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: PCK1

Gene summary for PCK1

Gene summary.

Gene information	Species	Human
	Gene symbol	PCK1
	Gene ID	5105
	Gene name	phosphoenolpyruvate carboxykinase 1
	Gene Alias	PCKDC
	Cytomap	20q13.31
	Gene Type	protein-coding
	GO ID	GO:0001101
	UniProtAcc	P35558

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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
5105	PCK1	HTA11_3410_2000001011	Human	Colorectum	AD	1.87e-07	-4.85e-01	0.0155
5105	PCK1	HTA11_347_2000001011	Human	Colorectum	AD	1.21e-37	1.24e+00	-0.1954
5105	PCK1	HTA11_411_2000001011	Human	Colorectum	SER	2.43e-05	1.52e+00	-0.2602
5105	PCK1	HTA11_5212_2000001011	Human	Colorectum	AD	4.34e-08	1.14e+00	-0.2061
5105	PCK1	HTA11_10711_2000001011	Human	Colorectum	AD	5.85e-03	-4.87e-01	0.0338
5105	PCK1	HTA11_7696_3000711011	Human	Colorectum	AD	2.20e-07	-4.46e-01	0.0674
5105	PCK1	HTA11_6818_2000001021	Human	Colorectum	AD	3.57e-07	-5.71e-01	0.0588
5105	PCK1	HTA11_99999971662_82457	Human	Colorectum	MSS	4.66e-03	7.00e-01	0.3859
5105	PCK1	HTA11_99999974143_84620	Human	Colorectum	MSS	6.92e-19	-5.62e-01	0.3005
5105	PCK1	F007	Human	Colorectum	FAP	6.22e-08	-5.44e-01	0.1176
5105	PCK1	A002-C-010	Human	Colorectum	FAP	1.27e-11	-5.35e-01	0.242
5105	PCK1	A001-C-207	Human	Colorectum	FAP	1.10e-07	-4.91e-01	0.1278
5105	PCK1	A015-C-203	Human	Colorectum	FAP	2.80e-09	-3.48e-01	-0.1294
5105	PCK1	A015-C-204	Human	Colorectum	FAP	2.78e-06	-4.73e-01	-0.0228
5105	PCK1	A002-C-201	Human	Colorectum	FAP	1.39e-14	-5.20e-01	0.0324
5105	PCK1	A002-C-203	Human	Colorectum	FAP	2.09e-21	-5.60e-01	0.2786
5105	PCK1	A001-C-119	Human	Colorectum	FAP	6.58e-04	-4.49e-01	-0.1557
5105	PCK1	A001-C-108	Human	Colorectum	FAP	1.41e-15	-5.23e-01	-0.0272
5105	PCK1	A002-C-205	Human	Colorectum	FAP	3.98e-15	-5.31e-01	-0.1236
5105	PCK1	A001-C-104	Human	Colorectum	FAP	2.10e-08	-4.07e-01	0.0184

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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
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

∗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:00060664	Colorectum	CRC	alcohol metabolic process	57/2078	353/18723	2.37e-03	2.27e-02	57
GO:00704824	Colorectum	CRC	response to oxygen levels	56/2078	347/18723	2.60e-03	2.40e-02	56
GO:00097495	Colorectum	CRC	response to glucose	37/2078	212/18723	3.54e-03	3.00e-02	37
GO:00713224	Colorectum	CRC	cellular response to carbohydrate stimulus	30/2078	163/18723	3.69e-03	3.12e-02	30
GO:00714534	Colorectum	CRC	cellular response to oxygen levels	32/2078	177/18723	3.69e-03	3.12e-02	32
GO:00442423	Colorectum	CRC	cellular lipid catabolic process	37/2078	214/18723	4.16e-03	3.40e-02	37
GO:00714561	Colorectum	CRC	cellular response to hypoxia	28/2078	151/18723	4.41e-03	3.47e-02	28
GO:00713203	Colorectum	CRC	cellular response to cAMP	13/2078	53/18723	4.42e-03	3.47e-02	13
GO:00362933	Colorectum	CRC	response to decreased oxygen levels	51/2078	322/18723	5.72e-03	4.28e-02	51
GO:0019751	Colorectum	CRC	polyol metabolic process	22/2078	114/18723	6.73e-03	4.77e-02	22
GO:0022407	Colorectum	CRC	regulation of cell-cell adhesion	67/2078	448/18723	6.86e-03	4.81e-02	67
GO:00463953	Liver	NAFLD	carboxylic acid catabolic process	73/1882	236/18723	4.16e-19	1.22e-15	73
GO:00160544	Liver	NAFLD	organic acid catabolic process	73/1882	240/18723	1.20e-18	2.34e-15	73
GO:00442825	Liver	NAFLD	small molecule catabolic process	91/1882	376/18723	8.96e-16	1.31e-12	91
GO:00066316	Liver	NAFLD	fatty acid metabolic process	92/1882	390/18723	3.38e-15	3.29e-12	92
GO:00723295	Liver	NAFLD	monocarboxylic acid catabolic process	39/1882	122/18723	2.40e-11	8.77e-09	39
GO:00485457	Liver	NAFLD	response to steroid hormone	75/1882	339/18723	3.44e-11	1.12e-08	75
GO:00090626	Liver	NAFLD	fatty acid catabolic process	34/1882	100/18723	6.81e-11	1.99e-08	34
GO:00713755	Liver	NAFLD	cellular response to peptide hormone stimulus	65/1882	290/18723	3.95e-10	9.62e-08	65
GO:00442425	Liver	NAFLD	cellular lipid catabolic process	52/1882	214/18723	1.15e-09	2.17e-07	52

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa00620	Colorectum	AD	Pyruvate metabolism	28/2092	47/8465	3.71e-07	5.41e-06	3.45e-06	28
hsa00020	Colorectum	AD	Citrate cycle (TCA cycle)	20/2092	30/8465	1.43e-06	1.77e-05	1.13e-05	20
hsa00010	Colorectum	AD	Glycolysis / Gluconeogenesis	34/2092	67/8465	3.63e-06	4.34e-05	2.77e-05	34
hsa04152	Colorectum	AD	AMPK signaling pathway	47/2092	121/8465	3.74e-04	2.82e-03	1.80e-03	47
hsa04922	Colorectum	AD	Glucagon signaling pathway	41/2092	107/8465	1.18e-03	7.75e-03	4.94e-03	41
hsa04964	Colorectum	AD	Proximal tubule bicarbonate reclamation	11/2092	23/8465	1.35e-02	4.86e-02	3.10e-02	11
hsa006201	Colorectum	AD	Pyruvate metabolism	28/2092	47/8465	3.71e-07	5.41e-06	3.45e-06	28
hsa000201	Colorectum	AD	Citrate cycle (TCA cycle)	20/2092	30/8465	1.43e-06	1.77e-05	1.13e-05	20
hsa000101	Colorectum	AD	Glycolysis / Gluconeogenesis	34/2092	67/8465	3.63e-06	4.34e-05	2.77e-05	34
hsa041521	Colorectum	AD	AMPK signaling pathway	47/2092	121/8465	3.74e-04	2.82e-03	1.80e-03	47
hsa049221	Colorectum	AD	Glucagon signaling pathway	41/2092	107/8465	1.18e-03	7.75e-03	4.94e-03	41
hsa049641	Colorectum	AD	Proximal tubule bicarbonate reclamation	11/2092	23/8465	1.35e-02	4.86e-02	3.10e-02	11
hsa006202	Colorectum	SER	Pyruvate metabolism	22/1580	47/8465	9.62e-06	1.33e-04	9.67e-05	22
hsa000202	Colorectum	SER	Citrate cycle (TCA cycle)	16/1580	30/8465	2.06e-05	2.74e-04	1.99e-04	16
hsa049222	Colorectum	SER	Glucagon signaling pathway	38/1580	107/8465	2.57e-05	3.28e-04	2.38e-04	38
hsa000102	Colorectum	SER	Glycolysis / Gluconeogenesis	24/1580	67/8465	6.62e-04	5.36e-03	3.89e-03	24
hsa049642	Colorectum	SER	Proximal tubule bicarbonate reclamation	10/1580	23/8465	5.33e-03	3.28e-02	2.38e-02	10
hsa006203	Colorectum	SER	Pyruvate metabolism	22/1580	47/8465	9.62e-06	1.33e-04	9.67e-05	22
hsa000203	Colorectum	SER	Citrate cycle (TCA cycle)	16/1580	30/8465	2.06e-05	2.74e-04	1.99e-04	16
hsa049223	Colorectum	SER	Glucagon signaling pathway	38/1580	107/8465	2.57e-05	3.28e-04	2.38e-04	38

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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

PCK1

SNV

Missense_Mutation

novel

c.85N>A

p.Glu29Lys

p.E29K

P35558

protein_coding

tolerated(0.59)

benign(0.003)

TCGA-A7-A4SA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PCK1

SNV

Missense_Mutation

c.689C>G

p.Ser230Cys

p.S230C

P35558

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PCK1

SNV

Missense_Mutation

c.521N>G

p.Thr174Arg

p.T174R

P35558

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A6IX-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

PCK1

SNV

Missense_Mutation

novel

c.369N>T

p.Glu123Asp

p.E123D

P35558

protein_coding

tolerated(0.57)

benign(0)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PCK1

SNV

Missense_Mutation

novel

c.1779N>T

p.Glu593Asp

p.E593D

P35558

protein_coding

tolerated(0.08)

benign(0)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PCK1

SNV

Missense_Mutation

c.650C>A

p.Thr217Lys

p.T217K

P35558

protein_coding

tolerated(0.87)

benign(0.213)

TCGA-AO-A0JD-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

PCK1

SNV

Missense_Mutation

c.584N>T

p.Ser195Phe

p.S195F

P35558

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-B6-A1KF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PCK1

SNV

Missense_Mutation

c.1180N>C

p.Glu394Gln

p.E394Q

P35558

protein_coding

tolerated(0.26)

benign(0.019)

TCGA-BH-A0HK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

PCK1

SNV

Missense_Mutation

novel

c.715T>C

p.Ser239Pro

p.S239P

P35558

protein_coding

deleterious(0)

probably_damaging(0.973)

TCGA-C8-A1HG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PCK1

SNV

Missense_Mutation

novel

c.971N>T

p.Arg324Met

p.R324M

P35558

protein_coding

tolerated(0.05)

possibly_damaging(0.904)

TCGA-OL-A97C-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

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