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: ANP32B

Gene summary for ANP32B

Gene summary.

Gene information	Species	Human
	Gene symbol	ANP32B
	Gene ID	10541
	Gene name	acidic nuclear phosphoprotein 32 family member B
	Gene Alias	APRIL
	Cytomap	9q22.33
	Gene Type	protein-coding
	GO ID	GO:0001944
	UniProtAcc	Q92688

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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
10541	ANP32B	GSM4909281	Human	Breast	IDC	9.69e-28	6.26e-01	0.21
10541	ANP32B	GSM4909282	Human	Breast	IDC	6.53e-19	5.03e-01	-0.0288
10541	ANP32B	GSM4909285	Human	Breast	IDC	3.38e-45	7.78e-01	0.21
10541	ANP32B	GSM4909286	Human	Breast	IDC	1.80e-09	3.38e-01	0.1081
10541	ANP32B	GSM4909288	Human	Breast	IDC	8.94e-09	2.96e-01	0.0988
10541	ANP32B	GSM4909294	Human	Breast	IDC	4.28e-05	-1.80e-01	0.2022
10541	ANP32B	GSM4909296	Human	Breast	IDC	4.70e-11	-9.31e-02	0.1524
10541	ANP32B	GSM4909297	Human	Breast	IDC	1.36e-17	-1.79e-01	0.1517
10541	ANP32B	GSM4909301	Human	Breast	IDC	1.43e-02	-1.43e-01	0.1577
10541	ANP32B	GSM4909311	Human	Breast	IDC	2.04e-30	-3.63e-01	0.1534
10541	ANP32B	GSM4909312	Human	Breast	IDC	1.17e-11	-6.52e-02	0.1552
10541	ANP32B	GSM4909319	Human	Breast	IDC	1.54e-44	-4.20e-01	0.1563
10541	ANP32B	GSM4909320	Human	Breast	IDC	1.64e-05	-4.35e-01	0.1575
10541	ANP32B	GSM4909321	Human	Breast	IDC	2.72e-15	-2.80e-01	0.1559
10541	ANP32B	M1	Human	Breast	IDC	2.59e-03	3.39e-01	0.1577
10541	ANP32B	M2	Human	Breast	IDC	1.67e-13	6.17e-01	0.21
10541	ANP32B	NCCBC14	Human	Breast	DCIS	1.74e-10	1.38e-01	0.2021
10541	ANP32B	NCCBC2	Human	Breast	DCIS	1.66e-04	-1.73e-01	0.1554
10541	ANP32B	NCCBC3	Human	Breast	DCIS	1.13e-09	2.44e-01	0.1198
10541	ANP32B	NCCBC5	Human	Breast	DCIS	2.05e-18	1.20e-01	0.2046

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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:005254812	Liver	Cirrhotic	regulation of endopeptidase activity	172/4634	432/18723	2.12e-12	1.58e-10	172
GO:190495112	Liver	Cirrhotic	positive regulation of establishment of protein localization	135/4634	319/18723	3.20e-12	2.28e-10	135
GO:005122212	Liver	Cirrhotic	positive regulation of protein transport	126/4634	303/18723	6.85e-11	3.77e-09	126
GO:003238811	Liver	Cirrhotic	positive regulation of intracellular transport	92/4634	202/18723	8.60e-11	4.66e-09	92
GO:009031611	Liver	Cirrhotic	positive regulation of intracellular protein transport	77/4634	160/18723	1.17e-10	6.21e-09	77
GO:00432817	Liver	Cirrhotic	regulation of cysteine-type endopeptidase activity involved in apoptotic process	91/4634	209/18723	1.91e-09	7.98e-08	91
GO:20001167	Liver	Cirrhotic	regulation of cysteine-type endopeptidase activity	97/4634	235/18723	1.61e-08	5.99e-07	97
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:004682211	Liver	Cirrhotic	regulation of nucleocytoplasmic transport	51/4634	106/18723	1.54e-07	4.12e-06	51
GO:005116812	Liver	Cirrhotic	nuclear export	67/4634	154/18723	2.57e-07	6.41e-06	67
GO:00109527	Liver	Cirrhotic	positive regulation of peptidase activity	81/4634	197/18723	2.89e-07	7.03e-06	81
GO:00109507	Liver	Cirrhotic	positive regulation of endopeptidase activity	70/4634	179/18723	1.42e-05	1.97e-04	70
GO:00468246	Liver	Cirrhotic	positive regulation of nucleocytoplasmic transport	29/4634	62/18723	1.34e-04	1.31e-03	29
GO:00432806	Liver	Cirrhotic	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	51/4634	129/18723	1.42e-04	1.38e-03	51
GO:00066114	Liver	Cirrhotic	protein export from nucleus	27/4634	57/18723	1.74e-04	1.63e-03	27
GO:00468256	Liver	Cirrhotic	regulation of protein export from nucleus	17/4634	30/18723	1.87e-04	1.74e-03	17
GO:20010566	Liver	Cirrhotic	positive regulation of cysteine-type endopeptidase activity	55/4634	148/18723	5.12e-04	4.06e-03	55
GO:00069191	Liver	Cirrhotic	activation of cysteine-type endopeptidase activity involved in apoptotic process	31/4634	78/18723	2.43e-03	1.46e-02	31
GO:003238621	Liver	HCC	regulation of intracellular transport	231/7958	337/18723	1.99e-22	3.40e-20	231

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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

ANP32B

SNV

Missense_Mutation

novel

c.185A>T

p.Lys62Met

p.K62M

Q92688

protein_coding

deleterious(0)

probably_damaging(0.931)

TCGA-A2-A4S3-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

novel

c.178N>A

p.Leu60Ile

p.L60I

Q92688

protein_coding

deleterious(0.03)

possibly_damaging(0.818)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

c.616G>A

p.Asp206Asn

p.D206N

Q92688

protein_coding

tolerated(0.16)

benign(0.011)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

c.697N>C

p.Glu233Gln

p.E233Q

Q92688

protein_coding

tolerated(0.1)

benign(0.259)

TCGA-IR-A3LH-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ANP32B

SNV

Missense_Mutation

c.241G>C

p.Asp81His

p.D81H

Q92688

protein_coding

deleterious(0.02)

possibly_damaging(0.869)

TCGA-MY-A5BD-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

ANP32B

SNV

Missense_Mutation

c.623N>G

p.Glu208Gly

p.E208G

Q92688

protein_coding

tolerated(0.17)

probably_damaging(0.932)

TCGA-AD-6895-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

ANP32B

SNV

Missense_Mutation

c.179N>G

p.Leu60Arg

p.L60R

Q92688

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AZ-5403-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

rs761031783

c.619N>A

p.Asp207Asn

p.D207N

Q92688

protein_coding

tolerated(0.23)

benign(0.142)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

c.753N>G

p.Asp251Glu

p.D251E

Q92688

protein_coding

deleterious_low_confidence(0)

benign(0.225)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ANP32B

SNV

Missense_Mutation

novel

c.598N>A

p.Val200Ile

p.V200I

Q92688

protein_coding

tolerated(0.42)

benign(0.001)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

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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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