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: SMC6

Gene summary for SMC6

Gene summary.

Gene information	Species	Human
	Gene symbol	SMC6
	Gene ID	79677
	Gene name	structural maintenance of chromosomes 6
	Gene Alias	SMC-6
	Cytomap	2p24.2
	Gene Type	protein-coding
	GO ID	GO:0000722
	UniProtAcc	Q96SB8

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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
79677	SMC6	CA_HPV_1	Human	Cervix	CC	1.40e-05	1.93e-01	0.0264
79677	SMC6	CCI_1	Human	Cervix	CC	6.73e-03	8.19e-01	0.528
79677	SMC6	CCI_2	Human	Cervix	CC	5.15e-10	1.01e+00	0.5249
79677	SMC6	CCI_3	Human	Cervix	CC	4.28e-08	6.74e-01	0.516
79677	SMC6	sample3	Human	Cervix	CC	4.48e-03	2.44e-01	0.1387
79677	SMC6	T3	Human	Cervix	CC	4.49e-03	2.56e-01	0.1389
79677	SMC6	LZE4T	Human	Esophagus	ESCC	4.08e-15	4.42e-01	0.0811
79677	SMC6	LZE7T	Human	Esophagus	ESCC	8.22e-08	4.45e-01	0.0667
79677	SMC6	LZE8T	Human	Esophagus	ESCC	2.56e-12	1.29e-01	0.067
79677	SMC6	LZE20T	Human	Esophagus	ESCC	3.25e-07	3.09e-02	0.0662
79677	SMC6	LZE22D1	Human	Esophagus	HGIN	1.33e-02	-4.45e-02	0.0595
79677	SMC6	LZE22T	Human	Esophagus	ESCC	1.70e-03	2.01e-01	0.068
79677	SMC6	LZE24T	Human	Esophagus	ESCC	1.53e-13	4.31e-01	0.0596
79677	SMC6	LZE21T	Human	Esophagus	ESCC	1.86e-08	5.38e-01	0.0655
79677	SMC6	LZE6T	Human	Esophagus	ESCC	1.87e-05	3.19e-02	0.0845
79677	SMC6	P1T-E	Human	Esophagus	ESCC	1.25e-06	5.88e-01	0.0875
79677	SMC6	P2T-E	Human	Esophagus	ESCC	1.46e-32	7.12e-01	0.1177
79677	SMC6	P4T-E	Human	Esophagus	ESCC	2.55e-30	7.31e-01	0.1323
79677	SMC6	P5T-E	Human	Esophagus	ESCC	5.47e-13	2.89e-01	0.1327
79677	SMC6	P8T-E	Human	Esophagus	ESCC	4.19e-19	2.22e-01	0.0889

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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
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:20001423	Oral cavity	OSCC	regulation of DNA-templated transcription, initiation	26/7305	40/18723	7.79e-04	4.23e-03	26
GO:20001442	Oral cavity	OSCC	positive regulation of DNA-templated transcription, initiation	21/7305	31/18723	1.13e-03	5.75e-03	21
GO:007084116	Oral cavity	OSCC	inclusion body assembly	17/7305	24/18723	1.59e-03	7.56e-03	17
GO:00602602	Oral cavity	OSCC	regulation of transcription initiation from RNA polymerase II promoter	21/7305	33/18723	3.63e-03	1.51e-02	21
GO:0000725	Oral cavity	OSCC	recombinational repair	70/7305	140/18723	5.22e-03	2.03e-02	70
GO:0000724	Oral cavity	OSCC	double-strand break repair via homologous recombination	69/7305	138/18723	5.52e-03	2.14e-02	69
GO:00903983	Oral cavity	OSCC	cellular senescence	48/7305	93/18723	9.03e-03	3.26e-02	48
GO:00602611	Oral cavity	OSCC	positive regulation of transcription initiation from RNA polymerase II promoter	16/7305	25/18723	1.00e-02	3.49e-02	16
GO:0010498110	Oral cavity	LP	proteasomal protein catabolic process	224/4623	490/18723	9.57e-25	4.00e-22	224
GO:0043161110	Oral cavity	LP	proteasome-mediated ubiquitin-dependent protein catabolic process	190/4623	412/18723	1.08e-21	2.93e-19	190
GO:0034976110	Oral cavity	LP	response to endoplasmic reticulum stress	133/4623	256/18723	3.84e-21	9.24e-19	133
GO:0042176110	Oral cavity	LP	regulation of protein catabolic process	177/4623	391/18723	3.00e-19	5.87e-17	177
GO:0045862110	Oral cavity	LP	positive regulation of proteolysis	165/4623	372/18723	5.40e-17	8.46e-15	165
GO:1903362110	Oral cavity	LP	regulation of cellular protein catabolic process	119/4623	255/18723	1.52e-14	1.76e-12	119
GO:1903050110	Oral cavity	LP	regulation of proteolysis involved in cellular protein catabolic process	101/4623	221/18723	7.00e-12	5.48e-10	101
GO:0061136110	Oral cavity	LP	regulation of proteasomal protein catabolic process	89/4623	187/18723	8.05e-12	6.15e-10	89
GO:003043313	Oral cavity	LP	ubiquitin-dependent ERAD pathway	50/4623	85/18723	2.12e-11	1.48e-09	50
GO:0009896110	Oral cavity	LP	positive regulation of catabolic process	187/4623	492/18723	2.30e-11	1.58e-09	187
GO:0045732110	Oral cavity	LP	positive regulation of protein catabolic process	103/4623	231/18723	2.68e-11	1.81e-09	103
GO:003650314	Oral cavity	LP	ERAD pathway	57/4623	107/18723	1.99e-10	1.08e-08	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

SMC6

SNV

Missense_Mutation

novel

c.179N>T

p.Ser60Leu

p.S60L

Q96SB8

protein_coding

deleterious(0.01)

possibly_damaging(0.783)

TCGA-5L-AAT0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

SMC6

SNV

Missense_Mutation

rs376248274

c.2819N>A

p.Arg940Gln

p.R940Q

Q96SB8

protein_coding

tolerated(0.22)

possibly_damaging(0.596)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC6

SNV

Missense_Mutation

rs373857118

c.745N>T

p.Arg249Cys

p.R249C

Q96SB8

protein_coding

deleterious(0)

benign(0.133)

TCGA-AR-A0TS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SMC6

SNV

Missense_Mutation

novel

c.1570N>A

p.Glu524Lys

p.E524K

Q96SB8

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

SMC6

SNV

Missense_Mutation

c.2240A>G

p.Glu747Gly

p.E747G

Q96SB8

protein_coding

deleterious(0)

possibly_damaging(0.745)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC6

SNV

Missense_Mutation

c.1694C>T

p.Ser565Phe

p.S565F

Q96SB8

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-EW-A1PB-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

SMC6

SNV

Missense_Mutation

novel

c.1041N>T

p.Met347Ile

p.M347I

Q96SB8

protein_coding

tolerated(1)

benign(0)

TCGA-S3-A6ZH-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

SMC6

insertion

Frame_Shift_Ins

novel

c.1867_1868insATCTTCTAAGTCAT

p.Val623AspfsTer6

p.V623Dfs*6

Q96SB8

protein_coding

TCGA-AQ-A04H-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

SMC6

SNV

Missense_Mutation

novel

c.2837A>G

p.Asp946Gly

p.D946G

Q96SB8

protein_coding

deleterious(0.02)

benign(0.092)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SMC6

SNV

Missense_Mutation

novel

c.2482A>G

p.Thr828Ala

p.T828A

Q96SB8

protein_coding

tolerated(0.45)

benign(0.05)

TCGA-2W-A8YY-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

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