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: ANP32A

Gene summary for ANP32A

Gene summary.

Gene information	Species	Human
	Gene symbol	ANP32A
	Gene ID	8125
	Gene name	acidic nuclear phosphoprotein 32 family member A
	Gene Alias	C15orf1
	Cytomap	15q23
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	P39687

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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
8125	ANP32A	Pt14.d	Human	Liver	HCC	1.57e-02	1.37e-01	0.0143
8125	ANP32A	S014	Human	Liver	HCC	1.62e-46	1.53e+00	0.2254
8125	ANP32A	S015	Human	Liver	HCC	4.78e-33	1.96e+00	0.2375
8125	ANP32A	S016	Human	Liver	HCC	5.75e-44	1.63e+00	0.2243
8125	ANP32A	S027	Human	Liver	HCC	6.69e-19	1.84e+00	0.2446
8125	ANP32A	S028	Human	Liver	HCC	8.71e-39	1.69e+00	0.2503
8125	ANP32A	S029	Human	Liver	HCC	7.97e-29	1.76e+00	0.2581
8125	ANP32A	C04	Human	Oral cavity	OSCC	7.03e-22	1.35e+00	0.2633
8125	ANP32A	C21	Human	Oral cavity	OSCC	3.51e-57	2.15e+00	0.2678
8125	ANP32A	C30	Human	Oral cavity	OSCC	2.05e-38	2.21e+00	0.3055
8125	ANP32A	C38	Human	Oral cavity	OSCC	2.94e-04	9.78e-01	0.172
8125	ANP32A	C43	Human	Oral cavity	OSCC	6.12e-47	1.06e+00	0.1704
8125	ANP32A	C46	Human	Oral cavity	OSCC	1.88e-19	6.54e-01	0.1673
8125	ANP32A	C51	Human	Oral cavity	OSCC	4.94e-21	1.36e+00	0.2674
8125	ANP32A	C57	Human	Oral cavity	OSCC	1.13e-04	5.11e-01	0.1679
8125	ANP32A	C06	Human	Oral cavity	OSCC	5.49e-08	1.52e+00	0.2699
8125	ANP32A	C07	Human	Oral cavity	OSCC	1.32e-02	1.18e+00	0.2491
8125	ANP32A	C08	Human	Oral cavity	OSCC	1.49e-53	1.30e+00	0.1919
8125	ANP32A	C09	Human	Oral cavity	OSCC	2.45e-06	4.64e-01	0.1431
8125	ANP32A	LN22	Human	Oral cavity	OSCC	7.43e-10	1.34e+00	0.1733

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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
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
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
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: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:00069131	Colorectum	SER	nucleocytoplasmic transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00511691	Colorectum	SER	nuclear transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00069132	Colorectum	MSS	nucleocytoplasmic transport	99/3467	301/18723	1.35e-09	1.03e-07	99
GO:00511692	Colorectum	MSS	nuclear transport	99/3467	301/18723	1.35e-09	1.03e-07	99
GO:00069134	Colorectum	FAP	nucleocytoplasmic transport	77/2622	301/18723	6.15e-08	4.54e-06	77
GO:00511694	Colorectum	FAP	nuclear transport	77/2622	301/18723	6.15e-08	4.54e-06	77
GO:00069135	Colorectum	CRC	nucleocytoplasmic transport	57/2078	301/18723	3.71e-05	9.18e-04	57
GO:00511695	Colorectum	CRC	nuclear transport	57/2078	301/18723	3.71e-05	9.18e-04	57
GO:000691310	Endometrium	AEH	nucleocytoplasmic transport	54/2100	301/18723	3.24e-04	3.62e-03	54
GO:005116910	Endometrium	AEH	nuclear transport	54/2100	301/18723	3.24e-04	3.62e-03	54
GO:000691314	Endometrium	EEC	nucleocytoplasmic transport	59/2168	301/18723	3.31e-05	5.65e-04	59
GO:005116914	Endometrium	EEC	nuclear transport	59/2168	301/18723	3.31e-05	5.65e-04	59
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:000691312	Liver	Cirrhotic	nucleocytoplasmic transport	118/4634	301/18723	1.71e-08	6.27e-07	118
GO:005116912	Liver	Cirrhotic	nuclear transport	118/4634	301/18723	1.71e-08	6.27e-07	118
GO:000691322	Liver	HCC	nucleocytoplasmic transport	208/7958	301/18723	5.51e-21	8.12e-19	208
GO:005116922	Liver	HCC	nuclear transport	208/7958	301/18723	5.51e-21	8.12e-19	208

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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

ANP32A

SNV

Missense_Mutation

novel

c.206N>G

p.Leu69Arg

p.L69R

P39687

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AQ-A54O-01

Breast

breast invasive carcinoma

Male

<65

I/II

Chemotherapy

adriamycin

ANP32A

insertion

Frame_Shift_Ins

novel

c.412_413insATAA

p.Leu138HisfsTer13

p.L138Hfs*13

P39687

protein_coding

TCGA-A2-A0D1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

ANP32A

insertion

Frame_Shift_Ins

novel

c.411_412insTCCCATGCTCATGGAAATATCCTGAGATTCTCCAACTG

p.Leu138SerfsTer61

p.L138Sfs*61

P39687

protein_coding

TCGA-A2-A0D1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

ANP32A

SNV

Missense_Mutation

novel

c.739N>A

p.Asp247Asn

p.D247N

P39687

protein_coding

deleterious_low_confidence(0.02)

benign(0.048)

TCGA-VS-A8EL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ANP32A

SNV

Missense_Mutation

c.311G>A

p.Ser104Asn

p.S104N

P39687

protein_coding

tolerated(0.1)

benign(0.014)

TCGA-AA-3864-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

ANP32A

SNV

Missense_Mutation

c.646N>A

p.Asp216Asn

p.D216N

P39687

protein_coding

tolerated_low_confidence(0.14)

benign(0.01)

TCGA-EI-6882-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

ANP32A

SNV

Missense_Mutation

novel

c.638N>A

p.Gly213Asp

p.G213D

P39687

protein_coding

tolerated(0.28)

benign(0.001)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

ANP32A

SNV

Missense_Mutation

novel

c.348N>T

p.Lys116Asn

p.K116N

P39687

protein_coding

deleterious(0)

possibly_damaging(0.891)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

ANP32A

SNV

Missense_Mutation

novel

c.731N>G

p.Glu244Gly

p.E244G

P39687

protein_coding

tolerated_low_confidence(0.06)

benign(0)

TCGA-AP-A0LS-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ANP32A

SNV

Missense_Mutation

novel

c.113N>T

p.Thr38Ile

p.T38I

P39687

protein_coding

deleterious(0.02)

possibly_damaging(0.879)

TCGA-AX-A3G8-01

Endometrium

uterine corpus endometrioid 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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