

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-E9-A295-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

PTPRJ

insertion

In_Frame_Ins

novel

c.2397_2398insCCTGGCCGG

p.Gly799_Lys800insProGlyArg

p.G799_K800insPGR

Q12913

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PTPRJ

insertion

Frame_Shift_Ins

novel

c.2398_2399insAGTCATTCTGTACAGGTGAGTGT

p.Met801SerfsTer41

p.M801Sfs*41

Q12913

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

PTPRJ

insertion

In_Frame_Ins

novel

c.461_462insCTCTTC

p.Lys154delinsAsnSerSer

p.K154delinsNSS

Q12913

protein_coding

TCGA-AN-A0FN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PTPRJ

insertion

Frame_Shift_Ins

novel

c.462_463insGTTTCTGGTTGTTACTCCTCAGTCTT

p.His155ValfsTer45

p.H155Vfs*45

Q12913

protein_coding

TCGA-AN-A0FN-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

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