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:00903163	Colorectum	MSI-H	positive regulation of intracellular protein transport	24/1319	160/18723	3.51e-04	8.20e-03	24
GO:00109503	Colorectum	MSI-H	positive regulation of endopeptidase activity	23/1319	179/18723	3.75e-03	4.37e-02	23
GO:00468253	Colorectum	MSI-H	regulation of protein export from nucleus	7/1319	30/18723	4.10e-03	4.67e-02	7
GO:19049514	Colorectum	FAP	positive regulation of establishment of protein localization	82/2622	319/18723	1.83e-08	1.87e-06	82
GO:00512224	Colorectum	FAP	positive regulation of protein transport	78/2622	303/18723	3.79e-08	3.23e-06	78
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:00323884	Colorectum	FAP	positive regulation of intracellular transport	53/2622	202/18723	2.99e-06	1.10e-04	53
GO:00468224	Colorectum	FAP	regulation of nucleocytoplasmic transport	32/2622	106/18723	1.30e-05	3.53e-04	32
GO:00903164	Colorectum	FAP	positive regulation of intracellular protein transport	43/2622	160/18723	1.30e-05	3.53e-04	43
GO:00323864	Colorectum	FAP	regulation of intracellular transport	75/2622	337/18723	2.38e-05	5.60e-04	75
GO:00458624	Colorectum	FAP	positive regulation of proteolysis	81/2622	372/18723	2.64e-05	6.08e-04	81
GO:00331574	Colorectum	FAP	regulation of intracellular protein transport	55/2622	229/18723	3.20e-05	7.20e-04	55
GO:00063253	Colorectum	FAP	chromatin organization	84/2622	409/18723	1.62e-04	2.47e-03	84
GO:00468244	Colorectum	FAP	positive regulation of nucleocytoplasmic transport	20/2622	62/18723	1.95e-04	2.83e-03	20
GO:00511684	Colorectum	FAP	nuclear export	37/2622	154/18723	5.81e-04	6.46e-03	37
GO:00432814	Colorectum	FAP	regulation of cysteine-type endopeptidase activity involved in apoptotic process	46/2622	209/18723	1.06e-03	1.03e-02	46
GO:20001164	Colorectum	FAP	regulation of cysteine-type endopeptidase activity	50/2622	235/18723	1.45e-03	1.31e-02	50
GO:00525474	Colorectum	FAP	regulation of peptidase activity	86/2622	461/18723	2.98e-03	2.27e-02	86
GO:00109524	Colorectum	FAP	positive regulation of peptidase activity	41/2622	197/18723	5.49e-03	3.56e-02	41

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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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