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: SMC4

Gene summary for SMC4

Gene summary.

Gene information	Species	Human
	Gene symbol	SMC4
	Gene ID	10051
	Gene name	structural maintenance of chromosomes 4
	Gene Alias	CAP-C
	Cytomap	3q25.33
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	Q58F29

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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
10051	SMC4	P10_cSCC	Human	Skin	cSCC	1.19e-20	1.11e+00	0.1017
10051	SMC4	cSCC_p9	Human	Skin	cSCC	1.68e-02	8.32e-02	-0.1991
10051	SMC4	male-WTA	Human	Thyroid	PTC	6.18e-23	1.05e-01	0.1037
10051	SMC4	PTC01	Human	Thyroid	PTC	2.34e-12	6.26e-02	0.1899
10051	SMC4	PTC03	Human	Thyroid	PTC	3.47e-06	2.15e-01	0.1784
10051	SMC4	PTC04	Human	Thyroid	PTC	6.67e-08	1.85e-01	0.1927
10051	SMC4	PTC05	Human	Thyroid	PTC	2.72e-08	5.43e-01	0.2065
10051	SMC4	PTC06	Human	Thyroid	PTC	9.26e-13	5.01e-01	0.2057
10051	SMC4	PTC07	Human	Thyroid	PTC	2.94e-11	2.27e-01	0.2044
10051	SMC4	ATC08	Human	Thyroid	ATC	2.00e-02	3.52e-02	0.0541
10051	SMC4	ATC11	Human	Thyroid	ATC	3.15e-05	1.25e+00	0.3386
10051	SMC4	ATC12	Human	Thyroid	ATC	2.34e-29	1.18e+00	0.34
10051	SMC4	ATC13	Human	Thyroid	ATC	3.85e-22	4.54e-01	0.34
10051	SMC4	ATC2	Human	Thyroid	ATC	2.42e-12	2.18e+00	0.34
10051	SMC4	ATC3	Human	Thyroid	ATC	1.10e-07	8.58e-01	0.338
10051	SMC4	ATC4	Human	Thyroid	ATC	1.03e-35	1.54e+00	0.34
10051	SMC4	ATC5	Human	Thyroid	ATC	2.51e-28	6.28e-01	0.34

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:004217610	Cervix	CC	regulation of protein catabolic process	104/2311	391/18723	9.39e-15	9.36e-12	104
GO:004586210	Cervix	CC	positive regulation of proteolysis	95/2311	372/18723	1.84e-12	6.86e-10	95
GO:190336210	Cervix	CC	regulation of cellular protein catabolic process	72/2311	255/18723	5.98e-12	2.10e-09	72
GO:004573210	Cervix	CC	positive regulation of protein catabolic process	65/2311	231/18723	7.44e-11	1.39e-08	65
GO:001049810	Cervix	CC	proteasomal protein catabolic process	111/2311	490/18723	8.98e-11	1.58e-08	111
GO:000989610	Cervix	CC	positive regulation of catabolic process	109/2311	492/18723	5.26e-10	6.99e-08	109
GO:190305010	Cervix	CC	regulation of proteolysis involved in cellular protein catabolic process	60/2311	221/18723	1.82e-09	1.98e-07	60
GO:004316110	Cervix	CC	proteasome-mediated ubiquitin-dependent protein catabolic process	91/2311	412/18723	1.65e-08	1.25e-06	91
GO:003133110	Cervix	CC	positive regulation of cellular catabolic process	91/2311	427/18723	9.64e-08	5.25e-06	91
GO:190336410	Cervix	CC	positive regulation of cellular protein catabolic process	43/2311	155/18723	1.80e-07	8.28e-06	43
GO:006113610	Cervix	CC	regulation of proteasomal protein catabolic process	48/2311	187/18723	4.63e-07	1.77e-05	48
GO:19030528	Cervix	CC	positive regulation of proteolysis involved in cellular protein catabolic process	34/2311	133/18723	2.28e-05	4.01e-04	34
GO:00017018	Cervix	CC	in utero embryonic development	71/2311	367/18723	7.21e-05	1.00e-03	71
GO:19018008	Cervix	CC	positive regulation of proteasomal protein catabolic process	29/2311	114/18723	9.71e-05	1.27e-03	29
GO:01400143	Cervix	CC	mitotic nuclear division	50/2311	287/18723	7.27e-03	3.91e-02	50
GO:00482851	Cervix	CC	organelle fission	78/2311	488/18723	9.70e-03	4.79e-02	78
GO:0042176	Colorectum	AD	regulation of protein catabolic process	160/3918	391/18723	1.06e-19	7.34e-17	160
GO:0009896	Colorectum	AD	positive regulation of catabolic process	180/3918	492/18723	4.33e-16	1.94e-13	180
GO:1903362	Colorectum	AD	regulation of cellular protein catabolic process	109/3918	255/18723	2.14e-15	6.08e-13	109
GO:0010498	Colorectum	AD	proteasomal protein catabolic process	174/3918	490/18723	3.18e-14	7.66e-12	174

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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

SMC4

SNV

Missense_Mutation

c.160N>C

p.Asp54His

p.D54H

Q9NTJ3

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A8-A094-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC4

SNV

Missense_Mutation

novel

c.1980N>C

p.Arg660Ser

p.R660S

Q9NTJ3

protein_coding

tolerated(0.21)

benign(0.079)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC4

SNV

Missense_Mutation

rs753147258

c.641N>A

p.Arg214Gln

p.R214Q

Q9NTJ3

protein_coding

deleterious(0)

benign(0.315)

TCGA-BH-A18P-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMC4

SNV

Missense_Mutation

c.2726N>G

p.Ile909Arg

p.I909R

Q9NTJ3

protein_coding

deleterious(0)

probably_damaging(0.917)

TCGA-C8-A12W-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SMC4

SNV

Missense_Mutation

rs748833024

c.2083N>C

p.Asp695His

p.D695H

Q9NTJ3

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-D8-A1JC-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

SMC4

SNV

Missense_Mutation

c.1189N>A

p.Asp397Asn

p.D397N

Q9NTJ3

protein_coding

deleterious(0.03)

possibly_damaging(0.658)

TCGA-JL-A3YW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMC4

SNV

Missense_Mutation

c.3253N>A

p.Glu1085Lys

p.E1085K

Q9NTJ3

protein_coding

tolerated(0.29)

benign(0.009)

TCGA-C5-A1MK-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

carboplatin

SMC4

SNV

Missense_Mutation

novel

c.606N>C

p.Lys202Asn

p.K202N

Q9NTJ3

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-C5-A2LZ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Unknown

SMC4

SNV

Missense_Mutation

novel

c.2188C>G

p.Gln730Glu

p.Q730E

Q9NTJ3

protein_coding

tolerated(0.31)

benign(0.009)

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

SMC4

SNV

Missense_Mutation

c.3676N>C

p.Asp1226His

p.D1226H

Q9NTJ3

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-EK-A2PG-01

Cervix

cervical & endocervical cancer

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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