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: NUP153

Gene summary for NUP153

Gene summary.

Gene information	Species	Human
	Gene symbol	NUP153
	Gene ID	9972
	Gene name	nucleoporin 153
	Gene Alias	HNUP153
	Cytomap	6p22.3
	Gene Type	protein-coding
	GO ID	GO:0006403
	UniProtAcc	P49790

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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
9972	NUP153	CCI_1	Human	Cervix	CC	8.96e-08	7.23e-01	0.528
9972	NUP153	CCI_2	Human	Cervix	CC	1.32e-11	9.90e-01	0.5249
9972	NUP153	CCI_3	Human	Cervix	CC	3.50e-05	5.64e-01	0.516
9972	NUP153	AEH-subject1	Human	Endometrium	AEH	5.36e-09	3.54e-01	-0.3059
9972	NUP153	AEH-subject4	Human	Endometrium	AEH	3.23e-13	4.97e-01	-0.2657
9972	NUP153	AEH-subject5	Human	Endometrium	AEH	1.09e-27	7.09e-01	-0.2953
9972	NUP153	EEC-subject1	Human	Endometrium	EEC	6.27e-11	4.73e-01	-0.2682
9972	NUP153	EEC-subject5	Human	Endometrium	EEC	4.27e-04	3.20e-01	-0.249
9972	NUP153	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	5.82e-03	3.14e-02	-0.1869
9972	NUP153	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	9.94e-04	1.63e-02	-0.1883
9972	NUP153	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	2.52e-02	5.53e-02	-0.1934
9972	NUP153	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	1.93e-04	1.74e-02	-0.1917
9972	NUP153	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	4.22e-07	7.15e-02	-0.1916
9972	NUP153	LZE4T	Human	Esophagus	ESCC	4.87e-03	6.26e-02	0.0811
9972	NUP153	LZE7T	Human	Esophagus	ESCC	9.80e-08	6.12e-01	0.0667
9972	NUP153	LZE8T	Human	Esophagus	ESCC	4.59e-09	1.96e-02	0.067
9972	NUP153	LZE22T	Human	Esophagus	ESCC	9.13e-03	1.17e-01	0.068
9972	NUP153	LZE24T	Human	Esophagus	ESCC	3.95e-03	1.09e-01	0.0596
9972	NUP153	P1T-E	Human	Esophagus	ESCC	1.80e-02	3.10e-01	0.0875
9972	NUP153	P2T-E	Human	Esophagus	ESCC	1.73e-24	5.16e-01	0.1177

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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
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

∗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:005117021	Oral cavity	EOLP	import into nucleus	42/2218	159/18723	3.47e-07	1.01e-05	42
GO:000660621	Oral cavity	EOLP	protein import into nucleus	41/2218	155/18723	4.58e-07	1.27e-05	41
GO:004683121	Oral cavity	EOLP	regulation of RNA export from nucleus	8/2218	12/18723	1.22e-05	2.09e-04	8
GO:000640521	Oral cavity	EOLP	RNA export from nucleus	24/2218	84/18723	2.70e-05	3.95e-04	24
GO:004440325	Oral cavity	EOLP	biological process involved in symbiotic interaction	57/2218	290/18723	7.75e-05	9.39e-04	57
GO:00322391	Oral cavity	EOLP	regulation of nucleobase-containing compound transport	8/2218	15/18723	1.14e-04	1.27e-03	8
GO:00510517	Oral cavity	EOLP	negative regulation of transport	80/2218	470/18723	5.11e-04	4.44e-03	80
GO:000699721	Oral cavity	EOLP	nucleus organization	29/2218	133/18723	7.82e-04	6.24e-03	29
GO:005170126	Oral cavity	EOLP	biological process involved in interaction with host	40/2218	203/18723	8.05e-04	6.31e-03	40
GO:004440926	Oral cavity	EOLP	entry into host	31/2218	151/18723	1.50e-03	1.01e-02	31
GO:004476612	Oral cavity	EOLP	multi-organism transport	8/2218	21/18723	1.87e-03	1.21e-02	8
GO:190257912	Oral cavity	EOLP	multi-organism localization	8/2218	21/18723	1.87e-03	1.21e-02	8
GO:005212626	Oral cavity	EOLP	movement in host environment	34/2218	175/18723	2.43e-03	1.48e-02	34
GO:003238721	Oral cavity	EOLP	negative regulation of intracellular transport	15/2218	58/18723	2.52e-03	1.53e-02	15
GO:004671826	Oral cavity	EOLP	viral entry into host cell	29/2218	144/18723	2.82e-03	1.68e-02	29
GO:000699911	Oral cavity	EOLP	nuclear pore organization	6/2218	14/18723	3.54e-03	2.01e-02	6
GO:00467941	Oral cavity	EOLP	transport of virus	7/2218	19/18723	4.48e-03	2.42e-02	7
GO:00757331	Oral cavity	EOLP	intracellular transport of virus	5/2218	11/18723	5.79e-03	2.94e-02	5
GO:001603233	Oral cavity	NEOLP	viral process	101/2005	415/18723	1.08e-15	5.85e-13	101
GO:004682231	Oral cavity	NEOLP	regulation of nucleocytoplasmic transport	39/2005	106/18723	1.14e-12	2.60e-10	39

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501418	Cervix	CC	Amyotrophic lateral sclerosis	103/1267	364/8465	1.79e-11	4.47e-10	2.64e-10	103
hsa0501419	Cervix	CC	Amyotrophic lateral sclerosis	103/1267	364/8465	1.79e-11	4.47e-10	2.64e-10	103
hsa0501420	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa05014110	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa0501425	Endometrium	EEC	Amyotrophic lateral sclerosis	128/1237	364/8465	9.83e-24	4.04e-22	3.01e-22	128
hsa0501435	Endometrium	EEC	Amyotrophic lateral sclerosis	128/1237	364/8465	9.83e-24	4.04e-22	3.01e-22	128
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
hsa032509	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
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
hsa0325014	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa0501414	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
hsa0501415	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
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
hsa032502	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
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
hsa0325011	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46

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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

NUP153

SNV

Missense_Mutation

novel

c.4027N>C

p.Ala1343Pro

p.A1343P

P49790

protein_coding

deleterious(0.02)

possibly_damaging(0.675)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

NUP153

SNV

Missense_Mutation

c.211N>A

p.Asp71Asn

p.D71N

P49790

protein_coding

tolerated(0.07)

benign(0.015)

TCGA-A2-A0YG-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

NUP153

SNV

Missense_Mutation

rs568893774

c.2384C>T

p.Ser795Leu

p.S795L

P49790

protein_coding

tolerated(0.11)

benign(0.062)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP153

SNV

Missense_Mutation

c.3250N>T

p.Ile1084Leu

p.I1084L

P49790

protein_coding

tolerated(0.18)

benign(0)

TCGA-AN-A0G0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUP153

SNV

Missense_Mutation

c.3458N>A

p.Ala1153Asp

p.A1153D

P49790

protein_coding

deleterious(0)

possibly_damaging(0.782)

TCGA-AR-A1AO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

NUP153

SNV

Missense_Mutation

c.1006C>G

p.Leu336Val

p.L336V

P49790

protein_coding

deleterious(0.04)

benign(0.082)

TCGA-BH-A0BF-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUP153

SNV

Missense_Mutation

c.2395G>C

p.Glu799Gln

p.E799Q

P49790

protein_coding

tolerated(0.43)

benign(0.123)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

NUP153

SNV

Missense_Mutation

c.2105N>T

p.Asn702Ile

p.N702I

P49790

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-C8-A12P-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUP153

SNV

Missense_Mutation

c.3403G>A

p.Glu1135Lys

p.E1135K

P49790

protein_coding

deleterious(0.01)

probably_damaging(0.919)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

NUP153

SNV

Missense_Mutation

c.4278N>G

p.Phe1426Leu

p.F1426L

P49790

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=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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