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:000641733	Lung	MIAC	regulation of translation	51/967	468/18723	3.94e-07	6.52e-05	51
GO:00064146	Lung	MIAC	translational elongation	10/967	55/18723	4.52e-04	1.25e-02	10
GO:004316123	Lung	MIAC	proteasome-mediated ubiquitin-dependent protein catabolic process	37/967	412/18723	7.87e-04	1.76e-02	37
GO:005116823	Lung	MIAC	nuclear export	18/967	154/18723	1.01e-03	2.07e-02	18
GO:001049823	Lung	MIAC	proteasomal protein catabolic process	40/967	490/18723	2.92e-03	3.99e-02	40
GO:001049820	Oral cavity	OSCC	proteasomal protein catabolic process	336/7305	490/18723	5.45e-41	8.63e-38	336
GO:004316120	Oral cavity	OSCC	proteasome-mediated ubiquitin-dependent protein catabolic process	285/7305	412/18723	5.68e-36	5.99e-33	285
GO:000691317	Oral cavity	OSCC	nucleocytoplasmic transport	204/7305	301/18723	2.65e-24	6.98e-22	204
GO:005116917	Oral cavity	OSCC	nuclear transport	204/7305	301/18723	2.65e-24	6.98e-22	204
GO:000641720	Oral cavity	OSCC	regulation of translation	274/7305	468/18723	4.39e-18	4.63e-16	274
GO:005116817	Oral cavity	OSCC	nuclear export	112/7305	154/18723	1.70e-17	1.56e-15	112
GO:000641416	Oral cavity	OSCC	translational elongation	37/7305	55/18723	2.03e-05	1.94e-04	37
GO:0010498110	Oral cavity	LP	proteasomal protein catabolic process	224/4623	490/18723	9.57e-25	4.00e-22	224
GO:0043161110	Oral cavity	LP	proteasome-mediated ubiquitin-dependent protein catabolic process	190/4623	412/18723	1.08e-21	2.93e-19	190
GO:000691318	Oral cavity	LP	nucleocytoplasmic transport	130/4623	301/18723	1.19e-12	9.77e-11	130
GO:005116918	Oral cavity	LP	nuclear transport	130/4623	301/18723	1.19e-12	9.77e-11	130
GO:0006417110	Oral cavity	LP	regulation of translation	175/4623	468/18723	4.49e-10	2.22e-08	175
GO:005116818	Oral cavity	LP	nuclear export	68/4623	154/18723	9.55e-08	3.13e-06	68
GO:000641417	Oral cavity	LP	translational elongation	25/4623	55/18723	6.27e-04	5.71e-03	25
GO:000691323	Oral cavity	EOLP	nucleocytoplasmic transport	87/2218	301/18723	7.30e-16	4.37e-13	87

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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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