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: NOL10

Gene summary for NOL10

Gene summary.

Gene information	Species	Human
	Gene symbol	NOL10
	Gene ID	79954
	Gene name	nucleolar protein 10
	Gene Alias	PQBP5
	Cytomap	2p25.1
	Gene Type	protein-coding
	GO ID	GO:0000462
	UniProtAcc	Q9BSC4

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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
79954	NOL10	P32T-E	Human	Esophagus	ESCC	1.67e-23	4.90e-01	0.1666
79954	NOL10	P36T-E	Human	Esophagus	ESCC	4.43e-19	4.55e-01	0.1187
79954	NOL10	P37T-E	Human	Esophagus	ESCC	4.92e-16	3.02e-01	0.1371
79954	NOL10	P38T-E	Human	Esophagus	ESCC	1.39e-03	2.13e-01	0.127
79954	NOL10	P39T-E	Human	Esophagus	ESCC	8.64e-13	2.12e-01	0.0894
79954	NOL10	P40T-E	Human	Esophagus	ESCC	4.51e-07	1.04e-01	0.109
79954	NOL10	P42T-E	Human	Esophagus	ESCC	8.36e-20	4.88e-01	0.1175
79954	NOL10	P44T-E	Human	Esophagus	ESCC	3.88e-10	1.70e-01	0.1096
79954	NOL10	P47T-E	Human	Esophagus	ESCC	2.00e-13	1.02e-01	0.1067
79954	NOL10	P48T-E	Human	Esophagus	ESCC	3.72e-14	1.99e-01	0.0959
79954	NOL10	P49T-E	Human	Esophagus	ESCC	4.82e-09	9.20e-01	0.1768
79954	NOL10	P52T-E	Human	Esophagus	ESCC	1.37e-21	5.30e-01	0.1555
79954	NOL10	P54T-E	Human	Esophagus	ESCC	5.96e-20	4.54e-01	0.0975
79954	NOL10	P56T-E	Human	Esophagus	ESCC	4.47e-05	8.27e-01	0.1613
79954	NOL10	P57T-E	Human	Esophagus	ESCC	2.52e-13	1.96e-01	0.0926
79954	NOL10	P61T-E	Human	Esophagus	ESCC	3.60e-13	2.18e-01	0.099
79954	NOL10	P62T-E	Human	Esophagus	ESCC	1.21e-31	5.25e-01	0.1302
79954	NOL10	P65T-E	Human	Esophagus	ESCC	2.55e-12	1.86e-01	0.0978
79954	NOL10	P74T-E	Human	Esophagus	ESCC	9.22e-29	6.95e-01	0.1479
79954	NOL10	P75T-E	Human	Esophagus	ESCC	4.05e-20	3.81e-01	0.1125

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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
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
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ

∗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:004227410	Cervix	CC	ribosomal small subunit biogenesis	23/2311	73/18723	1.33e-05	2.68e-04	23
GO:002261310	Cervix	CC	ribonucleoprotein complex biogenesis	88/2311	463/18723	2.11e-05	3.82e-04	88
GO:004225410	Cervix	CC	ribosome biogenesis	62/2311	299/18723	2.48e-05	4.27e-04	62
GO:00160727	Cervix	CC	rRNA metabolic process	42/2311	236/18723	9.12e-03	4.60e-02	42
GO:0022613	Colorectum	AD	ribonucleoprotein complex biogenesis	151/3918	463/18723	1.96e-09	1.39e-07	151
GO:0042254	Colorectum	AD	ribosome biogenesis	84/3918	299/18723	1.82e-03	1.50e-02	84
GO:0042274	Colorectum	AD	ribosomal small subunit biogenesis	25/3918	73/18723	5.69e-03	3.64e-02	25
GO:00226134	Colorectum	FAP	ribonucleoprotein complex biogenesis	91/2622	463/18723	4.28e-04	5.12e-03	91
GO:00226135	Colorectum	CRC	ribonucleoprotein complex biogenesis	76/2078	463/18723	3.04e-04	4.78e-03	76
GO:00422743	Colorectum	CRC	ribosomal small subunit biogenesis	18/2078	73/18723	8.33e-04	1.04e-02	18
GO:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:0042254111	Esophagus	ESCC	ribosome biogenesis	252/8552	299/18723	3.27e-44	1.04e-40	252
GO:003447015	Esophagus	ESCC	ncRNA processing	300/8552	395/18723	3.09e-35	3.26e-32	300
GO:0016072110	Esophagus	ESCC	rRNA metabolic process	197/8552	236/18723	1.31e-33	1.18e-30	197
GO:0006364110	Esophagus	ESCC	rRNA processing	189/8552	225/18723	4.88e-33	3.87e-30	189
GO:003466012	Esophagus	ESCC	ncRNA metabolic process	346/8552	485/18723	4.35e-31	2.51e-28	346
GO:0042274111	Esophagus	ESCC	ribosomal small subunit biogenesis	67/8552	73/18723	6.62e-17	5.38e-15	67
GO:00304904	Esophagus	ESCC	maturation of SSU-rRNA	45/8552	50/18723	5.07e-11	1.63e-09	45
GO:00004623	Esophagus	ESCC	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	32/8552	37/18723	2.96e-07	4.23e-06	32
GO:002261322	Liver	HCC	ribonucleoprotein complex biogenesis	355/7958	463/18723	7.76e-52	4.92e-48	355

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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

NOL10

SNV

Missense_Mutation

novel

c.56C>T

p.Ser19Phe

p.S19F

Q9BSC4

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

NOL10

SNV

Missense_Mutation

novel

c.792N>C

p.Leu264Phe

p.L264F

Q9BSC4

protein_coding

tolerated(0.41)

benign(0)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

NOL10

SNV

Missense_Mutation

novel

c.790N>G

p.Leu264Val

p.L264V

Q9BSC4

protein_coding

tolerated(0.11)

benign(0)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

NOL10

SNV

Missense_Mutation

c.1491N>A

p.Asp497Glu

p.D497E

Q9BSC4

protein_coding

deleterious(0.02)

probably_damaging(0.997)

TCGA-BH-A0DT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

NOL10

SNV

Missense_Mutation

c.30N>C

p.Lys10Asn

p.K10N

Q9BSC4

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-BH-A208-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NOL10

insertion

In_Frame_Ins

novel

c.1991_2008dupGACAAGAAAGGAAAAGAC

p.Arg664_Arg669dup

p.R664_R669dup

Q9BSC4

protein_coding

TCGA-AO-A0JB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

NOL10

insertion

Nonsense_Mutation

novel

c.1345_1346insAAAAACAATAATCTAAACGT

p.Val449GlufsTer4

p.V449Efs*4

Q9BSC4

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NOL10

SNV

Missense_Mutation

c.1780N>C

p.Glu594Gln

p.E594Q

Q9BSC4

protein_coding

tolerated(0.2)

benign(0.051)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

NOL10

SNV

Missense_Mutation

c.212N>A

p.Gly71Glu

p.G71E

Q9BSC4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

NOL10

SNV

Missense_Mutation

novel

c.286N>C

p.Glu96Gln

p.E96Q

Q9BSC4

protein_coding

deleterious(0.01)

benign(0.217)

TCGA-VS-A9V2-01

Cervix

cervical & endocervical cancer

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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