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: SAMHD1

Gene summary for SAMHD1

Gene summary.

Gene information	Species	Human
	Gene symbol	SAMHD1
	Gene ID	25939
	Gene name	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1
	Gene Alias	CHBL2
	Cytomap	20q11.23
	Gene Type	protein-coding
	GO ID	GO:0000724
	UniProtAcc	Q59H15

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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
25939	SAMHD1	HTA11_2487_2000001011	Human	Colorectum	SER	1.18e-15	7.70e-01	-0.1808
25939	SAMHD1	HTA11_1938_2000001011	Human	Colorectum	AD	6.05e-03	4.16e-01	-0.0811
25939	SAMHD1	HTA11_78_2000001011	Human	Colorectum	AD	1.18e-02	3.31e-01	-0.1088
25939	SAMHD1	HTA11_347_2000001011	Human	Colorectum	AD	2.58e-47	1.21e+00	-0.1954
25939	SAMHD1	HTA11_411_2000001011	Human	Colorectum	SER	4.18e-05	1.10e+00	-0.2602
25939	SAMHD1	HTA11_3361_2000001011	Human	Colorectum	AD	3.31e-05	4.74e-01	-0.1207
25939	SAMHD1	HTA11_83_2000001011	Human	Colorectum	SER	1.47e-21	1.03e+00	-0.1526
25939	SAMHD1	HTA11_696_2000001011	Human	Colorectum	AD	1.76e-23	7.91e-01	-0.1464
25939	SAMHD1	HTA11_866_2000001011	Human	Colorectum	AD	2.84e-18	6.60e-01	-0.1001
25939	SAMHD1	HTA11_1391_2000001011	Human	Colorectum	AD	1.15e-11	5.64e-01	-0.059
25939	SAMHD1	HTA11_2992_2000001011	Human	Colorectum	SER	4.06e-02	6.43e-01	-0.1706
25939	SAMHD1	HTA11_5212_2000001011	Human	Colorectum	AD	4.08e-04	7.20e-01	-0.2061
25939	SAMHD1	HTA11_546_2000001011	Human	Colorectum	AD	2.88e-09	8.09e-01	-0.0842
25939	SAMHD1	HTA11_10623_2000001011	Human	Colorectum	AD	5.18e-07	7.47e-01	-0.0177
25939	SAMHD1	HTA11_7696_3000711011	Human	Colorectum	AD	6.18e-03	2.92e-01	0.0674
25939	SAMHD1	HTA11_99999970781_79442	Human	Colorectum	MSS	1.84e-05	3.85e-01	0.294
25939	SAMHD1	HTA11_99999965062_69753	Human	Colorectum	MSI-H	4.80e-04	1.03e+00	0.3487
25939	SAMHD1	HTA11_99999965104_69814	Human	Colorectum	MSS	5.98e-11	6.43e-01	0.281
25939	SAMHD1	HTA11_99999971662_82457	Human	Colorectum	MSS	4.36e-27	1.02e+00	0.3859
25939	SAMHD1	HTA11_99999973899_84307	Human	Colorectum	MSS	3.78e-04	5.77e-01	0.2585

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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
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
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:0006163	Colorectum	AD	purine nucleotide metabolic process	149/3918	396/18723	1.08e-14	2.80e-12	149
GO:0072521	Colorectum	AD	purine-containing compound metabolic process	153/3918	416/18723	4.34e-14	1.01e-11	153
GO:0009117	Colorectum	AD	nucleotide metabolic process	168/3918	489/18723	2.20e-12	3.36e-10	168
GO:0006753	Colorectum	AD	nucleoside phosphate metabolic process	169/3918	497/18723	4.99e-12	6.98e-10	169
GO:0044270	Colorectum	AD	cellular nitrogen compound catabolic process	147/3918	451/18723	3.35e-09	2.23e-07	147
GO:0046700	Colorectum	AD	heterocycle catabolic process	145/3918	445/18723	4.37e-09	2.84e-07	145
GO:0009144	Colorectum	AD	purine nucleoside triphosphate metabolic process	43/3918	88/18723	5.05e-09	3.19e-07	43
GO:0034655	Colorectum	AD	nucleobase-containing compound catabolic process	133/3918	407/18723	1.56e-08	9.12e-07	133
GO:0019439	Colorectum	AD	aromatic compound catabolic process	146/3918	467/18723	7.48e-08	3.84e-06	146
GO:1901361	Colorectum	AD	organic cyclic compound catabolic process	153/3918	495/18723	8.23e-08	4.18e-06	153
GO:0009141	Colorectum	AD	nucleoside triphosphate metabolic process	48/3918	112/18723	1.27e-07	6.02e-06	48
GO:0034340	Colorectum	AD	response to type I interferon	22/3918	58/18723	2.23e-03	1.75e-02	22
GO:0006195	Colorectum	AD	purine nucleotide catabolic process	18/3918	46/18723	3.67e-03	2.60e-02	18
GO:0060337	Colorectum	AD	type I interferon signaling pathway	19/3918	50/18723	4.23e-03	2.91e-02	19
GO:0071357	Colorectum	AD	cellular response to type I interferon	19/3918	52/18723	6.92e-03	4.26e-02	19
GO:0072523	Colorectum	AD	purine-containing compound catabolic process	19/3918	52/18723	6.92e-03	4.26e-02	19
GO:00061631	Colorectum	SER	purine nucleotide metabolic process	109/2897	396/18723	4.26e-10	5.44e-08	109
GO:00725211	Colorectum	SER	purine-containing compound metabolic process	113/2897	416/18723	4.80e-10	5.68e-08	113
GO:00091441	Colorectum	SER	purine nucleoside triphosphate metabolic process	38/2897	88/18723	4.82e-10	5.68e-08	38
GO:00091171	Colorectum	SER	nucleotide metabolic process	122/2897	489/18723	2.50e-08	1.76e-06	122

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05170	Colorectum	AD	Human immunodeficiency virus 1 infection	72/2092	212/8465	1.40e-03	8.46e-03	5.39e-03	72
hsa051701	Colorectum	AD	Human immunodeficiency virus 1 infection	72/2092	212/8465	1.40e-03	8.46e-03	5.39e-03	72
hsa051702	Colorectum	SER	Human immunodeficiency virus 1 infection	58/1580	212/8465	1.08e-03	8.56e-03	6.21e-03	58
hsa051703	Colorectum	SER	Human immunodeficiency virus 1 infection	58/1580	212/8465	1.08e-03	8.56e-03	6.21e-03	58
hsa051704	Colorectum	MSS	Human immunodeficiency virus 1 infection	69/1875	212/8465	2.66e-04	1.98e-03	1.21e-03	69
hsa03250	Colorectum	MSS	Viral life cycle - HIV-1	23/1875	63/8465	6.55e-03	2.64e-02	1.62e-02	23
hsa051705	Colorectum	MSS	Human immunodeficiency virus 1 infection	69/1875	212/8465	2.66e-04	1.98e-03	1.21e-03	69
hsa032501	Colorectum	MSS	Viral life cycle - HIV-1	23/1875	63/8465	6.55e-03	2.64e-02	1.62e-02	23
hsa051706	Colorectum	FAP	Human immunodeficiency virus 1 infection	51/1404	212/8465	2.98e-03	1.29e-02	7.87e-03	51
hsa051707	Colorectum	FAP	Human immunodeficiency virus 1 infection	51/1404	212/8465	2.98e-03	1.29e-02	7.87e-03	51
hsa032509	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa05170210	Esophagus	ESCC	Human immunodeficiency virus 1 infection	147/4205	212/8465	3.37e-09	3.53e-08	1.81e-08	147
hsa046234	Esophagus	ESCC	Cytosolic DNA-sensing pathway	49/4205	75/8465	4.35e-03	1.12e-02	5.74e-03	49
hsa0325014	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa0517038	Esophagus	ESCC	Human immunodeficiency virus 1 infection	147/4205	212/8465	3.37e-09	3.53e-08	1.81e-08	147
hsa0462311	Esophagus	ESCC	Cytosolic DNA-sensing pathway	49/4205	75/8465	4.35e-03	1.12e-02	5.74e-03	49
hsa032502	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
hsa051709	Liver	HCC	Human immunodeficiency virus 1 infection	125/4020	212/8465	4.51e-04	1.94e-03	1.08e-03	125
hsa0325011	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
hsa0517012	Liver	HCC	Human immunodeficiency virus 1 infection	125/4020	212/8465	4.51e-04	1.94e-03	1.08e-03	125

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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

SAMHD1

SNV

Missense_Mutation

c.652N>C

p.Asp218His

p.D218H

Q9Y3Z3

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A094-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SAMHD1

SNV

Missense_Mutation

c.1756N>A

p.Val586Ile

p.V586I

Q9Y3Z3

protein_coding

tolerated(0.51)

benign(0.003)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

SAMHD1

SNV

Missense_Mutation

c.746N>A

p.Gly249Glu

p.G249E

Q9Y3Z3

protein_coding

tolerated(0.23)

benign(0.012)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SAMHD1

SNV

Missense_Mutation

c.1287G>C

p.Glu429Asp

p.E429D

Q9Y3Z3

protein_coding

deleterious(0.05)

benign(0.017)

TCGA-E9-A1N5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SAMHD1

insertion

Frame_Shift_Ins

novel

c.1839_1840insGGAGTGA

p.Ser614GlyfsTer11

p.S614Gfs*11

Q9Y3Z3

protein_coding

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SAMHD1

insertion

Nonsense_Mutation

novel

c.1837_1838insGTGCCAGGTTGGGGTAAAGAGTTGGAGATGATGGC

p.Ala613GlyfsTer6

p.A613Gfs*6

Q9Y3Z3

protein_coding

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SAMHD1

insertion

Nonsense_Mutation

novel

c.1583_1584insGTAGGTGGCCTGTTACTCACAAACTTTGCACAATTTTTTATT

p.Arg528_Ala529insTer

p.R528_A529ins*

Q9Y3Z3

protein_coding

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

SAMHD1

insertion

In_Frame_Ins

novel

c.1610_1611insCCA

p.Val537_Ser538insHis

p.V537_S538insH

Q9Y3Z3

protein_coding

TCGA-AR-A0U2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

SAMHD1

insertion

Frame_Shift_Ins

novel

c.1609_1610insACAATAATGCTAAACAGTA

p.Val537AspfsTer25

p.V537Dfs*25

Q9Y3Z3

protein_coding

TCGA-AR-A0U2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

SAMHD1

SNV

Missense_Mutation

novel

c.486N>G

p.His162Gln

p.H162Q

Q9Y3Z3

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-C5-A8XJ-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

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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
25939	SAMHD1	ENZYME, KINASE		stavudine	STAVUDINE	30273369

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