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: NUP107

Gene summary for NUP107

Gene summary.

Gene information	Species	Human
	Gene symbol	NUP107
	Gene ID	57122
	Gene name	nucleoporin 107
	Gene Alias	NPHS11
	Cytomap	12q15
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P57740

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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
57122	NUP107	C38	Human	Oral cavity	OSCC	3.63e-06	7.79e-01	0.172
57122	NUP107	C43	Human	Oral cavity	OSCC	1.01e-14	3.75e-01	0.1704
57122	NUP107	C46	Human	Oral cavity	OSCC	4.95e-12	4.86e-01	0.1673
57122	NUP107	C51	Human	Oral cavity	OSCC	3.94e-06	5.07e-01	0.2674
57122	NUP107	C57	Human	Oral cavity	OSCC	3.66e-02	2.78e-01	0.1679
57122	NUP107	C07	Human	Oral cavity	OSCC	2.67e-02	5.17e-01	0.2491
57122	NUP107	C08	Human	Oral cavity	OSCC	3.81e-09	4.07e-01	0.1919
57122	NUP107	LN22	Human	Oral cavity	OSCC	7.65e-11	1.05e+00	0.1733
57122	NUP107	LN46	Human	Oral cavity	OSCC	3.75e-07	4.35e-01	0.1666
57122	NUP107	SYSMH2	Human	Oral cavity	OSCC	2.56e-08	4.39e-01	0.2326
57122	NUP107	SYSMH3	Human	Oral cavity	OSCC	1.43e-15	4.04e-01	0.2442
57122	NUP107	P1_cSCC	Human	Skin	cSCC	2.10e-11	4.85e-01	0.0292
57122	NUP107	P2_cSCC	Human	Skin	cSCC	1.84e-10	3.54e-01	-0.024
57122	NUP107	P4_cSCC	Human	Skin	cSCC	4.88e-20	4.71e-01	-0.00290000000000005
57122	NUP107	P10_cSCC	Human	Skin	cSCC	5.66e-25	6.88e-01	0.1017
57122	NUP107	male-WTA	Human	Thyroid	PTC	1.20e-11	7.53e-02	0.1037
57122	NUP107	PTC01	Human	Thyroid	PTC	2.96e-06	9.80e-02	0.1899
57122	NUP107	PTC04	Human	Thyroid	PTC	8.68e-07	5.73e-02	0.1927
57122	NUP107	PTC05	Human	Thyroid	PTC	3.70e-13	3.70e-01	0.2065
57122	NUP107	PTC06	Human	Thyroid	PTC	4.84e-14	2.34e-01	0.2057

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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
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:00725949	Cervix	CC	establishment of protein localization to organelle	99/2311	422/18723	1.23e-10	2.11e-08	99
GO:00069139	Cervix	CC	nucleocytoplasmic transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00511699	Cervix	CC	nuclear transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00345048	Cervix	CC	protein localization to nucleus	68/2311	290/18723	9.91e-08	5.25e-06	68
GO:00614588	Cervix	CC	reproductive system development	87/2311	427/18723	1.37e-06	4.55e-05	87
GO:00486088	Cervix	CC	reproductive structure development	86/2311	424/18723	1.90e-06	5.97e-05	86
GO:00170388	Cervix	CC	protein import	48/2311	206/18723	8.62e-06	1.98e-04	48
GO:00511689	Cervix	CC	nuclear export	38/2311	154/18723	1.86e-05	3.46e-04	38
GO:00511707	Cervix	CC	import into nucleus	38/2311	159/18723	3.98e-05	6.18e-04	38
GO:00512368	Cervix	CC	establishment of RNA localization	39/2311	166/18723	4.76e-05	7.25e-04	39
GO:00066067	Cervix	CC	protein import into nucleus	37/2311	155/18723	5.13e-05	7.71e-04	37
GO:00506578	Cervix	CC	nucleic acid transport	38/2311	163/18723	7.06e-05	9.85e-04	38
GO:00506588	Cervix	CC	RNA transport	38/2311	163/18723	7.06e-05	9.85e-04	38
GO:000640310	Cervix	CC	RNA localization	43/2311	201/18723	2.00e-04	2.29e-03	43
GO:00510284	Cervix	CC	mRNA transport	31/2311	130/18723	2.05e-04	2.33e-03	31
GO:00469312	Cervix	CC	pore complex assembly	9/2311	20/18723	3.06e-04	3.27e-03	9
GO:00159318	Cervix	CC	nucleobase-containing compound transport	43/2311	222/18723	1.72e-03	1.30e-02	43
GO:00069991	Cervix	CC	nuclear pore organization	6/2311	14/18723	4.36e-03	2.67e-02	6
GO:00714262	Cervix	CC	ribonucleoprotein complex export from nucleus	18/2311	76/18723	4.45e-03	2.71e-02	18
GO:00711662	Cervix	CC	ribonucleoprotein complex localization	18/2311	77/18723	5.15e-03	3.03e-02	18

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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
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

NUP107

SNV

Missense_Mutation

c.2620T>C

p.Cys874Arg

p.C874R

P57740

protein_coding

deleterious(0)

probably_damaging(0.958)

TCGA-A2-A1FZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Arimidex

NUP107

SNV

Missense_Mutation

novel

c.1265N>T

p.Arg422Ile

p.R422I

P57740

protein_coding

tolerated(0.33)

benign(0.112)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP107

SNV

Missense_Mutation

novel

c.2379N>T

p.Lys793Asn

p.K793N

P57740

protein_coding

deleterious(0.02)

benign(0.152)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP107

SNV

Missense_Mutation

rs375498676

c.2420A>G

p.Asp807Gly

p.D807G

P57740

protein_coding

tolerated(0.18)

benign(0.074)

TCGA-B6-A0RT-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

NUP107

SNV

Missense_Mutation

rs753777420

c.2588N>T

p.Thr863Met

p.T863M

P57740

protein_coding

deleterious(0.01)

possibly_damaging(0.701)

TCGA-BH-A1FC-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NUP107

SNV

Missense_Mutation

c.847N>A

p.Glu283Lys

p.E283K

P57740

protein_coding

tolerated(0.06)

benign(0.041)

TCGA-C8-A1HM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

doxorubicin

NUP107

SNV

Missense_Mutation

c.83N>G

p.Ala28Gly

p.A28G

P57740

protein_coding

tolerated_low_confidence(0.08)

benign(0.086)

TCGA-D8-A140-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin+cyclophosphamid

NUP107

SNV

Missense_Mutation

c.2088G>A

p.Met696Ile

p.M696I

P57740

protein_coding

tolerated(0.17)

benign(0.058)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

NUP107

SNV

Missense_Mutation

rs139969249

c.937G>A

p.Val313Ile

p.V313I

P57740

protein_coding

tolerated(0.93)

benign(0)

TCGA-LD-A66U-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

NUP107

SNV

Missense_Mutation

novel

c.1966N>A

p.Leu656Met

p.L656M

P57740

protein_coding

tolerated(0.11)

benign(0.047)

TCGA-2W-A8YY-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
57122	NUP107	TRANSPORTER		Platinum compounds		28562428

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