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: SLTM

Gene summary for SLTM

Gene summary.

Gene information	Species	Human
	Gene symbol	SLTM
	Gene ID	79811
	Gene name	SAFB like transcription modulator
	Gene Alias	Met
	Cytomap	15q22.1
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q9NWH9

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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
79811	SLTM	HTA11_3410_2000001011	Human	Colorectum	AD	2.75e-21	-6.90e-01	0.0155
79811	SLTM	HTA11_2487_2000001011	Human	Colorectum	SER	2.79e-06	-5.38e-01	-0.1808
79811	SLTM	HTA11_3361_2000001011	Human	Colorectum	AD	1.45e-04	-5.52e-01	-0.1207
79811	SLTM	HTA11_83_2000001011	Human	Colorectum	SER	1.66e-03	-4.78e-01	-0.1526
79811	SLTM	HTA11_696_2000001011	Human	Colorectum	AD	3.48e-11	-5.22e-01	-0.1464
79811	SLTM	HTA11_866_2000001011	Human	Colorectum	AD	7.86e-14	-5.17e-01	-0.1001
79811	SLTM	HTA11_1391_2000001011	Human	Colorectum	AD	4.55e-02	-3.94e-01	-0.059
79811	SLTM	HTA11_5212_2000001011	Human	Colorectum	AD	1.97e-02	-6.40e-01	-0.2061
79811	SLTM	HTA11_7862_2000001011	Human	Colorectum	AD	2.96e-02	-5.35e-01	-0.0179
79811	SLTM	HTA11_866_3004761011	Human	Colorectum	AD	2.68e-09	-4.73e-01	0.096
79811	SLTM	HTA11_8622_2000001021	Human	Colorectum	SER	7.07e-03	-6.48e-01	0.0528
79811	SLTM	HTA11_10711_2000001011	Human	Colorectum	AD	5.68e-07	-5.85e-01	0.0338
79811	SLTM	HTA11_7696_3000711011	Human	Colorectum	AD	4.57e-08	-4.46e-01	0.0674
79811	SLTM	HTA11_6818_2000001021	Human	Colorectum	AD	1.62e-03	-5.45e-01	0.0588
79811	SLTM	HTA11_99999971662_82457	Human	Colorectum	MSS	4.49e-06	-4.67e-01	0.3859
79811	SLTM	HTA11_99999973899_84307	Human	Colorectum	MSS	5.27e-04	-5.19e-01	0.2585
79811	SLTM	HTA11_99999974143_84620	Human	Colorectum	MSS	5.03e-19	-6.01e-01	0.3005
79811	SLTM	A015-C-203	Human	Colorectum	FAP	3.06e-22	-1.93e-01	-0.1294
79811	SLTM	A015-C-204	Human	Colorectum	FAP	9.61e-03	4.04e-02	-0.0228
79811	SLTM	A002-C-201	Human	Colorectum	FAP	2.32e-09	-7.90e-02	0.0324

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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
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
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:1903311	Colorectum	AD	regulation of mRNA metabolic process	117/3918	288/18723	1.69e-14	4.23e-12	117
GO:0050684	Colorectum	AD	regulation of mRNA processing	61/3918	137/18723	4.23e-10	3.58e-08	61
GO:19033111	Colorectum	SER	regulation of mRNA metabolic process	78/2897	288/18723	2.61e-07	1.43e-05	78
GO:00506841	Colorectum	SER	regulation of mRNA processing	42/2897	137/18723	5.57e-06	2.01e-04	42
GO:19033112	Colorectum	MSS	regulation of mRNA metabolic process	115/3467	288/18723	1.23e-17	6.41e-15	115
GO:00506842	Colorectum	MSS	regulation of mRNA processing	57/3467	137/18723	2.88e-10	2.68e-08	57
GO:19033114	Colorectum	FAP	regulation of mRNA metabolic process	97/2622	288/18723	1.35e-17	4.13e-14	97
GO:00506844	Colorectum	FAP	regulation of mRNA processing	51/2622	137/18723	9.70e-12	4.96e-09	51
GO:19033115	Colorectum	CRC	regulation of mRNA metabolic process	80/2078	288/18723	3.21e-15	6.40e-12	80
GO:00506845	Colorectum	CRC	regulation of mRNA processing	41/2078	137/18723	1.57e-09	5.23e-07	41
GO:190331120	Esophagus	HGIN	regulation of mRNA metabolic process	91/2587	288/18723	5.06e-15	9.78e-13	91
GO:005068419	Esophagus	HGIN	regulation of mRNA processing	55/2587	137/18723	2.17e-14	3.94e-12	55
GO:1903311110	Esophagus	ESCC	regulation of mRNA metabolic process	210/8552	288/18723	3.25e-21	5.56e-19	210
GO:0050684110	Esophagus	ESCC	regulation of mRNA processing	109/8552	137/18723	3.51e-16	2.59e-14	109
GO:19033116	Liver	NAFLD	regulation of mRNA metabolic process	66/1882	288/18723	1.06e-10	2.96e-08	66
GO:00506846	Liver	NAFLD	regulation of mRNA processing	33/1882	137/18723	1.47e-06	6.73e-05	33
GO:190331111	Liver	Cirrhotic	regulation of mRNA metabolic process	140/4634	288/18723	1.07e-18	1.91e-16	140
GO:005068411	Liver	Cirrhotic	regulation of mRNA processing	81/4634	137/18723	1.05e-17	1.60e-15	81
GO:190331121	Liver	HCC	regulation of mRNA metabolic process	205/7958	288/18723	3.38e-23	6.90e-21	205
GO:005068421	Liver	HCC	regulation of mRNA processing	106/7958	137/18723	7.64e-17	7.12e-15	106

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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

SLTM

SNV

Missense_Mutation

c.507N>T

p.Glu169Asp

p.E169D

Q9NWH9

protein_coding

tolerated(0.36)

benign(0)

TCGA-A2-A0CM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SLTM

SNV

Missense_Mutation

novel

c.2596N>T

p.His866Tyr

p.H866Y

Q9NWH9

protein_coding

deleterious(0.03)

probably_damaging(0.977)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SLTM

SNV

Missense_Mutation

c.1277N>A

p.Cys426Tyr

p.C426Y

Q9NWH9

protein_coding

deleterious(0.01)

probably_damaging(0.999)

TCGA-BH-A204-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SLTM

SNV

Missense_Mutation

rs775663177

c.2377C>T

p.Arg793Trp

p.R793W

Q9NWH9

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-E9-A5UO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SLTM

SNV

Missense_Mutation

novel

c.1360N>A

p.Leu454Met

p.L454M

Q9NWH9

protein_coding

tolerated(0.22)

benign(0.025)

TCGA-GM-A2DL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

SLTM

SNV

Missense_Mutation

novel

c.1018N>G

p.Lys340Glu

p.K340E

Q9NWH9

protein_coding

deleterious(0.04)

probably_damaging(0.985)

TCGA-JL-A3YW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SLTM

insertion

In_Frame_Ins

novel

c.1306_1307insGTAAGAAAATAA

p.Ser435_Thr436insSerLysLysIle

p.S435_T436insSKKI

Q9NWH9

protein_coding

TCGA-A8-A0A1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

SLTM

insertion

In_Frame_Ins

novel

c.1324_1325insAAAATAAATCCTTAC

p.Ile442delinsLysAsnLysSerLeuLeu

p.I442delinsKNKSLL

Q9NWH9

protein_coding

TCGA-AR-A0TU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Doxorubicin

SLTM

insertion

Frame_Shift_Ins

novel

c.1530_1531insCCTGGACTCTTGGAACCTAAGG

p.Glu511ProfsTer16

p.E511Pfs*16

Q9NWH9

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SLTM

insertion

Nonsense_Mutation

novel

c.403_404insGAAAAAAGCCTTAAAACTT

p.Glu135GlyfsTer5

p.E135Gfs*5

Q9NWH9

protein_coding

TCGA-AR-A0U0-01

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

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