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	GSM4909281	Human	Breast	IDC	7.12e-04	3.36e-01	0.21
10051	SMC4	GSM4909282	Human	Breast	IDC	4.45e-23	6.19e-01	-0.0288
10051	SMC4	GSM4909285	Human	Breast	IDC	2.99e-10	3.58e-01	0.21
10051	SMC4	GSM4909287	Human	Breast	IDC	2.31e-02	2.55e-01	0.2057
10051	SMC4	GSM4909290	Human	Breast	IDC	3.91e-09	3.78e-01	0.2096
10051	SMC4	GSM4909308	Human	Breast	IDC	6.43e-06	2.94e-01	0.158
10051	SMC4	GSM4909311	Human	Breast	IDC	3.51e-04	-1.15e-01	0.1534
10051	SMC4	GSM4909319	Human	Breast	IDC	9.51e-05	3.65e-02	0.1563
10051	SMC4	M1	Human	Breast	IDC	1.28e-03	2.87e-01	0.1577
10051	SMC4	M2	Human	Breast	IDC	5.51e-10	7.55e-01	0.21
10051	SMC4	P2	Human	Breast	IDC	2.18e-05	4.30e-01	0.21
10051	SMC4	DCIS2	Human	Breast	DCIS	1.51e-11	4.79e-03	0.0085
10051	SMC4	CA_HPV_2	Human	Cervix	CC	1.22e-02	2.93e-01	0.0391
10051	SMC4	HSIL_HPV_2	Human	Cervix	HSIL_HPV	1.06e-05	3.19e-01	0.0208
10051	SMC4	CCI_2	Human	Cervix	CC	2.06e-10	1.68e+00	0.5249
10051	SMC4	CCI_3	Human	Cervix	CC	1.87e-11	1.10e+00	0.516
10051	SMC4	sample3	Human	Cervix	CC	2.44e-11	3.91e-01	0.1387
10051	SMC4	H2	Human	Cervix	HSIL_HPV	1.28e-03	2.70e-01	0.0632
10051	SMC4	T1	Human	Cervix	CC	1.55e-02	3.98e-01	0.0918
10051	SMC4	T3	Human	Cervix	CC	1.21e-12	3.88e-01	0.1389

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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:19030521	Colorectum	SER	positive regulation of proteolysis involved in cellular protein catabolic process	47/2897	133/18723	1.30e-08	1.02e-06	47
GO:00431611	Colorectum	SER	proteasome-mediated ubiquitin-dependent protein catabolic process	105/2897	412/18723	7.48e-08	4.70e-06	105
GO:19018001	Colorectum	SER	positive regulation of proteasomal protein catabolic process	38/2897	114/18723	1.65e-06	7.23e-05	38
GO:00017011	Colorectum	SER	in utero embryonic development	77/2897	367/18723	2.77e-03	2.48e-02	77
GO:00421762	Colorectum	MSS	regulation of protein catabolic process	145/3467	391/18723	2.03e-18	1.17e-15	145
GO:00098962	Colorectum	MSS	positive regulation of catabolic process	163/3467	492/18723	3.10e-15	9.22e-13	163
GO:19033622	Colorectum	MSS	regulation of cellular protein catabolic process	99/3467	255/18723	1.90e-14	5.37e-12	99
GO:00104982	Colorectum	MSS	proteasomal protein catabolic process	157/3467	490/18723	2.39e-13	5.25e-11	157
GO:00313312	Colorectum	MSS	positive regulation of cellular catabolic process	140/3467	427/18723	7.02e-13	1.33e-10	140
GO:00457322	Colorectum	MSS	positive regulation of protein catabolic process	85/3467	231/18723	3.66e-11	4.57e-09	85
GO:19030502	Colorectum	MSS	regulation of proteolysis involved in cellular protein catabolic process	82/3467	221/18723	4.97e-11	5.64e-09	82
GO:00458622	Colorectum	MSS	positive regulation of proteolysis	119/3467	372/18723	2.14e-10	2.09e-08	119
GO:00431612	Colorectum	MSS	proteasome-mediated ubiquitin-dependent protein catabolic process	127/3467	412/18723	7.70e-10	6.32e-08	127
GO:00611362	Colorectum	MSS	regulation of proteasomal protein catabolic process	67/3467	187/18723	1.45e-08	8.47e-07	67
GO:19033642	Colorectum	MSS	positive regulation of cellular protein catabolic process	57/3467	155/18723	6.01e-08	3.15e-06	57
GO:19030522	Colorectum	MSS	positive regulation of proteolysis involved in cellular protein catabolic process	48/3467	133/18723	1.21e-06	4.06e-05	48
GO:19018002	Colorectum	MSS	positive regulation of proteasomal protein catabolic process	40/3467	114/18723	1.96e-05	4.19e-04	40
GO:00017012	Colorectum	MSS	in utero embryonic development	99/3467	367/18723	3.71e-05	7.10e-04	99
GO:00421763	Colorectum	MSI-H	regulation of protein catabolic process	65/1319	391/18723	6.96e-11	1.29e-08	65
GO:19033623	Colorectum	MSI-H	regulation of cellular protein catabolic process	49/1319	255/18723	9.82e-11	1.66e-08	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

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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