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: SON

Gene summary for SON

Gene summary.

Gene information	Species	Human
	Gene symbol	SON
	Gene ID	6651
	Gene name	SON DNA and RNA binding protein
	Gene Alias	BASS1
	Cytomap	21q22.11
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	P18583

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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
6651	SON	HTA11_3410_2000001011	Human	Colorectum	AD	5.81e-09	-4.21e-01	0.0155
6651	SON	HTA11_347_2000001011	Human	Colorectum	AD	2.45e-08	4.38e-01	-0.1954
6651	SON	HTA11_99999965104_69814	Human	Colorectum	MSS	2.60e-13	7.54e-01	0.281
6651	SON	A002-C-010	Human	Colorectum	FAP	3.02e-06	-1.11e-01	0.242
6651	SON	A001-C-207	Human	Colorectum	FAP	3.39e-04	1.93e-01	0.1278
6651	SON	A015-C-203	Human	Colorectum	FAP	1.47e-34	1.61e-01	-0.1294
6651	SON	A015-C-204	Human	Colorectum	FAP	2.10e-07	2.04e-01	-0.0228
6651	SON	A014-C-040	Human	Colorectum	FAP	7.23e-05	2.69e-01	-0.1184
6651	SON	A002-C-201	Human	Colorectum	FAP	1.25e-15	2.66e-01	0.0324
6651	SON	A002-C-203	Human	Colorectum	FAP	4.32e-06	2.69e-01	0.2786
6651	SON	A001-C-119	Human	Colorectum	FAP	6.21e-07	1.23e-01	-0.1557
6651	SON	A001-C-108	Human	Colorectum	FAP	1.89e-26	4.21e-01	-0.0272
6651	SON	A002-C-021	Human	Colorectum	FAP	6.28e-06	3.75e-01	0.1171
6651	SON	A002-C-205	Human	Colorectum	FAP	8.06e-30	3.34e-01	-0.1236
6651	SON	A001-C-104	Human	Colorectum	FAP	7.57e-08	3.24e-01	0.0184
6651	SON	A015-C-005	Human	Colorectum	FAP	1.11e-07	3.42e-01	-0.0336
6651	SON	A015-C-006	Human	Colorectum	FAP	1.80e-16	1.37e-01	-0.0994
6651	SON	A015-C-106	Human	Colorectum	FAP	3.21e-15	2.47e-01	-0.0511
6651	SON	A002-C-114	Human	Colorectum	FAP	7.35e-23	2.83e-01	-0.1561
6651	SON	A015-C-104	Human	Colorectum	FAP	9.82e-42	3.09e-01	-0.1899

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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
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:00616405	Oral cavity	OSCC	cytoskeleton-dependent cytokinesis	60/7305	100/18723	1.69e-05	1.67e-04	60
GO:0010389	Oral cavity	OSCC	regulation of G2/M transition of mitotic cell cycle	57/7305	94/18723	1.75e-05	1.71e-04	57
GO:00000774	Oral cavity	OSCC	DNA damage checkpoint	67/7305	115/18723	2.20e-05	2.08e-04	67
GO:00062611	Oral cavity	OSCC	DNA-dependent DNA replication	84/7305	151/18723	2.46e-05	2.30e-04	84
GO:00447744	Oral cavity	OSCC	mitotic DNA integrity checkpoint	52/7305	85/18723	2.86e-05	2.64e-04	52
GO:00447734	Oral cavity	OSCC	mitotic DNA damage checkpoint	50/7305	81/18723	2.87e-05	2.64e-04	50
GO:00062753	Oral cavity	OSCC	regulation of DNA replication	62/7305	107/18723	5.49e-05	4.54e-04	62
GO:1902749	Oral cavity	OSCC	regulation of cell cycle G2/M phase transition	59/7305	102/18723	8.81e-05	6.72e-04	59
GO:0010972	Oral cavity	OSCC	negative regulation of G2/M transition of mitotic cell cycle	38/7305	60/18723	1.17e-04	8.46e-04	38
GO:1902750	Oral cavity	OSCC	negative regulation of cell cycle G2/M phase transition	39/7305	62/18723	1.19e-04	8.54e-04	39
GO:0044818	Oral cavity	OSCC	mitotic G2/M transition checkpoint	28/7305	46/18723	2.19e-03	9.95e-03	28
GO:0007095	Oral cavity	OSCC	mitotic G2 DNA damage checkpoint	21/7305	34/18723	6.02e-03	2.28e-02	21
GO:0008380110	Oral cavity	LP	RNA splicing	237/4623	434/18723	1.82e-41	3.79e-38	237
GO:0000375110	Oral cavity	LP	RNA splicing, via transesterification reactions	181/4623	324/18723	1.36e-33	1.70e-30	181
GO:0000377110	Oral cavity	LP	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	179/4623	320/18723	2.48e-33	2.22e-30	179
GO:0000398110	Oral cavity	LP	mRNA splicing, via spliceosome	179/4623	320/18723	2.48e-33	2.22e-30	179
GO:0043484110	Oral cavity	LP	regulation of RNA splicing	81/4623	148/18723	4.34e-15	5.79e-13	81
GO:005068418	Oral cavity	LP	regulation of mRNA processing	76/4623	137/18723	1.14e-14	1.35e-12	76
GO:190331119	Oral cavity	LP	regulation of mRNA metabolic process	129/4623	288/18723	5.70e-14	6.10e-12	129
GO:0048024110	Oral cavity	LP	regulation of mRNA splicing, via spliceosome	57/4623	101/18723	9.06e-12	6.84e-10	57

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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

SON

SNV

Missense_Mutation

novel

c.220N>C

p.Asp74His

p.D74H

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.999)

TCGA-3C-AALI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Poly E

Complete Response

SON

SNV

Missense_Mutation

c.7184A>G

p.Asp2395Gly

p.D2395G

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.972)

TCGA-A7-A0CE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SON

SNV

Missense_Mutation

c.2183C>A

p.Ser728Tyr

p.S728Y

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.993)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SON

SNV

Missense_Mutation

novel

c.1003N>A

p.Glu335Lys

p.E335K

P18583

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.704)

TCGA-AC-A8OS-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SON

SNV

Missense_Mutation

c.496N>A

p.Ala166Thr

p.A166T

P18583

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.843)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SON

SNV

Missense_Mutation

rs200910529

c.5510N>A

p.Arg1837His

p.R1837H

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.948)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SON

SNV

Missense_Mutation

c.5519C>T

p.Thr1840Ile

p.T1840I

P18583

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.86)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

SON

SNV

Missense_Mutation

c.5680N>C

p.Ser1894Pro

p.S1894P

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.994)

TCGA-BH-A18V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SON

SNV

Missense_Mutation

c.2268N>T

p.Leu756Phe

p.L756F

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.994)

TCGA-C8-A12U-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SON

SNV

Missense_Mutation

c.1169N>G

p.Ser390Cys

p.S390C

P18583

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.963)

TCGA-C8-A26Y-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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