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: GNAS

Gene summary for GNAS

Gene summary.

Gene information	Species	Human
	Gene symbol	GNAS
	Gene ID	2778
	Gene name	GNAS complex locus
	Gene Alias	AHO
	Cytomap	20q13.32
	Gene Type	protein-coding
	GO ID	GO:0001501
	UniProtAcc	A0A0S2Z3H8

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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
2778	GNAS	GSM4909286	Human	Breast	IDC	6.71e-08	-1.78e-01	0.1081
2778	GNAS	GSM4909293	Human	Breast	IDC	2.50e-09	3.32e-01	0.1581
2778	GNAS	GSM4909294	Human	Breast	IDC	4.70e-06	-7.31e-02	0.2022
2778	GNAS	GSM4909296	Human	Breast	IDC	1.66e-07	2.08e-02	0.1524
2778	GNAS	GSM4909297	Human	Breast	IDC	3.87e-19	-4.92e-01	0.1517
2778	GNAS	GSM4909303	Human	Breast	IDC	1.60e-05	5.04e-01	0.0438
2778	GNAS	GSM4909304	Human	Breast	IDC	6.31e-33	5.16e-01	0.1636
2778	GNAS	GSM4909306	Human	Breast	IDC	1.30e-07	-4.55e-01	0.1564
2778	GNAS	GSM4909308	Human	Breast	IDC	6.55e-04	-1.31e-01	0.158
2778	GNAS	GSM4909311	Human	Breast	IDC	4.01e-46	-4.84e-01	0.1534
2778	GNAS	GSM4909312	Human	Breast	IDC	5.09e-14	-4.55e-01	0.1552
2778	GNAS	GSM4909313	Human	Breast	IDC	2.95e-02	-2.66e-01	0.0391
2778	GNAS	GSM4909316	Human	Breast	IDC	2.82e-03	2.20e-01	0.21
2778	GNAS	GSM4909317	Human	Breast	IDC	2.69e-04	3.24e-01	0.1355
2778	GNAS	GSM4909318	Human	Breast	IDC	1.61e-04	3.66e-01	0.2031
2778	GNAS	GSM4909319	Human	Breast	IDC	4.03e-52	-4.26e-01	0.1563
2778	GNAS	GSM4909320	Human	Breast	IDC	1.39e-05	-3.56e-01	0.1575
2778	GNAS	GSM4909321	Human	Breast	IDC	1.74e-10	-2.31e-01	0.1559
2778	GNAS	brca3	Human	Breast	Precancer	8.88e-06	-1.39e-01	-0.0263
2778	GNAS	M2	Human	Breast	IDC	3.36e-33	9.39e-01	0.21

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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
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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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:00341099	Breast	Precancer	homotypic cell-cell adhesion	18/1080	90/18723	3.15e-06	1.03e-04	18
GO:00420609	Breast	Precancer	wound healing	48/1080	422/18723	5.48e-06	1.63e-04	48
GO:00508789	Breast	Precancer	regulation of body fluid levels	40/1080	379/18723	1.68e-04	2.77e-03	40
GO:00705278	Breast	Precancer	platelet aggregation	12/1080	67/18723	4.02e-04	5.43e-03	12
GO:00075995	Breast	Precancer	hemostasis	24/1080	222/18723	2.31e-03	2.15e-02	24
GO:00075965	Breast	Precancer	blood coagulation	23/1080	217/18723	3.61e-03	2.98e-02	23
GO:00508175	Breast	Precancer	coagulation	23/1080	222/18723	4.78e-03	3.64e-02	23
GO:0030168	Breast	Precancer	platelet activation	15/1080	123/18723	4.80e-03	3.64e-02	15
GO:003410913	Breast	IDC	homotypic cell-cell adhesion	20/1434	90/18723	1.20e-05	3.17e-04	20
GO:004206014	Breast	IDC	wound healing	55/1434	422/18723	7.27e-05	1.45e-03	55
GO:005087813	Breast	IDC	regulation of body fluid levels	50/1434	379/18723	1.12e-04	2.10e-03	50
GO:007052713	Breast	IDC	platelet aggregation	12/1434	67/18723	4.53e-03	3.49e-02	12
GO:005087823	Breast	DCIS	regulation of body fluid levels	50/1390	379/18723	5.17e-05	1.06e-03	50
GO:004206024	Breast	DCIS	wound healing	54/1390	422/18723	6.09e-05	1.22e-03	54
GO:003410923	Breast	DCIS	homotypic cell-cell adhesion	18/1390	90/18723	9.33e-05	1.71e-03	18
GO:004206010	Cervix	CC	wound healing	109/2311	422/18723	1.84e-14	1.57e-11	109
GO:005087810	Cervix	CC	regulation of body fluid levels	78/2311	379/18723	3.20e-06	8.77e-05	78
GO:003410910	Cervix	CC	homotypic cell-cell adhesion	26/2311	90/18723	2.12e-05	3.82e-04	26
GO:00705279	Cervix	CC	platelet aggregation	19/2311	67/18723	3.42e-04	3.58e-03	19
GO:00508176	Cervix	CC	coagulation	45/2311	222/18723	5.08e-04	4.94e-03	45

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501218	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0471418	Breast	Precancer	Thermogenesis	68/684	232/8465	4.40e-22	1.26e-20	9.69e-21	68
hsa0491518	Breast	Precancer	Estrogen signaling pathway	28/684	138/8465	4.10e-06	5.39e-05	4.13e-05	28
hsa05031	Breast	Precancer	Amphetamine addiction	14/684	69/8465	1.05e-03	7.35e-03	5.63e-03	14
hsa0516316	Breast	Precancer	Human cytomegalovirus infection	32/684	225/8465	1.13e-03	7.57e-03	5.80e-03	32
hsa0496110	Breast	Precancer	Endocrine and other factor-regulated calcium reabsorption	11/684	53/8465	2.92e-03	1.81e-02	1.39e-02	11
hsa0501219	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0471419	Breast	Precancer	Thermogenesis	68/684	232/8465	4.40e-22	1.26e-20	9.69e-21	68
hsa0491519	Breast	Precancer	Estrogen signaling pathway	28/684	138/8465	4.10e-06	5.39e-05	4.13e-05	28
hsa050311	Breast	Precancer	Amphetamine addiction	14/684	69/8465	1.05e-03	7.35e-03	5.63e-03	14
hsa0516317	Breast	Precancer	Human cytomegalovirus infection	32/684	225/8465	1.13e-03	7.57e-03	5.80e-03	32
hsa0496111	Breast	Precancer	Endocrine and other factor-regulated calcium reabsorption	11/684	53/8465	2.92e-03	1.81e-02	1.39e-02	11
hsa0501224	Breast	IDC	Parkinson disease	107/867	266/8465	2.57e-39	8.36e-37	6.26e-37	107
hsa0471424	Breast	IDC	Thermogenesis	75/867	232/8465	8.41e-21	3.04e-19	2.27e-19	75
hsa0491523	Breast	IDC	Estrogen signaling pathway	35/867	138/8465	2.55e-07	5.18e-06	3.88e-06	35
hsa0511022	Breast	IDC	Vibrio cholerae infection	17/867	50/8465	4.82e-06	6.82e-05	5.10e-05	17
hsa050312	Breast	IDC	Amphetamine addiction	18/867	69/8465	1.42e-04	1.36e-03	1.01e-03	18
hsa0516324	Breast	IDC	Human cytomegalovirus infection	39/867	225/8465	6.66e-04	5.41e-03	4.05e-03	39
hsa0497122	Breast	IDC	Gastric acid secretion	16/867	76/8465	3.80e-03	2.33e-02	1.74e-02	16
hsa049704	Breast	IDC	Salivary secretion	18/867	93/8465	5.69e-03	3.13e-02	2.34e-02	18

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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

GNAS

SNV

Missense_Mutation

rs11554273

c.2530C>T

p.Arg844Cys

p.R844C

Q5JWF2

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-A8-A09T-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

GNAS

SNV

Missense_Mutation

c.437N>A

p.Gly146Asp

p.G146D

Q5JWF2

protein_coding

tolerated_low_confidence(0.09)

benign(0.003)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GNAS

SNV

Missense_Mutation

c.964C>G

p.Pro322Ala

p.P322A

Q5JWF2

protein_coding

tolerated_low_confidence(0.08)

benign(0.013)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GNAS

SNV

Missense_Mutation

c.3094N>T

p.Arg1032Cys

p.R1032C

Q5JWF2

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GNAS

SNV

Missense_Mutation

c.2782A>G

p.Ile928Val

p.I928V

Q5JWF2

protein_coding

deleterious(0.04)

probably_damaging(0.935)

TCGA-AR-A1AW-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

GNAS

SNV

Missense_Mutation

c.1004C>T

p.Pro335Leu

p.P335L

Q5JWF2

protein_coding

deleterious_low_confidence(0.03)

benign(0.02)

TCGA-E2-A570-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

GNAS

SNV

Missense_Mutation

c.3057C>G

p.Phe1019Leu

p.F1019L

Q5JWF2

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

GNAS

SNV

Missense_Mutation

c.513G>C

p.Gln171His

p.Q171H

Q5JWF2

protein_coding

deleterious_low_confidence(0.04)

benign(0.01)

TCGA-PE-A5DE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

GNAS

insertion

Frame_Shift_Ins

novel

c.2106_2107insA

p.Met703AsnfsTer7

p.M703Nfs*7

Q5JWF2

protein_coding

TCGA-AN-A0FF-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

GNAS

insertion

Frame_Shift_Ins

novel

c.1827dupC

p.Asn610GlnfsTer15

p.N610Qfs*15

Q5JWF2

protein_coding

TCGA-AO-A1KT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

fluorouracil

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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
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		GARCINONE E	GARCINONE E
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		BAS 01152706	CHEMBL2002487
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		N-(3,4-DICHLOROPHENYL)BENZAMIDE	CHEMBL560296
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		TETRAETHYLAMMONIUM CHLORIDE	TETRAETHYLAMMONIUM CHLORIDE
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		TCMDC-125620	CHEMBL530291
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		CISPLATIN	CISPLATIN	19274060
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		TCMDC-124353	CHEMBL529918
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		FLUOROURACIL	FLUOROURACIL	19274060
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		NICLOSAMIDE	NICLOSAMIDE
2778	GNAS	DRUGGABLE GENOME, CLINICALLY ACTIONABLE, G PROTEIN COUPLED RECEPTOR, DRUG RESISTANCE, TRANSPORTER		9,10-PHENANTHRENEQUINONE	9,10-PHENANTHRENEQUINONE

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