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: SAMSN1

Gene summary for SAMSN1

Gene summary.

Gene information	Species	Human
	Gene symbol	SAMSN1
	Gene ID	64092
	Gene name	SAM domain, SH3 domain and nuclear localization signals 1
	Gene Alias	HACS1
	Cytomap	21q11.2
	Gene Type	protein-coding
	GO ID	GO:0001775
	UniProtAcc	Q9NSI8

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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
64092	SAMSN1	CA_HPV_1	Human	Cervix	CC	1.40e-06	-4.84e-01	0.0264
64092	SAMSN1	CA_HPV_3	Human	Cervix	CC	2.56e-04	-3.96e-01	0.0414
64092	SAMSN1	N_HPV_2	Human	Cervix	N_HPV	2.74e-05	-1.35e-01	-0.0131
64092	SAMSN1	CCI_1	Human	Cervix	CC	2.95e-05	-7.59e-01	0.528
64092	SAMSN1	CCI_2	Human	Cervix	CC	1.10e-03	-7.53e-01	0.5249
64092	SAMSN1	CCI_3	Human	Cervix	CC	1.06e-07	-7.04e-01	0.516
64092	SAMSN1	CCII_1	Human	Cervix	CC	5.99e-15	-8.40e-01	0.3249
64092	SAMSN1	Tumor	Human	Cervix	CC	8.28e-32	-8.40e-01	0.1241
64092	SAMSN1	sample1	Human	Cervix	CC	2.19e-12	-8.40e-01	0.0959
64092	SAMSN1	sample3	Human	Cervix	CC	1.02e-27	-8.27e-01	0.1387
64092	SAMSN1	H2	Human	Cervix	HSIL_HPV	5.10e-23	-7.69e-01	0.0632
64092	SAMSN1	L1	Human	Cervix	CC	2.24e-14	-8.30e-01	0.0802
64092	SAMSN1	T1	Human	Cervix	CC	3.82e-23	-8.19e-01	0.0918
64092	SAMSN1	T2	Human	Cervix	CC	1.33e-06	-8.40e-01	0.0709
64092	SAMSN1	T3	Human	Cervix	CC	1.36e-27	-8.33e-01	0.1389
64092	SAMSN1	LZE4T	Human	Esophagus	ESCC	1.60e-05	7.21e-01	0.0811
64092	SAMSN1	LZE6T	Human	Esophagus	ESCC	2.46e-13	1.15e+00	0.0845
64092	SAMSN1	C21	Human	Oral cavity	OSCC	1.15e-10	4.00e-01	0.2678
64092	SAMSN1	C30	Human	Oral cavity	OSCC	7.46e-06	1.83e-01	0.3055
64092	SAMSN1	C38	Human	Oral cavity	OSCC	1.43e-07	1.09e+00	0.172

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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
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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

∗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:00026837	Cervix	CC	negative regulation of immune system process	94/2311	434/18723	2.63e-08	1.87e-06	94
GO:004593610	Cervix	CC	negative regulation of phosphate metabolic process	88/2311	441/18723	2.92e-06	8.27e-05	88
GO:001056310	Cervix	CC	negative regulation of phosphorus metabolic process	88/2311	442/18723	3.21e-06	8.77e-05	88
GO:004232610	Cervix	CC	negative regulation of phosphorylation	77/2311	385/18723	1.09e-05	2.38e-04	77
GO:0051250	Cervix	CC	negative regulation of lymphocyte activation	39/2311	157/18723	1.23e-05	2.57e-04	39
GO:000193310	Cervix	CC	negative regulation of protein phosphorylation	69/2311	342/18723	2.29e-05	4.01e-04	69
GO:0002695	Cervix	CC	negative regulation of leukocyte activation	43/2311	187/18723	3.47e-05	5.60e-04	43
GO:0050866	Cervix	CC	negative regulation of cell activation	44/2311	210/18723	2.76e-04	3.02e-03	44
GO:00507773	Cervix	CC	negative regulation of immune response	41/2311	194/18723	3.63e-04	3.76e-03	41
GO:0002819	Cervix	CC	regulation of adaptive immune response	35/2311	183/18723	5.38e-03	3.11e-02	35
GO:000268312	Cervix	HSIL_HPV	negative regulation of immune system process	39/737	434/18723	1.51e-06	6.60e-05	39
GO:004593615	Cervix	HSIL_HPV	negative regulation of phosphate metabolic process	36/737	441/18723	3.12e-05	8.94e-04	36
GO:001056315	Cervix	HSIL_HPV	negative regulation of phosphorus metabolic process	36/737	442/18723	3.27e-05	9.16e-04	36
GO:000193314	Cervix	HSIL_HPV	negative regulation of protein phosphorylation	30/737	342/18723	3.80e-05	1.03e-03	30
GO:004232614	Cervix	HSIL_HPV	negative regulation of phosphorylation	32/737	385/18723	6.03e-05	1.44e-03	32
GO:0050864	Cervix	HSIL_HPV	regulation of B cell activation	19/737	198/18723	3.19e-04	5.15e-03	19
GO:00028191	Cervix	HSIL_HPV	regulation of adaptive immune response	17/737	183/18723	9.31e-04	1.18e-02	17
GO:00026951	Cervix	HSIL_HPV	negative regulation of leukocyte activation	17/737	187/18723	1.18e-03	1.41e-02	17
GO:00512501	Cervix	HSIL_HPV	negative regulation of lymphocyte activation	15/737	157/18723	1.37e-03	1.56e-02	15
GO:00508661	Cervix	HSIL_HPV	negative regulation of cell activation	18/737	210/18723	1.68e-03	1.81e-02	18

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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

SAMSN1

SNV

Missense_Mutation

c.662G>T

p.Arg221Leu

p.R221L

Q9NSI8

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A2-A0EM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

SAMSN1

SNV

Missense_Mutation

c.1138G>A

p.Glu380Lys

p.E380K

Q9NSI8

protein_coding

tolerated(0.1)

benign(0.015)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

SAMSN1

SNV

Missense_Mutation

c.1049N>C

p.Ile350Thr

p.I350T

Q9NSI8

protein_coding

tolerated(0.43)

possibly_damaging(0.466)

TCGA-EW-A2FW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

exemestane

SAMSN1

SNV

Missense_Mutation

novel

c.200N>G

p.Ser67Cys

p.S67C

Q9NSI8

protein_coding

tolerated_low_confidence(0.19)

benign(0)

TCGA-LL-A5YL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SAMSN1

insertion

Frame_Shift_Ins

novel

c.1016_1017insGAAAGCATGCAGGCATTTTACTTGT

p.Asp340LysfsTer20

p.D340Kfs*20

Q9NSI8

protein_coding

TCGA-AO-A03T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SAMSN1

insertion

Nonsense_Mutation

novel

c.370_371insTTTCTGAGTGTCAGTTTCTTCTGTTAAAATG

p.Gln124LeufsTer11

p.Q124Lfs*11

Q9NSI8

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SAMSN1

SNV

Missense_Mutation

novel

c.710N>C

p.Arg237Thr

p.R237T

Q9NSI8

protein_coding

deleterious(0)

benign(0.382)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

SAMSN1

SNV

Missense_Mutation

novel

c.493N>C

p.Asp165His

p.D165H

Q9NSI8

protein_coding

deleterious(0.01)

possibly_damaging(0.66)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SAMSN1

SNV

Missense_Mutation

novel

c.1114G>A

p.Glu372Lys

p.E372K

Q9NSI8

protein_coding

deleterious(0.01)

benign(0.006)

TCGA-JX-A3Q0-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

SAMSN1

SNV

Missense_Mutation

novel

c.1152N>T

p.Glu384Asp

p.E384D

Q9NSI8

protein_coding

tolerated(0.59)

benign(0.036)

TCGA-UC-A7PG-06

Cervix

cervical & endocervical cancer

Female

<65

III/IV

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

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