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: COASY

Gene summary for COASY

Gene summary.

Gene information	Species	Human
	Gene symbol	COASY
	Gene ID	80347
	Gene name	Coenzyme A synthase
	Gene Alias	DPCK
	Cytomap	17q21.2
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q13057

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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
80347	COASY	LZE4T	Human	Esophagus	ESCC	6.55e-09	3.71e-01	0.0811
80347	COASY	LZE7T	Human	Esophagus	ESCC	1.97e-13	6.25e-01	0.0667
80347	COASY	LZE8T	Human	Esophagus	ESCC	5.12e-06	3.84e-01	0.067
80347	COASY	LZE20T	Human	Esophagus	ESCC	1.65e-03	1.43e-01	0.0662
80347	COASY	LZE22T	Human	Esophagus	ESCC	7.14e-05	5.44e-01	0.068
80347	COASY	LZE24T	Human	Esophagus	ESCC	1.28e-30	7.90e-01	0.0596
80347	COASY	LZE21T	Human	Esophagus	ESCC	6.21e-03	3.83e-01	0.0655
80347	COASY	LZE6T	Human	Esophagus	ESCC	4.08e-02	2.24e-01	0.0845
80347	COASY	P1T-E	Human	Esophagus	ESCC	9.42e-10	5.13e-01	0.0875
80347	COASY	P2T-E	Human	Esophagus	ESCC	6.46e-27	5.19e-01	0.1177
80347	COASY	P4T-E	Human	Esophagus	ESCC	2.59e-21	5.43e-01	0.1323
80347	COASY	P5T-E	Human	Esophagus	ESCC	3.13e-09	3.49e-01	0.1327
80347	COASY	P8T-E	Human	Esophagus	ESCC	2.67e-38	6.78e-01	0.0889
80347	COASY	P9T-E	Human	Esophagus	ESCC	5.09e-13	2.69e-01	0.1131
80347	COASY	P10T-E	Human	Esophagus	ESCC	9.82e-12	3.01e-01	0.116
80347	COASY	P11T-E	Human	Esophagus	ESCC	2.27e-15	7.01e-01	0.1426
80347	COASY	P12T-E	Human	Esophagus	ESCC	2.51e-27	5.58e-01	0.1122
80347	COASY	P15T-E	Human	Esophagus	ESCC	5.42e-29	7.00e-01	0.1149
80347	COASY	P16T-E	Human	Esophagus	ESCC	2.03e-25	5.02e-01	0.1153
80347	COASY	P17T-E	Human	Esophagus	ESCC	3.94e-14	6.17e-01	0.1278

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:0009117110	Oral cavity	LP	nucleotide metabolic process	158/4623	489/18723	7.17e-05	9.49e-04	158
GO:0019693110	Oral cavity	LP	ribose phosphate metabolic process	128/4623	396/18723	3.26e-04	3.28e-03	128
GO:0072521110	Oral cavity	LP	purine-containing compound metabolic process	130/4623	416/18723	1.30e-03	1.05e-02	130
GO:004639018	Oral cavity	LP	ribose phosphate biosynthetic process	65/4623	190/18723	1.97e-03	1.47e-02	65
GO:190129315	Oral cavity	LP	nucleoside phosphate biosynthetic process	84/4623	256/18723	1.98e-03	1.47e-02	84
GO:0009259110	Oral cavity	LP	ribonucleotide metabolic process	120/4623	385/18723	2.15e-03	1.57e-02	120
GO:000916515	Oral cavity	LP	nucleotide biosynthetic process	83/4623	254/18723	2.38e-03	1.71e-02	83
GO:0006163110	Oral cavity	LP	purine nucleotide metabolic process	122/4623	396/18723	3.10e-03	2.11e-02	122
GO:0009150110	Oral cavity	LP	purine ribonucleotide metabolic process	114/4623	368/18723	3.41e-03	2.28e-02	114
GO:007252210	Oral cavity	LP	purine-containing compound biosynthetic process	66/4623	200/18723	4.84e-03	3.05e-02	66
GO:000926018	Oral cavity	LP	ribonucleotide biosynthetic process	60/4623	182/18723	7.12e-03	4.00e-02	60
GO:000616410	Oral cavity	LP	purine nucleotide biosynthetic process	62/4623	191/18723	9.12e-03	4.86e-02	62
GO:0019693112	Skin	cSCC	ribose phosphate metabolic process	146/4864	396/18723	9.28e-07	1.68e-05	146
GO:000675324	Skin	cSCC	nucleoside phosphate metabolic process	176/4864	497/18723	1.55e-06	2.62e-05	176
GO:0046390111	Skin	cSCC	ribose phosphate biosynthetic process	79/4864	190/18723	1.86e-06	3.10e-05	79
GO:000911724	Skin	cSCC	nucleotide metabolic process	173/4864	489/18723	2.03e-06	3.35e-05	173
GO:0072521112	Skin	cSCC	purine-containing compound metabolic process	150/4864	416/18723	2.88e-06	4.54e-05	150
GO:0009259112	Skin	cSCC	ribonucleotide metabolic process	138/4864	385/18723	1.00e-05	1.30e-04	138
GO:0006163112	Skin	cSCC	purine nucleotide metabolic process	140/4864	396/18723	1.93e-05	2.27e-04	140
GO:0009260111	Skin	cSCC	ribonucleotide biosynthetic process	73/4864	182/18723	2.01e-05	2.36e-04	73

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa012405	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa0124012	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
hsa01240	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012401	Liver	Cirrhotic	Biosynthesis of cofactors	66/2530	153/8465	3.11e-04	1.99e-03	1.23e-03	66
hsa012402	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa007702	Liver	HCC	Pantothenate and CoA biosynthesis	16/4020	21/8465	7.16e-03	1.97e-02	1.09e-02	16
hsa012403	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa007703	Liver	HCC	Pantothenate and CoA biosynthesis	16/4020	21/8465	7.16e-03	1.97e-02	1.09e-02	16
hsa012404	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124011	Oral cavity	OSCC	Biosynthesis of cofactors	88/3704	153/8465	3.84e-04	1.20e-03	6.12e-04	88
hsa0124021	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57
hsa0124031	Oral cavity	LP	Biosynthesis of cofactors	57/2418	153/8465	1.17e-02	3.91e-02	2.52e-02	57

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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

COASY

SNV

Missense_Mutation

rs781118243

c.616N>C

p.Ala206Pro

p.A206P

Q13057

protein_coding

tolerated(0.16)

benign(0.005)

TCGA-BH-A0BZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

COASY

SNV

Missense_Mutation

c.418N>A

p.Pro140Thr

p.P140T

Q13057

protein_coding

tolerated(0.18)

probably_damaging(0.982)

TCGA-D8-A1JM-01

Breast

breast invasive carcinoma

Female

<65

I/II

ChemotherapyHormone Therapy

doxorubicine

COASY

SNV

Missense_Mutation

novel

c.638C>T

p.Pro213Leu

p.P213L

Q13057

protein_coding

tolerated(0.12)

benign(0.058)

TCGA-D8-A4Z1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

COASY

deletion

In_Frame_Del

c.512_514delNNN

p.Cys173del

p.C173del

Q13057

protein_coding

TCGA-E2-A1L6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

COASY

SNV

Missense_Mutation

rs755520740

c.964N>T

p.Arg322Cys

p.R322C

Q13057

protein_coding

deleterious(0)

probably_damaging(0.975)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

COASY

SNV

Missense_Mutation

c.148N>G

p.Arg50Gly

p.R50G

Q13057

protein_coding

deleterious(0.02)

probably_damaging(0.969)

TCGA-C5-A1BL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

COASY

SNV

Missense_Mutation

novel

c.20G>C

p.Arg7Thr

p.R7T

Q13057

protein_coding

tolerated_low_confidence(0.08)

benign(0)

TCGA-VS-A9UH-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

COASY

SNV

Missense_Mutation

novel

c.554N>G

p.Tyr185Cys

p.Y185C

Q13057

protein_coding

tolerated(0.07)

possibly_damaging(0.794)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

COASY

SNV

Missense_Mutation

c.1112G>A

p.Gly371Glu

p.G371E

Q13057

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D5-6930-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

COASY

SNV

Missense_Mutation

c.1048C>A

p.Leu350Ile

p.L350I

Q13057

protein_coding

tolerated(0.18)

benign(0.044)

TCGA-G4-6588-01

Colorectum

colon adenocarcinoma

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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