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: JARID2

Gene summary for JARID2

Gene summary.

Gene information	Species	Human
	Gene symbol	JARID2
	Gene ID	3720
	Gene name	jumonji and AT-rich interaction domain containing 2
	Gene Alias	JMJ
	Cytomap	6p22.3
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	Q92833

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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
3720	JARID2	N_HPV_2	Human	Cervix	N_HPV	5.19e-03	1.39e-01	-0.0131
3720	JARID2	CCI_1	Human	Cervix	CC	8.70e-15	1.62e+00	0.528
3720	JARID2	CCI_2	Human	Cervix	CC	3.84e-18	2.48e+00	0.5249
3720	JARID2	CCI_3	Human	Cervix	CC	1.45e-18	1.18e+00	0.516
3720	JARID2	HTA11_3410_2000001011	Human	Colorectum	AD	1.21e-19	-5.20e-01	0.0155
3720	JARID2	HTA11_2487_2000001011	Human	Colorectum	SER	2.15e-06	-5.22e-01	-0.1808
3720	JARID2	HTA11_78_2000001011	Human	Colorectum	AD	1.80e-05	-3.18e-01	-0.1088
3720	JARID2	HTA11_3361_2000001011	Human	Colorectum	AD	1.32e-06	-5.78e-01	-0.1207
3720	JARID2	HTA11_2992_2000001011	Human	Colorectum	SER	2.26e-02	-4.21e-01	-0.1706
3720	JARID2	HTA11_5212_2000001011	Human	Colorectum	AD	1.26e-02	-6.46e-01	-0.2061
3720	JARID2	HTA11_5216_2000001011	Human	Colorectum	SER	1.10e-03	-6.39e-01	-0.1462
3720	JARID2	HTA11_546_2000001011	Human	Colorectum	AD	1.54e-08	-3.33e-01	-0.0842
3720	JARID2	HTA11_8622_2000001021	Human	Colorectum	SER	4.59e-02	-4.72e-01	0.0528
3720	JARID2	HTA11_99999970781_79442	Human	Colorectum	MSS	7.46e-12	-4.29e-01	0.294
3720	JARID2	HTA11_99999965104_69814	Human	Colorectum	MSS	1.40e-02	5.55e-01	0.281
3720	JARID2	HTA11_99999974143_84620	Human	Colorectum	MSS	5.31e-09	-5.01e-01	0.3005
3720	JARID2	A001-C-207	Human	Colorectum	FAP	2.91e-02	-2.62e-01	0.1278
3720	JARID2	A015-C-203	Human	Colorectum	FAP	1.11e-30	-4.61e-01	-0.1294
3720	JARID2	A015-C-204	Human	Colorectum	FAP	6.97e-07	-4.21e-01	-0.0228
3720	JARID2	A014-C-040	Human	Colorectum	FAP	1.02e-05	-5.93e-01	-0.1184

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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
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:004873210	Cervix	CC	gland development	84/2311	436/18723	1.93e-05	3.54e-04	84
GO:00488634	Cervix	CC	stem cell differentiation	46/2311	206/18723	4.11e-05	6.36e-04	46
GO:00063257	Cervix	CC	chromatin organization	78/2311	409/18723	5.40e-05	8.02e-04	78
GO:00605375	Cervix	CC	muscle tissue development	76/2311	403/18723	9.76e-05	1.27e-03	76
GO:00165705	Cervix	CC	histone modification	84/2311	463/18723	1.70e-04	2.01e-03	84
GO:00147064	Cervix	CC	striated muscle tissue development	72/2311	384/18723	1.76e-04	2.07e-03	72
GO:00610089	Cervix	CC	hepaticobiliary system development	34/2311	150/18723	2.92e-04	3.14e-03	34
GO:00018899	Cervix	CC	liver development	33/2311	147/18723	4.27e-04	4.30e-03	33
GO:0033002	Cervix	CC	muscle cell proliferation	49/2311	248/18723	5.43e-04	5.24e-03	49
GO:00349685	Cervix	CC	histone lysine methylation	27/2311	115/18723	6.61e-04	6.09e-03	27
GO:00486386	Cervix	CC	regulation of developmental growth	61/2311	330/18723	7.69e-04	6.85e-03	61
GO:00310565	Cervix	CC	regulation of histone modification	33/2311	152/18723	7.97e-04	7.00e-03	33
GO:00165715	Cervix	CC	histone methylation	30/2311	141/18723	1.88e-03	1.39e-02	30
GO:19908234	Cervix	CC	response to leukemia inhibitory factor	22/2311	95/18723	2.40e-03	1.70e-02	22
GO:00180224	Cervix	CC	peptidyl-lysine methylation	28/2311	131/18723	2.43e-03	1.71e-02	28
GO:00064795	Cervix	CC	protein methylation	36/2311	181/18723	2.46e-03	1.71e-02	36
GO:00082135	Cervix	CC	protein alkylation	36/2311	181/18723	2.46e-03	1.71e-02	36
GO:00148963	Cervix	CC	muscle hypertrophy	23/2311	104/18723	3.63e-03	2.32e-02	23
GO:0014855	Cervix	CC	striated muscle cell proliferation	18/2311	76/18723	4.45e-03	2.71e-02	18
GO:19908304	Cervix	CC	cellular response to leukemia inhibitory factor	21/2311	94/18723	4.68e-03	2.82e-02	21

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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

JARID2

SNV

Missense_Mutation

c.2768N>C

p.Phe923Ser

p.F923S

Q92833

protein_coding

deleterious(0.03)

probably_damaging(0.999)

TCGA-DI-A0WH-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JARID2

SNV

Missense_Mutation

rs780593636

c.1447N>A

p.Gly483Arg

p.G483R

Q92833

protein_coding

deleterious_low_confidence(0)

benign(0.418)

TCGA-EO-A22R-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JARID2

SNV

Missense_Mutation

novel

c.1723N>A

p.Glu575Lys

p.E575K

Q92833

protein_coding

deleterious(0.01)

benign(0.202)

TCGA-EO-A22U-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

JARID2

SNV

Missense_Mutation

novel

c.2400N>T

p.Glu800Asp

p.E800D

Q92833

protein_coding

tolerated(0.1)

benign(0.001)

TCGA-EO-A3AV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

JARID2

SNV

Missense_Mutation

rs773374579

c.881G>A

p.Arg294Gln

p.R294Q

Q92833

protein_coding

deleterious_low_confidence(0.01)

benign(0.001)

TCGA-EO-A3KX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

JARID2

SNV

Missense_Mutation

rs144053937

c.3682N>A

p.Val1228Met

p.V1228M

Q92833

protein_coding

deleterious_low_confidence(0)

benign(0.046)

TCGA-EY-A1GU-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

JARID2

SNV

Missense_Mutation

novel

c.928A>G

p.Thr310Ala

p.T310A

Q92833

protein_coding

deleterious_low_confidence(0.03)

benign(0.192)

TCGA-FI-A2D0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

JARID2

SNV

Missense_Mutation

novel

c.851C>A

p.Ala284Asp

p.A284D

Q92833

protein_coding

deleterious_low_confidence(0.02)

benign(0.037)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

JARID2

SNV

Missense_Mutation

rs201283605

c.3728C>T

p.Ser1243Leu

p.S1243L

Q92833

protein_coding

deleterious_low_confidence(0)

benign(0.039)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

JARID2

deletion

Frame_Shift_Del

c.1186delG

p.Ala396ArgfsTer18

p.A396Rfs*18

Q92833

protein_coding

TCGA-A5-A0VQ-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

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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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