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: SMG7

Gene summary for SMG7

Gene summary.

Gene information	Species	Human
	Gene symbol	SMG7
	Gene ID	9887
	Gene name	SMG7 nonsense mediated mRNA decay factor
	Gene Alias	C1orf16
	Cytomap	1q25.3
	Gene Type	protein-coding
	GO ID	GO:0000184
	UniProtAcc	Q92540

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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
9887	SMG7	CCI_1	Human	Cervix	CC	1.53e-03	9.11e-01	0.528
9887	SMG7	CCI_2	Human	Cervix	CC	1.01e-09	1.19e+00	0.5249
9887	SMG7	CCI_3	Human	Cervix	CC	2.29e-14	8.02e-01	0.516
9887	SMG7	HTA11_3410_2000001011	Human	Colorectum	AD	1.06e-15	-5.39e-01	0.0155
9887	SMG7	HTA11_3361_2000001011	Human	Colorectum	AD	5.74e-07	-5.56e-01	-0.1207
9887	SMG7	HTA11_696_2000001011	Human	Colorectum	AD	1.22e-04	-3.65e-01	-0.1464
9887	SMG7	HTA11_866_2000001011	Human	Colorectum	AD	3.93e-03	-3.15e-01	-0.1001
9887	SMG7	HTA11_866_3004761011	Human	Colorectum	AD	3.66e-04	-3.86e-01	0.096
9887	SMG7	HTA11_7696_3000711011	Human	Colorectum	AD	4.51e-04	-2.89e-01	0.0674
9887	SMG7	HTA11_99999974143_84620	Human	Colorectum	MSS	1.97e-13	-4.45e-01	0.3005
9887	SMG7	A015-C-203	Human	Colorectum	FAP	4.90e-20	1.29e-03	-0.1294
9887	SMG7	A015-C-204	Human	Colorectum	FAP	2.44e-02	-7.30e-02	-0.0228
9887	SMG7	A014-C-040	Human	Colorectum	FAP	2.22e-02	-1.87e-01	-0.1184
9887	SMG7	A002-C-201	Human	Colorectum	FAP	1.67e-07	-1.13e-01	0.0324
9887	SMG7	A001-C-119	Human	Colorectum	FAP	3.03e-04	-2.46e-01	-0.1557
9887	SMG7	A001-C-108	Human	Colorectum	FAP	8.39e-10	-2.90e-02	-0.0272
9887	SMG7	A002-C-205	Human	Colorectum	FAP	2.43e-18	-3.03e-01	-0.1236
9887	SMG7	A015-C-005	Human	Colorectum	FAP	4.43e-02	-2.00e-01	-0.0336
9887	SMG7	A015-C-006	Human	Colorectum	FAP	2.20e-13	-3.29e-01	-0.0994
9887	SMG7	A015-C-106	Human	Colorectum	FAP	3.47e-08	3.04e-02	-0.0511

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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
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

∗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:00069139	Cervix	CC	nucleocytoplasmic transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00511699	Cervix	CC	nuclear transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00064029	Cervix	CC	mRNA catabolic process	56/2311	232/18723	4.81e-07	1.83e-05	56
GO:00064019	Cervix	CC	RNA catabolic process	62/2311	278/18723	2.18e-06	6.56e-05	62
GO:00511689	Cervix	CC	nuclear export	38/2311	154/18723	1.86e-05	3.46e-04	38
GO:00009567	Cervix	CC	nuclear-transcribed mRNA catabolic process	30/2311	112/18723	2.60e-05	4.37e-04	30
GO:00512368	Cervix	CC	establishment of RNA localization	39/2311	166/18723	4.76e-05	7.25e-04	39
GO:00506578	Cervix	CC	nucleic acid transport	38/2311	163/18723	7.06e-05	9.85e-04	38
GO:00506588	Cervix	CC	RNA transport	38/2311	163/18723	7.06e-05	9.85e-04	38
GO:003530310	Cervix	CC	regulation of dephosphorylation	31/2311	128/18723	1.52e-04	1.83e-03	31
GO:000640310	Cervix	CC	RNA localization	43/2311	201/18723	2.00e-04	2.29e-03	43
GO:00510284	Cervix	CC	mRNA transport	31/2311	130/18723	2.05e-04	2.33e-03	31
GO:00467008	Cervix	CC	heterocycle catabolic process	80/2311	445/18723	3.23e-04	3.42e-03	80
GO:00346559	Cervix	CC	nucleobase-containing compound catabolic process	74/2311	407/18723	3.77e-04	3.88e-03	74
GO:00442709	Cervix	CC	cellular nitrogen compound catabolic process	79/2311	451/18723	7.80e-04	6.91e-03	79
GO:00163117	Cervix	CC	dephosphorylation	73/2311	417/18723	1.23e-03	9.87e-03	73
GO:00159318	Cervix	CC	nucleobase-containing compound transport	43/2311	222/18723	1.72e-03	1.30e-02	43
GO:00194398	Cervix	CC	aromatic compound catabolic process	79/2311	467/18723	2.14e-03	1.54e-02	79
GO:00714262	Cervix	CC	ribonucleoprotein complex export from nucleus	18/2311	76/18723	4.45e-03	2.71e-02	18
GO:00711662	Cervix	CC	ribonucleoprotein complex localization	18/2311	77/18723	5.15e-03	3.03e-02	18

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa03015	Colorectum	AD	mRNA surveillance pathway	35/2092	97/8465	7.95e-03	3.13e-02	2.00e-02	35
hsa030151	Colorectum	AD	mRNA surveillance pathway	35/2092	97/8465	7.95e-03	3.13e-02	2.00e-02	35
hsa030152	Colorectum	FAP	mRNA surveillance pathway	26/1404	97/8465	7.11e-03	2.64e-02	1.60e-02	26
hsa030153	Colorectum	FAP	mRNA surveillance pathway	26/1404	97/8465	7.11e-03	2.64e-02	1.60e-02	26
hsa0301524	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa0301534	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa030154	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301511	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301521	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa0301531	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa030158	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301513	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301541	Oral cavity	EOLP	mRNA surveillance pathway	30/1218	97/8465	2.26e-05	1.20e-04	7.07e-05	30
hsa0301551	Oral cavity	EOLP	mRNA surveillance pathway	30/1218	97/8465	2.26e-05	1.20e-04	7.07e-05	30
hsa030156	Oral cavity	NEOLP	mRNA surveillance pathway	25/1112	97/8465	5.70e-04	3.18e-03	2.00e-03	25
hsa030157	Oral cavity	NEOLP	mRNA surveillance pathway	25/1112	97/8465	5.70e-04	3.18e-03	2.00e-03	25
hsa030155	Prostate	BPH	mRNA surveillance pathway	32/1718	97/8465	2.20e-03	8.63e-03	5.34e-03	32
hsa0301512	Prostate	BPH	mRNA surveillance pathway	32/1718	97/8465	2.20e-03	8.63e-03	5.34e-03	32
hsa0301522	Prostate	Tumor	mRNA surveillance pathway	33/1791	97/8465	2.18e-03	8.60e-03	5.33e-03	33
hsa0301532	Prostate	Tumor	mRNA surveillance pathway	33/1791	97/8465	2.18e-03	8.60e-03	5.33e-03	33

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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

SMG7

SNV

Missense_Mutation

novel

c.2414C>G

p.Pro805Arg

p.P805R

Q92540

protein_coding

deleterious_low_confidence(0)

benign(0.421)

TCGA-95-A4VN-01

Lung

lung adenocarcinoma

Female

<65

I/II

Unknown

SMG7

SNV

Missense_Mutation

c.1864N>T

p.Thr622Ser

p.T622S

Q92540

protein_coding

tolerated_low_confidence(0.07)

benign(0.015)

TCGA-21-1078-01

Lung

lung squamous cell carcinoma

Male

>=65

I/II

Unknown

SMG7

SNV

Missense_Mutation

c.1261N>A

p.Leu421Ile

p.L421I

Q92540

protein_coding

deleterious(0.02)

probably_damaging(0.998)

TCGA-39-5024-01

Lung

lung squamous cell carcinoma

Female

>=65

III/IV

Chemotherapy

carboplatin

SMG7

SNV

Missense_Mutation

c.2581C>T

p.Pro861Ser

p.P861S

Q92540

protein_coding

tolerated_low_confidence(0.41)

benign(0.027)

TCGA-39-5028-01

Lung

lung squamous cell carcinoma

Male

>=65

III/IV

Unknown

SMG7

SNV

Missense_Mutation

novel

c.2240A>G

p.Gln747Arg

p.Q747R

Q92540

protein_coding

deleterious_low_confidence(0)

benign(0.3)

TCGA-56-A49D-01

Lung

lung squamous cell carcinoma

Male

>=65

III/IV

Unknown

SMG7

SNV

Missense_Mutation

novel

c.1874N>C

p.Ile625Thr

p.I625T

Q92540

protein_coding

deleterious_low_confidence(0)

benign(0.1)

TCGA-60-2720-01

Lung

lung squamous cell carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

SMG7

SNV

Missense_Mutation

novel

c.2429N>T

p.Pro810Leu

p.P810L

Q92540

protein_coding

deleterious_low_confidence(0)

benign(0.14)

TCGA-63-A5MJ-01

Lung

lung squamous cell carcinoma

Male

<65

I/II

Chemotherapy

vinorelbine

SMG7

SNV

Missense_Mutation

c.733G>C

p.Gly245Arg

p.G245R

Q92540

protein_coding

tolerated(0.14)

benign(0.243)

TCGA-66-2757-01

Lung

lung squamous cell carcinoma

Female

>=65

I/II

Chemotherapy

gemcitabine

SMG7

SNV

Missense_Mutation

rs764737499

c.2308N>A

p.Val770Met

p.V770M

Q92540

protein_coding

tolerated_low_confidence(0.13)

benign(0.01)

TCGA-85-8353-01

Lung

lung squamous cell carcinoma

Male

>=65

III/IV

Unknown

SMG7

SNV

Missense_Mutation

novel

c.1452N>C

p.Leu484Phe

p.L484F

Q92540

protein_coding

deleterious(0.03)

possibly_damaging(0.601)

TCGA-94-8491-01

Lung

lung squamous cell carcinoma

Male

>=65

I/II

Chemotherapy

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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