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: NUP160

Gene summary for NUP160

Gene summary.

Gene information	Species	Human
	Gene symbol	NUP160
	Gene ID	23279
	Gene name	nucleoporin 160
	Gene Alias	NPHS19
	Cytomap	11p11.2
	Gene Type	protein-coding
	GO ID	GO:0001655
	UniProtAcc	Q12769

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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
23279	NUP160	LZE4T	Human	Esophagus	ESCC	1.28e-06	1.25e-01	0.0811
23279	NUP160	LZE7T	Human	Esophagus	ESCC	2.45e-12	2.92e-01	0.0667
23279	NUP160	LZE8T	Human	Esophagus	ESCC	6.16e-05	9.32e-02	0.067
23279	NUP160	LZE22T	Human	Esophagus	ESCC	4.72e-04	2.28e-01	0.068
23279	NUP160	LZE24T	Human	Esophagus	ESCC	5.82e-16	3.14e-01	0.0596
23279	NUP160	P2T-E	Human	Esophagus	ESCC	1.04e-14	3.26e-01	0.1177
23279	NUP160	P4T-E	Human	Esophagus	ESCC	3.00e-06	1.59e-01	0.1323
23279	NUP160	P5T-E	Human	Esophagus	ESCC	1.74e-09	5.82e-02	0.1327
23279	NUP160	P8T-E	Human	Esophagus	ESCC	2.54e-19	2.41e-01	0.0889
23279	NUP160	P9T-E	Human	Esophagus	ESCC	7.20e-10	1.95e-01	0.1131
23279	NUP160	P10T-E	Human	Esophagus	ESCC	3.02e-15	2.86e-01	0.116
23279	NUP160	P11T-E	Human	Esophagus	ESCC	1.22e-10	4.19e-01	0.1426
23279	NUP160	P12T-E	Human	Esophagus	ESCC	1.33e-18	4.78e-01	0.1122
23279	NUP160	P15T-E	Human	Esophagus	ESCC	4.85e-06	1.34e-01	0.1149
23279	NUP160	P16T-E	Human	Esophagus	ESCC	6.84e-21	1.90e-01	0.1153
23279	NUP160	P17T-E	Human	Esophagus	ESCC	7.60e-06	2.80e-01	0.1278
23279	NUP160	P19T-E	Human	Esophagus	ESCC	3.95e-03	3.27e-01	0.1662
23279	NUP160	P20T-E	Human	Esophagus	ESCC	3.51e-09	1.66e-01	0.1124
23279	NUP160	P21T-E	Human	Esophagus	ESCC	2.01e-12	3.16e-01	0.1617
23279	NUP160	P22T-E	Human	Esophagus	ESCC	4.61e-21	1.76e-01	0.1236

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:0006913110	Esophagus	ESCC	nucleocytoplasmic transport	230/8552	301/18723	6.04e-28	2.02e-25	230
GO:0051169110	Esophagus	ESCC	nuclear transport	230/8552	301/18723	6.04e-28	2.02e-25	230
GO:0006403110	Esophagus	ESCC	RNA localization	166/8552	201/18723	1.95e-27	6.18e-25	166
GO:005123617	Esophagus	ESCC	establishment of RNA localization	134/8552	166/18723	1.23e-20	1.81e-18	134
GO:0051168110	Esophagus	ESCC	nuclear export	126/8552	154/18723	1.88e-20	2.65e-18	126
GO:005102815	Esophagus	ESCC	mRNA transport	110/8552	130/18723	2.76e-20	3.80e-18	110
GO:005065717	Esophagus	ESCC	nucleic acid transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:005065817	Esophagus	ESCC	RNA transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:001593117	Esophagus	ESCC	nucleobase-containing compound transport	162/8552	222/18723	9.87e-17	7.93e-15	162
GO:007116612	Esophagus	ESCC	ribonucleoprotein complex localization	66/8552	77/18723	2.94e-13	1.38e-11	66
GO:007142612	Esophagus	ESCC	ribonucleoprotein complex export from nucleus	65/8552	76/18723	5.56e-13	2.50e-11	65
GO:000640512	Esophagus	ESCC	RNA export from nucleus	68/8552	84/18723	2.99e-11	1.01e-09	68
GO:00064064	Esophagus	ESCC	mRNA export from nucleus	51/8552	59/18723	7.98e-11	2.47e-09	51
GO:00714274	Esophagus	ESCC	mRNA-containing ribonucleoprotein complex export from nucleus	51/8552	59/18723	7.98e-11	2.47e-09	51
GO:003150314	Esophagus	ESCC	protein-containing complex localization	139/8552	220/18723	1.14e-07	1.85e-06	139
GO:00016559	Esophagus	ESCC	urogenital system development	177/8552	338/18723	7.51e-03	2.69e-02	177
GO:000640318	Oral cavity	OSCC	RNA localization	150/7305	201/18723	6.90e-25	1.98e-22	150
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:00510287	Oral cavity	OSCC	mRNA transport	101/7305	130/18723	2.19e-19	3.15e-17	101

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
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
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
hsa0501445	Oral cavity	EOLP	Amyotrophic lateral sclerosis	93/1218	364/8465	7.07e-09	1.14e-07	6.74e-08	93
hsa030134	Oral cavity	EOLP	Nucleocytoplasmic transport	34/1218	108/8465	4.24e-06	2.91e-05	1.72e-05	34
hsa0501455	Oral cavity	EOLP	Amyotrophic lateral sclerosis	93/1218	364/8465	7.07e-09	1.14e-07	6.74e-08	93
hsa030135	Oral cavity	EOLP	Nucleocytoplasmic transport	34/1218	108/8465	4.24e-06	2.91e-05	1.72e-05	34

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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

NUP160

SNV

Missense_Mutation

c.2173N>C

p.Ser725Arg

p.S725R

Q12769

protein_coding

tolerated(0.54)

benign(0.019)

TCGA-A2-A0YT-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

arimidex

NUP160

SNV

Missense_Mutation

c.4192G>A

p.Glu1398Lys

p.E1398K

Q12769

protein_coding

deleterious(0.02)

benign(0.201)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP160

SNV

Missense_Mutation

c.1513G>A

p.Glu505Lys

p.E505K

Q12769

protein_coding

deleterious(0.01)

probably_damaging(0.968)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP160

SNV

Missense_Mutation

rs199540952

c.1351C>G

p.Gln451Glu

p.Q451E

Q12769

protein_coding

tolerated(0.23)

probably_damaging(0.914)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP160

SNV

Missense_Mutation

c.2420C>G

p.Ser807Cys

p.S807C

Q12769

protein_coding

deleterious(0)

possibly_damaging(0.844)

TCGA-AN-A0XW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

NUP160

SNV

Missense_Mutation

novel

c.1711T>A

p.Ser571Thr

p.S571T

Q12769

protein_coding

tolerated(0.41)

benign(0.003)

TCGA-AR-A0U2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

NUP160

SNV

Missense_Mutation

c.2134N>A

p.Ala712Thr

p.A712T

Q12769

protein_coding

tolerated(0.11)

benign(0.003)

TCGA-BH-A0BP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP160

SNV

Missense_Mutation

rs754933075

c.3368N>G

p.Asn1123Ser

p.N1123S

Q12769

protein_coding

tolerated(0.1)

benign(0.003)

TCGA-BH-A0DP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

NUP160

SNV

Missense_Mutation

c.4051G>A

p.Val1351Met

p.V1351M

Q12769

protein_coding

deleterious(0.03)

possibly_damaging(0.635)

TCGA-BH-A0H3-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUP160

SNV

Missense_Mutation

c.779N>A

p.Ser260Asn

p.S260N

Q12769

protein_coding

deleterious(0.01)

benign(0.138)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

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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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