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: NUP62

Gene summary for NUP62

Gene summary.

Gene information	Species	Human
	Gene symbol	NUP62
	Gene ID	23636
	Gene name	nucleoporin 62
	Gene Alias	IBSN
	Cytomap	19q13.33
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	A0A024QZF1

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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
23636	NUP62	HTA11_3410_2000001011	Human	Colorectum	AD	1.75e-12	2.46e-01	0.0155
23636	NUP62	HTA11_2487_2000001011	Human	Colorectum	SER	1.65e-07	2.24e-01	-0.1808
23636	NUP62	HTA11_2951_2000001011	Human	Colorectum	AD	3.34e-04	3.63e-01	0.0216
23636	NUP62	HTA11_1938_2000001011	Human	Colorectum	AD	3.84e-10	3.09e-01	-0.0811
23636	NUP62	HTA11_78_2000001011	Human	Colorectum	AD	2.48e-07	2.13e-01	-0.1088
23636	NUP62	HTA11_347_2000001011	Human	Colorectum	AD	2.37e-14	2.95e-01	-0.1954
23636	NUP62	HTA11_411_2000001011	Human	Colorectum	SER	5.61e-03	2.94e-01	-0.2602
23636	NUP62	HTA11_2112_2000001011	Human	Colorectum	SER	1.90e-02	2.12e-01	-0.2196
23636	NUP62	HTA11_3361_2000001011	Human	Colorectum	AD	1.91e-05	2.02e-01	-0.1207
23636	NUP62	HTA11_83_2000001011	Human	Colorectum	SER	1.46e-11	4.07e-01	-0.1526
23636	NUP62	HTA11_696_2000001011	Human	Colorectum	AD	9.19e-18	3.23e-01	-0.1464
23636	NUP62	HTA11_866_2000001011	Human	Colorectum	AD	1.86e-11	2.63e-01	-0.1001
23636	NUP62	HTA11_1391_2000001011	Human	Colorectum	AD	6.55e-21	4.78e-01	-0.059
23636	NUP62	HTA11_546_2000001011	Human	Colorectum	AD	4.83e-08	3.18e-01	-0.0842
23636	NUP62	HTA11_7862_2000001011	Human	Colorectum	AD	3.08e-04	2.52e-01	-0.0179
23636	NUP62	HTA11_866_3004761011	Human	Colorectum	AD	3.43e-19	4.00e-01	0.096
23636	NUP62	HTA11_8622_2000001021	Human	Colorectum	SER	8.37e-05	2.67e-01	0.0528
23636	NUP62	HTA11_10623_2000001011	Human	Colorectum	AD	1.36e-03	2.44e-01	-0.0177
23636	NUP62	HTA11_6801_2000001011	Human	Colorectum	SER	2.21e-02	2.69e-01	0.0171
23636	NUP62	HTA11_10711_2000001011	Human	Colorectum	AD	1.10e-12	3.71e-01	0.0338

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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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:1903829	Colorectum	AD	positive regulation of cellular protein localization	110/3918	276/18723	4.58e-13	8.44e-11	110
GO:0072594	Colorectum	AD	establishment of protein localization to organelle	148/3918	422/18723	7.95e-12	1.04e-09	148
GO:0051495	Colorectum	AD	positive regulation of cytoskeleton organization	89/3918	226/18723	1.61e-10	1.56e-08	89
GO:0038127	Colorectum	AD	ERBB signaling pathway	55/3918	121/18723	1.19e-09	8.85e-08	55
GO:0051656	Colorectum	AD	establishment of organelle localization	131/3918	390/18723	3.00e-09	2.06e-07	131
GO:0007173	Colorectum	AD	epidermal growth factor receptor signaling pathway	50/3918	108/18723	3.08e-09	2.07e-07	50
GO:0006913	Colorectum	AD	nucleocytoplasmic transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0051169	Colorectum	AD	nuclear transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:1900180	Colorectum	AD	regulation of protein localization to nucleus	55/3918	136/18723	1.70e-07	7.34e-06	55
GO:0032386	Colorectum	AD	regulation of intracellular transport	109/3918	337/18723	5.33e-07	1.95e-05	109
GO:0033157	Colorectum	AD	regulation of intracellular protein transport	80/3918	229/18723	5.81e-07	2.09e-05	80
GO:0006403	Colorectum	AD	RNA localization	71/3918	201/18723	1.54e-06	4.76e-05	71
GO:1901185	Colorectum	AD	negative regulation of ERBB signaling pathway	19/3918	32/18723	2.39e-06	6.98e-05	19
GO:0034504	Colorectum	AD	protein localization to nucleus	94/3918	290/18723	2.83e-06	8.09e-05	94
GO:1901184	Colorectum	AD	regulation of ERBB signaling pathway	34/3918	79/18723	7.46e-06	1.82e-04	34
GO:0007265	Colorectum	AD	Ras protein signal transduction	104/3918	337/18723	1.01e-05	2.35e-04	104
GO:0010563	Colorectum	AD	negative regulation of phosphorus metabolic process	130/3918	442/18723	1.26e-05	2.76e-04	130
GO:0045936	Colorectum	AD	negative regulation of phosphate metabolic process	129/3918	441/18723	1.81e-05	3.76e-04	129
GO:0051056	Colorectum	AD	regulation of small GTPase mediated signal transduction	94/3918	302/18723	1.81e-05	3.76e-04	94
GO:0051236	Colorectum	AD	establishment of RNA localization	58/3918	166/18723	1.95e-05	4.01e-04	58

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05014	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050141	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050142	Colorectum	SER	Amyotrophic lateral sclerosis	138/1580	364/8465	9.89e-19	2.99e-17	2.17e-17	138
hsa050143	Colorectum	SER	Amyotrophic lateral sclerosis	138/1580	364/8465	9.89e-19	2.99e-17	2.17e-17	138
hsa050144	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050145	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050146	Colorectum	MSI-H	Amyotrophic lateral sclerosis	95/797	364/8465	2.31e-21	1.50e-19	1.26e-19	95
hsa050147	Colorectum	MSI-H	Amyotrophic lateral sclerosis	95/797	364/8465	2.31e-21	1.50e-19	1.26e-19	95
hsa05014210	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0301321	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0501438	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0301331	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0501422	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa03013	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81
hsa0501432	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa030131	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81
hsa0501428	Oral cavity	OSCC	Amyotrophic lateral sclerosis	246/3704	364/8465	6.65e-21	1.11e-18	5.67e-19	246
hsa030136	Oral cavity	OSCC	Nucleocytoplasmic transport	82/3704	108/8465	7.93e-12	1.33e-10	6.77e-11	82
hsa05014112	Oral cavity	OSCC	Amyotrophic lateral sclerosis	246/3704	364/8465	6.65e-21	1.11e-18	5.67e-19	246
hsa0301311	Oral cavity	OSCC	Nucleocytoplasmic transport	82/3704	108/8465	7.93e-12	1.33e-10	6.77e-11	82

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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

NUP62

SNV

Missense_Mutation

c.280N>T

p.Ala94Ser

p.A94S

P37198

protein_coding

tolerated(0.12)

benign(0.001)

TCGA-A1-A0SJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

NUP62

SNV

Missense_Mutation

c.1564G>C

p.Asp522His

p.D522H

P37198

protein_coding

deleterious(0)

possibly_damaging(0.824)

TCGA-A2-A0YM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP62

SNV

Missense_Mutation

novel

c.731N>T

p.Thr244Ile

p.T244I

P37198

protein_coding

deleterious(0)

possibly_damaging(0.708)

TCGA-AC-A3W5-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

NUP62

insertion

Frame_Shift_Ins

novel

c.254_255insG

p.Thr86AsnfsTer38

p.T86Nfs*38

P37198

protein_coding

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP62

SNV

Missense_Mutation

novel

c.137N>A

p.Ala46Asp

p.A46D

P37198

protein_coding

deleterious(0)

benign(0.027)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NUP62

SNV

Missense_Mutation

c.1312N>A

p.Glu438Lys

p.E438K

P37198

protein_coding

deleterious(0)

benign(0.168)

TCGA-C5-A1MK-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

carboplatin

NUP62

SNV

Missense_Mutation

novel

c.1543C>T

p.Arg515Cys

p.R515C

P37198

protein_coding

tolerated(0.05)

probably_damaging(0.948)

TCGA-EA-A3HS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NUP62

SNV

Missense_Mutation

c.98N>A

p.Ser33Tyr

p.S33Y

P37198

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NUP62

SNV

Missense_Mutation

c.1042G>A

p.Glu348Lys

p.E348K

P37198

protein_coding

deleterious(0)

possibly_damaging(0.85)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NUP62

SNV

Missense_Mutation

rs769926725

c.104N>T

p.Ser35Phe

p.S35F

P37198

protein_coding

deleterious(0.01)

probably_damaging(0.99)

TCGA-A6-6653-01

Colorectum

colon adenocarcinoma

Male

>=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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