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: NSMCE2

Gene summary for NSMCE2

Gene summary.

Gene information	Species	Human
	Gene symbol	NSMCE2
	Gene ID	286053
	Gene name	NSE2 (MMS21) homolog, SMC5-SMC6 complex SUMO ligase
	Gene Alias	C8orf36
	Cytomap	8q24.13
	Gene Type	protein-coding
	GO ID	GO:0000070
	UniProtAcc	A0A024R9J6

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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
286053	NSMCE2	CCI_1	Human	Cervix	CC	7.33e-09	1.10e+00	0.528
286053	NSMCE2	CCI_2	Human	Cervix	CC	7.47e-14	1.53e+00	0.5249
286053	NSMCE2	CCI_3	Human	Cervix	CC	1.97e-17	1.25e+00	0.516
286053	NSMCE2	HTA11_3410_2000001011	Human	Colorectum	AD	7.50e-12	-5.11e-01	0.0155
286053	NSMCE2	HTA11_347_2000001011	Human	Colorectum	AD	1.07e-02	4.38e-01	-0.1954
286053	NSMCE2	HTA11_99999965104_69814	Human	Colorectum	MSS	2.91e-03	5.14e-01	0.281
286053	NSMCE2	F007	Human	Colorectum	FAP	5.69e-07	-3.82e-01	0.1176
286053	NSMCE2	A001-C-207	Human	Colorectum	FAP	4.14e-08	-3.84e-01	0.1278
286053	NSMCE2	A015-C-203	Human	Colorectum	FAP	3.64e-30	-5.48e-01	-0.1294
286053	NSMCE2	A015-C-204	Human	Colorectum	FAP	3.53e-11	-4.75e-01	-0.0228
286053	NSMCE2	A014-C-040	Human	Colorectum	FAP	5.09e-07	-4.21e-01	-0.1184
286053	NSMCE2	A002-C-201	Human	Colorectum	FAP	2.38e-21	-4.83e-01	0.0324
286053	NSMCE2	A002-C-203	Human	Colorectum	FAP	3.37e-02	-1.97e-01	0.2786
286053	NSMCE2	A001-C-119	Human	Colorectum	FAP	3.47e-13	-5.98e-01	-0.1557
286053	NSMCE2	A001-C-108	Human	Colorectum	FAP	2.87e-24	-5.89e-01	-0.0272
286053	NSMCE2	A002-C-205	Human	Colorectum	FAP	4.75e-38	-7.57e-01	-0.1236
286053	NSMCE2	A001-C-104	Human	Colorectum	FAP	4.26e-06	-3.90e-01	0.0184
286053	NSMCE2	A015-C-005	Human	Colorectum	FAP	3.60e-04	-2.61e-01	-0.0336
286053	NSMCE2	A015-C-006	Human	Colorectum	FAP	4.88e-26	-7.55e-01	-0.0994
286053	NSMCE2	A015-C-106	Human	Colorectum	FAP	3.13e-13	-3.61e-01	-0.0511

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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
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

∗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:00447725	Cervix	CC	mitotic cell cycle phase transition	89/2311	424/18723	2.70e-07	1.12e-05	89
GO:00075689	Cervix	CC	aging	75/2311	339/18723	2.75e-07	1.13e-05	75
GO:00457876	Cervix	CC	positive regulation of cell cycle	66/2311	313/18723	7.78e-06	1.81e-04	66
GO:00073466	Cervix	CC	regulation of mitotic cell cycle	88/2311	457/18723	1.26e-05	2.60e-04	88
GO:19019903	Cervix	CC	regulation of mitotic cell cycle phase transition	63/2311	299/18723	1.27e-05	2.60e-04	63
GO:00459316	Cervix	CC	positive regulation of mitotic cell cycle	32/2311	121/18723	1.88e-05	3.47e-04	32
GO:00075695	Cervix	CC	cell aging	34/2311	132/18723	1.92e-05	3.53e-04	34
GO:19019922	Cervix	CC	positive regulation of mitotic cell cycle phase transition	26/2311	93/18723	3.97e-05	6.18e-04	26
GO:00070646	Cervix	CC	mitotic sister chromatid cohesion	12/2311	28/18723	5.47e-05	8.06e-04	12
GO:00900685	Cervix	CC	positive regulation of cell cycle process	50/2311	236/18723	8.25e-05	1.11e-03	50
GO:19019873	Cervix	CC	regulation of cell cycle phase transition	74/2311	390/18723	9.80e-05	1.27e-03	74
GO:00903981	Cervix	CC	cellular senescence	25/2311	93/18723	1.11e-04	1.40e-03	25
GO:00340864	Cervix	CC	maintenance of sister chromatid cohesion	7/2311	12/18723	1.94e-04	2.24e-03	7
GO:00340884	Cervix	CC	maintenance of mitotic sister chromatid cohesion	7/2311	12/18723	1.94e-04	2.24e-03	7
GO:19019892	Cervix	CC	positive regulation of cell cycle phase transition	28/2311	115/18723	2.82e-04	3.07e-03	28
GO:01400143	Cervix	CC	mitotic nuclear division	50/2311	287/18723	7.27e-03	3.91e-02	50
GO:00070625	Cervix	CC	sister chromatid cohesion	15/2311	62/18723	7.30e-03	3.92e-02	15
GO:00007239	Cervix	CC	telomere maintenance	26/2311	131/18723	9.33e-03	4.66e-02	26
GO:00482851	Cervix	CC	organelle fission	78/2311	488/18723	9.70e-03	4.79e-02	78
GO:00182054	Cervix	CC	peptidyl-lysine modification	62/2311	376/18723	1.04e-02	4.97e-02	62

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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

NSMCE2

SNV

Missense_Mutation

c.313N>C

p.Glu105Gln

p.E105Q

Q96MF7

protein_coding

tolerated(0.49)

benign(0.007)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

novel

c.571G>C

p.Glu191Gln

p.E191Q

Q96MF7

protein_coding

tolerated(0.18)

probably_damaging(0.927)

TCGA-BH-A18T-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

novel

c.672N>A

p.Asp224Glu

p.D224E

Q96MF7

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-EK-A2PM-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

rs140125530

c.11G>A

p.Arg4His

p.R4H

Q96MF7

protein_coding

deleterious_low_confidence(0.05)

benign(0)

TCGA-A5-A2K3-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

NSMCE2

SNV

Missense_Mutation

novel

c.133N>A

p.Ala45Thr

p.A45T

Q96MF7

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-AX-A1CE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

NSMCE2

SNV

Missense_Mutation

rs137953740

c.610N>T

p.Arg204Trp

p.R204W

Q96MF7

protein_coding

deleterious(0)

possibly_damaging(0.88)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

c.295G>A

p.Asp99Asn

p.D99N

Q96MF7

protein_coding

tolerated(0.33)

possibly_damaging(0.5)

TCGA-B5-A1MR-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Unknown

NSMCE2

SNV

Missense_Mutation

novel

c.321A>T

p.Lys107Asn

p.K107N

Q96MF7

protein_coding

deleterious(0.03)

benign(0.007)

TCGA-BS-A0UF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

novel

c.374N>C

p.Lys125Thr

p.K125T

Q96MF7

protein_coding

deleterious(0.04)

benign(0.193)

TCGA-D1-A103-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

NSMCE2

SNV

Missense_Mutation

novel

c.308N>C

p.Leu103Ser

p.L103S

Q96MF7

protein_coding

tolerated(0.19)

probably_damaging(0.946)

TCGA-D1-A175-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

paclitaxel

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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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