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: ATXN2

Gene summary for ATXN2

Gene summary.

Gene information	Species	Human
	Gene symbol	ATXN2
	Gene ID	6311
	Gene name	ataxin 2
	Gene Alias	ATX2
	Cytomap	12q24.12
	Gene Type	protein-coding
	GO ID	GO:0002090
	UniProtAcc	F8VQP2

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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
6311	ATXN2	CCI_1	Human	Cervix	CC	1.91e-06	9.49e-01	0.528
6311	ATXN2	CCI_2	Human	Cervix	CC	2.61e-12	1.29e+00	0.5249
6311	ATXN2	CCI_3	Human	Cervix	CC	2.94e-14	1.17e+00	0.516
6311	ATXN2	HTA11_3410_2000001011	Human	Colorectum	AD	4.85e-06	-4.32e-01	0.0155
6311	ATXN2	HTA11_347_2000001011	Human	Colorectum	AD	4.47e-07	4.75e-01	-0.1954
6311	ATXN2	HTA11_99999970781_79442	Human	Colorectum	MSS	4.38e-02	-3.10e-01	0.294
6311	ATXN2	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.78e-15	9.36e-01	0.3487
6311	ATXN2	HTA11_99999965104_69814	Human	Colorectum	MSS	3.81e-02	4.11e-01	0.281
6311	ATXN2	HTA11_99999974143_84620	Human	Colorectum	MSS	2.08e-04	-3.86e-01	0.3005
6311	ATXN2	A001-C-207	Human	Colorectum	FAP	1.48e-04	-3.16e-01	0.1278
6311	ATXN2	A015-C-203	Human	Colorectum	FAP	7.35e-33	-5.52e-01	-0.1294
6311	ATXN2	A015-C-204	Human	Colorectum	FAP	6.21e-07	-4.35e-01	-0.0228
6311	ATXN2	A014-C-040	Human	Colorectum	FAP	1.48e-09	-7.78e-01	-0.1184
6311	ATXN2	A002-C-201	Human	Colorectum	FAP	3.98e-16	-4.83e-01	0.0324
6311	ATXN2	A002-C-203	Human	Colorectum	FAP	2.21e-05	-2.21e-01	0.2786
6311	ATXN2	A001-C-119	Human	Colorectum	FAP	2.85e-07	-3.70e-01	-0.1557
6311	ATXN2	A001-C-108	Human	Colorectum	FAP	1.88e-18	-3.17e-01	-0.0272
6311	ATXN2	A002-C-205	Human	Colorectum	FAP	2.14e-28	-5.09e-01	-0.1236
6311	ATXN2	A015-C-006	Human	Colorectum	FAP	1.71e-18	-5.35e-01	-0.0994
6311	ATXN2	A015-C-106	Human	Colorectum	FAP	5.34e-11	-2.82e-01	-0.0511

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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
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
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
Prostate		BPH: Benign Prostatic Hyperplasia
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:000641710	Cervix	CC	regulation of translation	89/2311	468/18723	1.86e-05	3.46e-04	89
GO:00068987	Cervix	CC	receptor-mediated endocytosis	53/2311	244/18723	2.52e-05	4.29e-04	53
GO:00301008	Cervix	CC	regulation of endocytosis	47/2311	211/18723	3.65e-05	5.82e-04	47
GO:00512368	Cervix	CC	establishment of RNA localization	39/2311	166/18723	4.76e-05	7.25e-04	39
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:00431127	Cervix	CC	receptor metabolic process	37/2311	166/18723	2.31e-04	2.58e-03	37
GO:00159318	Cervix	CC	nucleobase-containing compound transport	43/2311	222/18723	1.72e-03	1.30e-02	43
GO:00482597	Cervix	CC	regulation of receptor-mediated endocytosis	24/2311	110/18723	3.62e-03	2.31e-02	24
GO:00316236	Cervix	CC	receptor internalization	24/2311	113/18723	5.18e-03	3.05e-02	24
GO:00339626	Cervix	CC	P-body assembly	7/2311	21/18723	1.04e-02	4.97e-02	7
GO:0043112	Colorectum	AD	receptor metabolic process	62/3918	166/18723	8.18e-07	2.85e-05	62
GO:0006417	Colorectum	AD	regulation of translation	141/3918	468/18723	1.32e-06	4.22e-05	141
GO:0006403	Colorectum	AD	RNA localization	71/3918	201/18723	1.54e-06	4.76e-05	71
GO:0051236	Colorectum	AD	establishment of RNA localization	58/3918	166/18723	1.95e-05	4.01e-04	58
GO:0015931	Colorectum	AD	nucleobase-containing compound transport	73/3918	222/18723	2.02e-05	4.10e-04	73
GO:0050657	Colorectum	AD	nucleic acid transport	57/3918	163/18723	2.22e-05	4.39e-04	57
GO:0050658	Colorectum	AD	RNA transport	57/3918	163/18723	2.22e-05	4.39e-04	57
GO:0006898	Colorectum	AD	receptor-mediated endocytosis	76/3918	244/18723	1.07e-04	1.59e-03	76

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0502218	Cervix	CC	Pathways of neurodegeneration - multiple diseases	128/1267	476/8465	2.87e-12	9.29e-11	5.50e-11	128
hsa0501418	Cervix	CC	Amyotrophic lateral sclerosis	103/1267	364/8465	1.79e-11	4.47e-10	2.64e-10	103
hsa0501716	Cervix	CC	Spinocerebellar ataxia	35/1267	143/8465	1.77e-03	7.21e-03	4.26e-03	35
hsa0502219	Cervix	CC	Pathways of neurodegeneration - multiple diseases	128/1267	476/8465	2.87e-12	9.29e-11	5.50e-11	128
hsa0501419	Cervix	CC	Amyotrophic lateral sclerosis	103/1267	364/8465	1.79e-11	4.47e-10	2.64e-10	103
hsa0501717	Cervix	CC	Spinocerebellar ataxia	35/1267	143/8465	1.77e-03	7.21e-03	4.26e-03	35
hsa05014	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa05022	Colorectum	AD	Pathways of neurodegeneration - multiple diseases	201/2092	476/8465	4.54e-18	1.27e-16	8.09e-17	201
hsa05017	Colorectum	AD	Spinocerebellar ataxia	60/2092	143/8465	3.78e-06	4.35e-05	2.78e-05	60
hsa050141	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050221	Colorectum	AD	Pathways of neurodegeneration - multiple diseases	201/2092	476/8465	4.54e-18	1.27e-16	8.09e-17	201
hsa050171	Colorectum	AD	Spinocerebellar ataxia	60/2092	143/8465	3.78e-06	4.35e-05	2.78e-05	60
hsa050224	Colorectum	MSS	Pathways of neurodegeneration - multiple diseases	192/1875	476/8465	2.79e-20	1.04e-18	6.36e-19	192
hsa050144	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050174	Colorectum	MSS	Spinocerebellar ataxia	60/1875	143/8465	7.14e-08	1.26e-06	7.71e-07	60
hsa050225	Colorectum	MSS	Pathways of neurodegeneration - multiple diseases	192/1875	476/8465	2.79e-20	1.04e-18	6.36e-19	192
hsa050145	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050175	Colorectum	MSS	Spinocerebellar ataxia	60/1875	143/8465	7.14e-08	1.26e-06	7.71e-07	60
hsa050146	Colorectum	MSI-H	Amyotrophic lateral sclerosis	95/797	364/8465	2.31e-21	1.50e-19	1.26e-19	95
hsa050226	Colorectum	MSI-H	Pathways of neurodegeneration - multiple diseases	107/797	476/8465	1.24e-18	5.72e-17	4.80e-17	107

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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

ATXN2

SNV

Missense_Mutation

novel

c.2126C>T

p.Ser709Phe

p.S709F

Q99700

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.915)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

ATXN2

SNV

Missense_Mutation

rs761520179

c.2810C>T

p.Ser937Leu

p.S937L

Q99700

protein_coding

tolerated(0.1)

probably_damaging(0.977)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

ATXN2

SNV

Missense_Mutation

c.3224N>A

p.Arg1075Lys

p.R1075K

Q99700

protein_coding

deleterious(0)

possibly_damaging(0.621)

TCGA-A8-A08L-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

ATXN2

SNV

Missense_Mutation

c.1024N>C

p.Asp342His

p.D342H

Q99700

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ATXN2

SNV

Missense_Mutation

c.3743A>G

p.Gln1248Arg

p.Q1248R

Q99700

protein_coding

deleterious(0)

benign(0.165)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

ATXN2

SNV

Missense_Mutation

c.1328N>C

p.Gln443Pro

p.Q443P

Q99700

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-B6-A0I8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ATXN2

SNV

Missense_Mutation

c.1326N>A

p.Asn442Lys

p.N442K

Q99700

protein_coding

tolerated(0.43)

benign(0.182)

TCGA-B6-A0I8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ATXN2

SNV

Missense_Mutation

c.3377N>T

p.Thr1126Met

p.T1126M

Q99700

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.925)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ATXN2

SNV

Missense_Mutation

c.1982C>G

p.Pro661Arg

p.P661R

Q99700

protein_coding

deleterious_low_confidence(0)

benign(0.174)

TCGA-C8-A1HN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ATXN2

SNV

Missense_Mutation

rs779112609

c.1541C>T

p.Pro514Leu

p.P514L

Q99700

protein_coding

deleterious(0)

possibly_damaging(0.688)

TCGA-D8-A1XQ-01

Breast

breast invasive 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
6311	ATXN2	NA		TCMDC-125298	CHEMBL581152
6311	ATXN2	NA		9,10-PHENANTHRENEQUINONE	9,10-PHENANTHRENEQUINONE
6311	ATXN2	NA		4'-EPICHAETOVIRIDIN A	CHEMBL1306556
6311	ATXN2	NA		ERBSTATIN	ERBSTATIN
6311	ATXN2	NA		TCMDC-125625	CHEMBL549208
6311	ATXN2	NA		R-N-PROPYLNORAPOMORPHINE	R-N-PROPYLNORAPOMORPHINE
6311	ATXN2	NA		SJ000154295	CHEMBL578502
6311	ATXN2	NA		PYRITHIONE	PYRITHIONE
6311	ATXN2	NA		SANGUINARIUM	SANGUINARIUM
6311	ATXN2	NA		(+/-)-OCTOCLOTHEPIN MALEATE	CHEMBL1256660

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