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:0008380	Colorectum	AD	RNA splicing	169/3918	434/18723	3.59e-18	2.04e-15	169
GO:0000377	Colorectum	AD	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000398	Colorectum	AD	mRNA splicing, via spliceosome	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000375	Colorectum	AD	RNA splicing, via transesterification reactions	131/3918	324/18723	7.11e-16	2.22e-13	131
GO:1903311	Colorectum	AD	regulation of mRNA metabolic process	117/3918	288/18723	1.69e-14	4.23e-12	117
GO:0043484	Colorectum	AD	regulation of RNA splicing	70/3918	148/18723	6.47e-13	1.16e-10	70
GO:0048024	Colorectum	AD	regulation of mRNA splicing, via spliceosome	50/3918	101/18723	1.62e-10	1.56e-08	50
GO:0050684	Colorectum	AD	regulation of mRNA processing	61/3918	137/18723	4.23e-10	3.58e-08	61
GO:0000910	Colorectum	AD	cytokinesis	59/3918	173/18723	3.74e-05	6.75e-04	59
GO:0061640	Colorectum	AD	cytoskeleton-dependent cytokinesis	37/3918	100/18723	1.58e-04	2.20e-03	37
GO:0000281	Colorectum	AD	mitotic cytokinesis	25/3918	71/18723	3.77e-03	2.65e-02	25
GO:00083802	Colorectum	MSS	RNA splicing	159/3467	434/18723	1.75e-19	1.22e-16	159
GO:19033112	Colorectum	MSS	regulation of mRNA metabolic process	115/3467	288/18723	1.23e-17	6.41e-15	115
GO:00003772	Colorectum	MSS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003982	Colorectum	MSS	mRNA splicing, via spliceosome	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003752	Colorectum	MSS	RNA splicing, via transesterification reactions	122/3467	324/18723	2.75e-16	8.58e-14	122
GO:00434842	Colorectum	MSS	regulation of RNA splicing	66/3467	148/18723	2.44e-13	5.25e-11	66
GO:00506842	Colorectum	MSS	regulation of mRNA processing	57/3467	137/18723	2.88e-10	2.68e-08	57
GO:00480242	Colorectum	MSS	regulation of mRNA splicing, via spliceosome	46/3467	101/18723	4.20e-10	3.49e-08	46
GO:00009102	Colorectum	MSS	cytokinesis	49/3467	173/18723	1.02e-03	1.02e-02	49

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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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