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: NEMF

Gene summary for NEMF

Gene summary.

Gene information	Species	Human
	Gene symbol	NEMF
	Gene ID	9147
	Gene name	nuclear export mediator factor
	Gene Alias	IDDSAPN
	Cytomap	14q21.3
	Gene Type	protein-coding
	GO ID	GO:0006412
	UniProtAcc	O60524

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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
9147	NEMF	HTA11_3410_2000001011	Human	Colorectum	AD	2.74e-14	-5.81e-01	0.0155
9147	NEMF	HTA11_3361_2000001011	Human	Colorectum	AD	5.69e-04	-5.15e-01	-0.1207
9147	NEMF	HTA11_696_2000001011	Human	Colorectum	AD	1.17e-02	-3.11e-01	-0.1464
9147	NEMF	HTA11_866_3004761011	Human	Colorectum	AD	7.03e-04	-3.83e-01	0.096
9147	NEMF	HTA11_8622_2000001021	Human	Colorectum	SER	2.95e-03	-6.18e-01	0.0528
9147	NEMF	HTA11_7696_3000711011	Human	Colorectum	AD	1.45e-06	-4.14e-01	0.0674
9147	NEMF	HTA11_99999970781_79442	Human	Colorectum	MSS	7.00e-16	-5.43e-01	0.294
9147	NEMF	HTA11_99999971662_82457	Human	Colorectum	MSS	5.67e-07	-4.21e-01	0.3859
9147	NEMF	HTA11_99999973899_84307	Human	Colorectum	MSS	6.74e-06	-6.52e-01	0.2585
9147	NEMF	HTA11_99999974143_84620	Human	Colorectum	MSS	8.24e-06	-4.38e-01	0.3005
9147	NEMF	F007	Human	Colorectum	FAP	7.19e-03	-4.27e-02	0.1176
9147	NEMF	A001-C-207	Human	Colorectum	FAP	2.11e-04	-8.76e-02	0.1278
9147	NEMF	A015-C-203	Human	Colorectum	FAP	5.73e-31	-2.19e-01	-0.1294
9147	NEMF	A015-C-204	Human	Colorectum	FAP	8.62e-10	-2.88e-01	-0.0228
9147	NEMF	A014-C-040	Human	Colorectum	FAP	7.95e-06	-6.51e-02	-0.1184
9147	NEMF	A002-C-201	Human	Colorectum	FAP	4.61e-17	-1.63e-01	0.0324
9147	NEMF	A002-C-203	Human	Colorectum	FAP	1.13e-06	-1.48e-01	0.2786
9147	NEMF	A001-C-119	Human	Colorectum	FAP	8.11e-09	6.68e-02	-0.1557
9147	NEMF	A001-C-108	Human	Colorectum	FAP	8.83e-19	4.06e-02	-0.0272
9147	NEMF	A002-C-205	Human	Colorectum	FAP	7.66e-29	-5.02e-02	-0.1236

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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
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
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:005116923	Oral cavity	EOLP	nuclear transport	87/2218	301/18723	7.30e-16	4.37e-13	87
GO:000641726	Oral cavity	EOLP	regulation of translation	108/2218	468/18723	4.04e-12	7.34e-10	108
GO:001049825	Oral cavity	EOLP	proteasomal protein catabolic process	108/2218	490/18723	7.79e-11	9.51e-09	108
GO:005116824	Oral cavity	EOLP	nuclear export	47/2218	154/18723	4.45e-10	3.76e-08	47
GO:004316125	Oral cavity	EOLP	proteasome-mediated ubiquitin-dependent protein catabolic process	92/2218	412/18723	9.87e-10	6.96e-08	92
GO:000641422	Oral cavity	EOLP	translational elongation	17/2218	55/18723	1.36e-04	1.48e-03	17
GO:000691331	Oral cavity	NEOLP	nucleocytoplasmic transport	75/2005	301/18723	1.56e-12	3.20e-10	75
GO:005116931	Oral cavity	NEOLP	nuclear transport	75/2005	301/18723	1.56e-12	3.20e-10	75
GO:001049831	Oral cavity	NEOLP	proteasomal protein catabolic process	103/2005	490/18723	1.08e-11	1.65e-09	103
GO:004316131	Oral cavity	NEOLP	proteasome-mediated ubiquitin-dependent protein catabolic process	89/2005	412/18723	6.27e-11	7.44e-09	89
GO:000641734	Oral cavity	NEOLP	regulation of translation	97/2005	468/18723	9.94e-11	1.05e-08	97
GO:005116832	Oral cavity	NEOLP	nuclear export	41/2005	154/18723	2.35e-08	1.03e-06	41
GO:000641431	Oral cavity	NEOLP	translational elongation	15/2005	55/18723	4.94e-04	4.39e-03	15
GO:000641718	Prostate	BPH	regulation of translation	157/3107	468/18723	9.09e-20	5.63e-17	157
GO:001049818	Prostate	BPH	proteasomal protein catabolic process	153/3107	490/18723	4.13e-16	7.51e-14	153
GO:004316118	Prostate	BPH	proteasome-mediated ubiquitin-dependent protein catabolic process	127/3107	412/18723	3.84e-13	3.60e-11	127
GO:000691315	Prostate	BPH	nucleocytoplasmic transport	92/3107	301/18723	1.09e-09	4.84e-08	92
GO:005116915	Prostate	BPH	nuclear transport	92/3107	301/18723	1.09e-09	4.84e-08	92
GO:005116815	Prostate	BPH	nuclear export	46/3107	154/18723	2.86e-05	3.32e-04	46
GO:000641410	Prostate	BPH	translational elongation	20/3107	55/18723	3.18e-04	2.43e-03	20

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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

NEMF

SNV

Missense_Mutation

novel

c.934N>T

p.Ala312Ser

p.A312S

O60524

protein_coding

tolerated(0.09)

benign(0.259)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NEMF

SNV

Missense_Mutation

c.788C>T

p.Pro263Leu

p.P263L

O60524

protein_coding

deleterious(0.03)

benign(0.124)

TCGA-AR-A1AV-01

Breast

breast invasive carcinoma

Male

>=65

I/II

Chemotherapy

cytoxan

NEMF

SNV

Missense_Mutation

c.2301N>T

p.Met767Ile

p.M767I

O60524

protein_coding

tolerated(0.19)

benign(0)

TCGA-B6-A0X5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NEMF

SNV

Missense_Mutation

c.1624N>G

p.Ile542Val

p.I542V

O60524

protein_coding

deleterious(0.03)

benign(0.073)

TCGA-BH-A1F6-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

NEMF

SNV

Missense_Mutation

rs370320203

c.1828N>G

p.Thr610Ala

p.T610A

O60524

protein_coding

tolerated(0.13)

possibly_damaging(0.669)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NEMF

SNV

Missense_Mutation

rs760379976

c.1634N>A

p.Arg545Gln

p.R545Q

O60524

protein_coding

deleterious(0)

probably_damaging(0.989)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NEMF

SNV

Missense_Mutation

rs764224132

c.1763G>A

p.Arg588Gln

p.R588Q

O60524

protein_coding

deleterious(0.01)

probably_damaging(0.957)

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

NEMF

SNV

Missense_Mutation

novel

c.2762N>A

p.Pro921His

p.P921H

O60524

protein_coding

tolerated(0.08)

benign(0.031)

TCGA-EA-A410-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NEMF

SNV

Missense_Mutation

c.2021N>A

p.Arg674Lys

p.R674K

O60524

protein_coding

tolerated(0.84)

benign(0)

TCGA-EA-A78R-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NEMF

SNV

Missense_Mutation

c.2781G>C

p.Gln927His

p.Q927H

O60524

protein_coding

deleterious(0.02)

benign(0.365)

TCGA-IR-A3LH-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

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

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