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: AKT1

Gene summary for AKT1

Gene summary.

Gene information	Species	Human
	Gene symbol	AKT1
	Gene ID	207
	Gene name	AKT serine/threonine kinase 1
	Gene Alias	AKT
	Cytomap	14q32.33
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	B0LPE5

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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
207	AKT1	HTA11_2487_2000001011	Human	Colorectum	SER	3.82e-07	4.27e-01	-0.1808
207	AKT1	HTA11_1938_2000001011	Human	Colorectum	AD	1.27e-07	4.56e-01	-0.0811
207	AKT1	HTA11_78_2000001011	Human	Colorectum	AD	4.14e-04	3.04e-01	-0.1088
207	AKT1	HTA11_347_2000001011	Human	Colorectum	AD	6.28e-14	4.37e-01	-0.1954
207	AKT1	HTA11_411_2000001011	Human	Colorectum	SER	5.15e-03	5.54e-01	-0.2602
207	AKT1	HTA11_83_2000001011	Human	Colorectum	SER	2.63e-03	3.35e-01	-0.1526
207	AKT1	HTA11_696_2000001011	Human	Colorectum	AD	1.25e-14	4.50e-01	-0.1464
207	AKT1	HTA11_866_2000001011	Human	Colorectum	AD	2.37e-03	2.38e-01	-0.1001
207	AKT1	HTA11_1391_2000001011	Human	Colorectum	AD	4.26e-10	4.42e-01	-0.059
207	AKT1	HTA11_2992_2000001011	Human	Colorectum	SER	1.68e-02	4.39e-01	-0.1706
207	AKT1	HTA11_546_2000001011	Human	Colorectum	AD	7.46e-04	3.74e-01	-0.0842
207	AKT1	HTA11_866_3004761011	Human	Colorectum	AD	1.70e-06	2.33e-01	0.096
207	AKT1	HTA11_10623_2000001011	Human	Colorectum	AD	3.02e-03	3.30e-01	-0.0177
207	AKT1	HTA11_7696_3000711011	Human	Colorectum	AD	1.20e-09	2.89e-01	0.0674
207	AKT1	HTA11_7469_2000001011	Human	Colorectum	AD	6.88e-03	4.96e-01	-0.0124
207	AKT1	HTA11_99999970781_79442	Human	Colorectum	MSS	7.38e-06	3.07e-01	0.294
207	AKT1	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.19e-02	7.01e-01	0.3487
207	AKT1	HTA11_99999965104_69814	Human	Colorectum	MSS	3.57e-09	4.13e-01	0.281
207	AKT1	HTA11_99999971662_82457	Human	Colorectum	MSS	1.03e-04	2.43e-01	0.3859
207	AKT1	HTA11_99999973899_84307	Human	Colorectum	MSS	2.32e-03	4.00e-01	0.2585

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:0006401112	Thyroid	PTC	RNA catabolic process	163/5968	278/18723	2.13e-20	3.27e-18	163
GO:0061136113	Thyroid	PTC	regulation of proteasomal protein catabolic process	121/5968	187/18723	2.25e-20	3.37e-18	121
GO:1903829113	Thyroid	PTC	positive regulation of cellular protein localization	162/5968	276/18723	2.40e-20	3.52e-18	162
GO:2001233113	Thyroid	PTC	regulation of apoptotic signaling pathway	197/5968	356/18723	2.58e-20	3.69e-18	197
GO:0006979113	Thyroid	PTC	response to oxidative stress	234/5968	446/18723	6.97e-20	9.77e-18	234
GO:0006091112	Thyroid	PTC	generation of precursor metabolites and energy	252/5968	490/18723	8.24e-20	1.13e-17	252
GO:0032434113	Thyroid	PTC	regulation of proteasomal ubiquitin-dependent protein catabolic process	94/5968	134/18723	9.17e-20	1.23e-17	94
GO:0045333112	Thyroid	PTC	cellular respiration	140/5968	230/18723	9.60e-20	1.26e-17	140
GO:0016236110	Thyroid	PTC	macroautophagy	167/5968	291/18723	1.51e-19	1.91e-17	167
GO:1903364113	Thyroid	PTC	positive regulation of cellular protein catabolic process	104/5968	155/18723	1.93e-19	2.39e-17	104
GO:000683928	Thyroid	PTC	mitochondrial transport	150/5968	254/18723	2.76e-19	3.34e-17	150
GO:0097193113	Thyroid	PTC	intrinsic apoptotic signaling pathway	164/5968	288/18723	9.17e-19	1.09e-16	164
GO:0006402112	Thyroid	PTC	mRNA catabolic process	139/5968	232/18723	9.59e-19	1.12e-16	139
GO:0015980111	Thyroid	PTC	energy derivation by oxidation of organic compounds	176/5968	318/18723	2.67e-18	2.90e-16	176
GO:0031396113	Thyroid	PTC	regulation of protein ubiquitination	128/5968	210/18723	3.06e-18	3.27e-16	128
GO:0051098113	Thyroid	PTC	regulation of binding	195/5968	363/18723	3.21e-18	3.37e-16	195
GO:0045862113	Thyroid	PTC	positive regulation of proteolysis	198/5968	372/18723	6.68e-18	6.91e-16	198
GO:0006417113	Thyroid	PTC	regulation of translation	236/5968	468/18723	2.70e-17	2.52e-15	236
GO:0034655112	Thyroid	PTC	nucleobase-containing compound catabolic process	211/5968	407/18723	2.72e-17	2.52e-15	211
GO:1901800112	Thyroid	PTC	positive regulation of proteasomal protein catabolic process	80/5968	114/18723	4.80e-17	4.27e-15	80

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05208	Colorectum	AD	Chemical carcinogenesis - reactive oxygen species	126/2092	223/8465	1.01e-24	1.68e-22	1.07e-22	126
hsa05415	Colorectum	AD	Diabetic cardiomyopathy	114/2092	203/8465	3.65e-22	3.06e-20	1.95e-20	114
hsa05010	Colorectum	AD	Alzheimer disease	174/2092	384/8465	1.82e-19	9.26e-18	5.91e-18	174
hsa04932	Colorectum	AD	Non-alcoholic fatty liver disease	90/2092	155/8465	4.83e-19	1.80e-17	1.15e-17	90
hsa05131	Colorectum	AD	Shigellosis	109/2092	247/8465	1.09e-11	2.44e-10	1.55e-10	109
hsa05132	Colorectum	AD	Salmonella infection	102/2092	249/8465	7.65e-09	1.28e-07	8.17e-08	102
hsa04666	Colorectum	AD	Fc gamma R-mediated phagocytosis	46/2092	97/8465	9.10e-07	1.22e-05	7.77e-06	46
hsa05017	Colorectum	AD	Spinocerebellar ataxia	60/2092	143/8465	3.78e-06	4.35e-05	2.78e-05	60
hsa05135	Colorectum	AD	Yersinia infection	58/2092	137/8465	3.90e-06	4.35e-05	2.78e-05	58
hsa04066	Colorectum	AD	HIF-1 signaling pathway	48/2092	109/8465	7.25e-06	7.84e-05	5.00e-05	48
hsa04919	Colorectum	AD	Thyroid hormone signaling pathway	51/2092	121/8465	1.71e-05	1.73e-04	1.10e-04	51
hsa04722	Colorectum	AD	Neurotrophin signaling pathway	50/2092	119/8465	2.28e-05	2.24e-04	1.43e-04	50
hsa05213	Colorectum	AD	Endometrial cancer	29/2092	58/8465	2.69e-05	2.57e-04	1.64e-04	29
hsa05230	Colorectum	AD	Central carbon metabolism in cancer	33/2092	70/8465	3.61e-05	3.19e-04	2.03e-04	33
hsa05418	Colorectum	AD	Fluid shear stress and atherosclerosis	54/2092	139/8465	1.41e-04	1.16e-03	7.37e-04	54
hsa04152	Colorectum	AD	AMPK signaling pathway	47/2092	121/8465	3.74e-04	2.82e-03	1.80e-03	47
hsa05210	Colorectum	AD	Colorectal cancer	35/2092	86/8465	7.54e-04	5.49e-03	3.50e-03	35
hsa04213	Colorectum	AD	Longevity regulating pathway - multiple species	27/2092	62/8465	8.72e-04	5.96e-03	3.80e-03	27
hsa04922	Colorectum	AD	Glucagon signaling pathway	41/2092	107/8465	1.18e-03	7.75e-03	4.94e-03	41
hsa05417	Colorectum	AD	Lipid and atherosclerosis	73/2092	215/8465	1.31e-03	8.27e-03	5.27e-03	73

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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

AKT1

SNV

Missense_Mutation

novel

c.618N>T

p.Arg206Ser

p.R206S

P31749

protein_coding

tolerated(0.32)

benign(0.023)

TCGA-A7-A13G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

AKT1

SNV

Missense_Mutation

rs121434592

c.49G>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A094-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

AKT1

SNV

Missense_Mutation

rs121434592

c.49G>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A6IX-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

AKT1

SNV

Missense_Mutation

c.155N>G

p.Leu52Arg

p.L52R

P31749

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-AN-A0XR-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

AKT1

SNV

Missense_Mutation

rs121434592

c.49G>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AO-A12H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

AKT1

SNV

Missense_Mutation

rs121434592

c.49G>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AR-A24X-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

AKT1

SNV

Missense_Mutation

rs121434592

c.49G>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-B6-A0WZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

AKT1

SNV

Missense_Mutation

rs121434592

c.49N>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0BR-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

AKT1

SNV

Missense_Mutation

rs121434592

c.49N>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0BS-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

AKT1

SNV

Missense_Mutation

rs121434592

c.49N>A

p.Glu17Lys

p.E17K

P31749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0W4-01

Breast

breast invasive carcinoma

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
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE	inhibitor	178101884	GSK-690693
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		AZD4547		26351323
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		PTX-200
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE	inhibitor	CHEMBL3137336	UPROSERTIB
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE	inhibitor	249565578	IPATASERTIB
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		Ipatasertib	IPATASERTIB	27872130
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		GAMBOGIC AMIDE	GAMBOGIC AMIDE	17911251
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		GDC-0068	IPATASERTIB
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE		SOTRASTAURIN	SOTRASTAURIN
207	AKT1	SERINE THREONINE KINASE, KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, TRANSPORTER, TRANSCRIPTION FACTOR, DRUG RESISTANCE	inhibitor	MK-2206	MK-2206

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