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: SMC5

Gene summary for SMC5

Gene summary.

Gene information	Species	Human
	Gene symbol	SMC5
	Gene ID	23137
	Gene name	structural maintenance of chromosomes 5
	Gene Alias	SMC5L1
	Cytomap	9q21.12
	Gene Type	protein-coding
	GO ID	GO:0000070
	UniProtAcc	Q8IY18

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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
23137	SMC5	CA_HPV_3	Human	Cervix	CC	3.95e-03	1.72e-01	0.0414
23137	SMC5	CCI_1	Human	Cervix	CC	1.82e-04	7.26e-01	0.528
23137	SMC5	CCI_2	Human	Cervix	CC	1.37e-11	1.24e+00	0.5249
23137	SMC5	CCI_3	Human	Cervix	CC	9.28e-16	1.05e+00	0.516
23137	SMC5	HTA11_3410_2000001011	Human	Colorectum	AD	2.37e-22	-7.11e-01	0.0155
23137	SMC5	HTA11_2487_2000001011	Human	Colorectum	SER	1.36e-07	-5.65e-01	-0.1808
23137	SMC5	HTA11_2951_2000001011	Human	Colorectum	AD	3.78e-02	-7.42e-01	0.0216
23137	SMC5	HTA11_3361_2000001011	Human	Colorectum	AD	4.07e-06	-6.16e-01	-0.1207
23137	SMC5	HTA11_696_2000001011	Human	Colorectum	AD	6.24e-05	-3.57e-01	-0.1464
23137	SMC5	HTA11_866_2000001011	Human	Colorectum	AD	1.94e-05	-3.87e-01	-0.1001
23137	SMC5	HTA11_5212_2000001011	Human	Colorectum	AD	2.92e-02	-5.62e-01	-0.2061
23137	SMC5	HTA11_866_3004761011	Human	Colorectum	AD	1.67e-11	-5.44e-01	0.096
23137	SMC5	HTA11_8622_2000001021	Human	Colorectum	SER	2.27e-03	-6.79e-01	0.0528
23137	SMC5	HTA11_10711_2000001011	Human	Colorectum	AD	1.52e-04	-5.42e-01	0.0338
23137	SMC5	HTA11_7696_3000711011	Human	Colorectum	AD	1.60e-19	-4.97e-01	0.0674
23137	SMC5	HTA11_6818_2000001021	Human	Colorectum	AD	4.08e-06	-6.39e-01	0.0588
23137	SMC5	HTA11_99999971662_82457	Human	Colorectum	MSS	4.25e-06	-4.12e-01	0.3859
23137	SMC5	HTA11_99999973899_84307	Human	Colorectum	MSS	3.88e-06	-6.77e-01	0.2585
23137	SMC5	HTA11_99999974143_84620	Human	Colorectum	MSS	8.38e-29	-6.83e-01	0.3005
23137	SMC5	A002-C-010	Human	Colorectum	FAP	2.08e-03	-2.46e-01	0.242

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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
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:00458629	Breast	Precancer	positive regulation of proteolysis	51/1080	372/18723	7.77e-09	5.70e-07	51
GO:00104989	Breast	Precancer	proteasomal protein catabolic process	58/1080	490/18723	1.54e-07	8.05e-06	58
GO:19033629	Breast	Precancer	regulation of cellular protein catabolic process	36/1080	255/18723	6.03e-07	2.55e-05	36
GO:00421769	Breast	Precancer	regulation of protein catabolic process	47/1080	391/18723	1.50e-06	5.58e-05	47
GO:19030509	Breast	Precancer	regulation of proteolysis involved in cellular protein catabolic process	31/1080	221/18723	4.10e-06	1.27e-04	31
GO:00611369	Breast	Precancer	regulation of proteasomal protein catabolic process	24/1080	187/18723	1.99e-04	3.14e-03	24
GO:00431619	Breast	Precancer	proteasome-mediated ubiquitin-dependent protein catabolic process	42/1080	412/18723	2.49e-04	3.72e-03	42
GO:00098969	Breast	Precancer	positive regulation of catabolic process	48/1080	492/18723	2.62e-04	3.84e-03	48
GO:00313319	Breast	Precancer	positive regulation of cellular catabolic process	43/1080	427/18723	2.75e-04	4.00e-03	43
GO:19033649	Breast	Precancer	positive regulation of cellular protein catabolic process	20/1080	155/18723	6.10e-04	7.67e-03	20
GO:19030527	Breast	Precancer	positive regulation of proteolysis involved in cellular protein catabolic process	17/1080	133/18723	1.68e-03	1.70e-02	17
GO:00457329	Breast	Precancer	positive regulation of protein catabolic process	25/1080	231/18723	1.87e-03	1.82e-02	25
GO:00708417	Breast	Precancer	inclusion body assembly	6/1080	24/18723	1.99e-03	1.90e-02	6
GO:00900836	Breast	Precancer	regulation of inclusion body assembly	5/1080	17/18723	2.19e-03	2.06e-02	5
GO:19018007	Breast	Precancer	positive regulation of proteasomal protein catabolic process	15/1080	114/18723	2.31e-03	2.15e-02	15
GO:004586214	Breast	IDC	positive regulation of proteolysis	66/1434	372/18723	9.76e-11	1.29e-08	66
GO:001049814	Breast	IDC	proteasomal protein catabolic process	75/1434	490/18723	5.59e-09	4.41e-07	75
GO:004217614	Breast	IDC	regulation of protein catabolic process	63/1434	391/18723	1.32e-08	9.61e-07	63
GO:190336214	Breast	IDC	regulation of cellular protein catabolic process	46/1434	255/18723	4.00e-08	2.68e-06	46
GO:190305014	Breast	IDC	regulation of proteolysis involved in cellular protein catabolic process	41/1434	221/18723	9.77e-08	5.84e-06	41

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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

SMC5

SNV

Missense_Mutation

c.1476N>T

p.Lys492Asn

p.K492N

Q8IY18

protein_coding

deleterious(0.01)

probably_damaging(0.965)

TCGA-A2-A0SY-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

arimidex

SMC5

SNV

Missense_Mutation

c.656N>C

p.Arg219Thr

p.R219T

Q8IY18

protein_coding

deleterious(0)

probably_damaging(0.941)

TCGA-A8-A08L-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

SMC5

SNV

Missense_Mutation

c.1854G>T

p.Lys618Asn

p.K618N

Q8IY18

protein_coding

deleterious(0.01)

probably_damaging(0.971)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC5

SNV

Missense_Mutation

c.2440N>G

p.Gln814Glu

p.Q814E

Q8IY18

protein_coding

tolerated(1)

benign(0.005)

TCGA-AO-A0J2-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SMC5

SNV

Missense_Mutation

c.2343G>C

p.Lys781Asn

p.K781N

Q8IY18

protein_coding

deleterious(0.02)

benign(0.129)

TCGA-B6-A0IJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMC5

SNV

Missense_Mutation

novel

c.2395N>A

p.Glu799Lys

p.E799K

Q8IY18

protein_coding

tolerated(0.13)

benign(0.318)

TCGA-BH-A0H5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

SMC5

SNV

Missense_Mutation

c.1141G>A

p.Glu381Lys

p.E381K

Q8IY18

protein_coding

tolerated(0.07)

possibly_damaging(0.472)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMC5

SNV

Missense_Mutation

rs749815955

c.2848N>T

p.Met950Leu

p.M950L

Q8IY18

protein_coding

tolerated(0.13)

probably_damaging(0.994)

TCGA-E2-A14S-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

SMC5

SNV

Missense_Mutation

novel

c.1397N>A

p.Ala466Asp

p.A466D

Q8IY18

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SMC5

SNV

Missense_Mutation

novel

c.2095N>C

p.Glu699Gln

p.E699Q

Q8IY18

protein_coding

deleterious(0.02)

probably_damaging(0.982)

TCGA-MA-AA41-01

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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