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: GOPC

Gene summary for GOPC

Gene summary.

Gene information	Species	Human
	Gene symbol	GOPC
	Gene ID	57120
	Gene name	golgi associated PDZ and coiled-coil motif containing
	Gene Alias	CAL
	Cytomap	6q22.1
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	Q9HD26

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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
57120	GOPC	LZE2T	Human	Esophagus	ESCC	2.43e-03	5.90e-01	0.082
57120	GOPC	LZE4T	Human	Esophagus	ESCC	4.23e-19	5.10e-01	0.0811
57120	GOPC	LZE7T	Human	Esophagus	ESCC	1.39e-05	3.86e-01	0.0667
57120	GOPC	LZE8T	Human	Esophagus	ESCC	1.38e-10	3.93e-01	0.067
57120	GOPC	LZE20T	Human	Esophagus	ESCC	4.17e-07	2.66e-01	0.0662
57120	GOPC	LZE22T	Human	Esophagus	ESCC	2.61e-04	5.25e-01	0.068
57120	GOPC	LZE24T	Human	Esophagus	ESCC	9.96e-19	6.18e-01	0.0596
57120	GOPC	LZE21T	Human	Esophagus	ESCC	1.18e-06	3.03e-01	0.0655
57120	GOPC	LZE6T	Human	Esophagus	ESCC	5.38e-04	5.10e-01	0.0845
57120	GOPC	P1T-E	Human	Esophagus	ESCC	6.08e-10	7.33e-01	0.0875
57120	GOPC	P2T-E	Human	Esophagus	ESCC	4.17e-57	8.73e-01	0.1177
57120	GOPC	P4T-E	Human	Esophagus	ESCC	1.11e-43	1.03e+00	0.1323
57120	GOPC	P5T-E	Human	Esophagus	ESCC	1.78e-39	7.26e-01	0.1327
57120	GOPC	P8T-E	Human	Esophagus	ESCC	1.93e-36	7.99e-01	0.0889
57120	GOPC	P9T-E	Human	Esophagus	ESCC	2.89e-13	3.85e-01	0.1131
57120	GOPC	P10T-E	Human	Esophagus	ESCC	4.18e-48	8.53e-01	0.116
57120	GOPC	P11T-E	Human	Esophagus	ESCC	2.06e-19	7.60e-01	0.1426
57120	GOPC	P12T-E	Human	Esophagus	ESCC	2.38e-58	9.48e-01	0.1122
57120	GOPC	P15T-E	Human	Esophagus	ESCC	7.90e-36	8.69e-01	0.1149
57120	GOPC	P16T-E	Human	Esophagus	ESCC	2.67e-51	1.07e+00	0.1153

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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:004819318	Esophagus	ESCC	Golgi vesicle transport	231/8552	296/18723	1.82e-30	9.63e-28	231
GO:0090150110	Esophagus	ESCC	establishment of protein localization to membrane	182/8552	260/18723	1.27e-15	8.19e-14	182
GO:000688815	Esophagus	ESCC	endoplasmic reticulum to Golgi vesicle-mediated transport	102/8552	130/18723	1.73e-14	9.22e-13	102
GO:0072659110	Esophagus	ESCC	protein localization to plasma membrane	193/8552	284/18723	1.95e-14	1.03e-12	193
GO:199077819	Esophagus	ESCC	protein localization to cell periphery	217/8552	333/18723	4.08e-13	1.88e-11	217
GO:000689215	Esophagus	ESCC	post-Golgi vesicle-mediated transport	82/8552	104/18723	4.00e-12	1.55e-10	82
GO:009887615	Esophagus	ESCC	vesicle-mediated transport to the plasma membrane	99/8552	136/18723	1.13e-10	3.39e-09	99
GO:0045185111	Esophagus	ESCC	maintenance of protein location	71/8552	94/18723	3.41e-09	7.24e-08	71
GO:0051235110	Esophagus	ESCC	maintenance of location	200/8552	327/18723	1.01e-08	2.02e-07	200
GO:190547519	Esophagus	ESCC	regulation of protein localization to membrane	117/8552	175/18723	1.14e-08	2.26e-07	117
GO:000689315	Esophagus	ESCC	Golgi to plasma membrane transport	48/8552	60/18723	5.11e-08	9.16e-07	48
GO:004300114	Esophagus	ESCC	Golgi to plasma membrane protein transport	34/8552	40/18723	3.00e-07	4.27e-06	34
GO:190437519	Esophagus	ESCC	regulation of protein localization to cell periphery	85/8552	125/18723	3.63e-07	5.06e-06	85
GO:1903076110	Esophagus	ESCC	regulation of protein localization to plasma membrane	72/8552	104/18723	9.74e-07	1.23e-05	72
GO:006195114	Esophagus	ESCC	establishment of protein localization to plasma membrane	44/8552	60/18723	1.25e-05	1.15e-04	44
GO:19038289	Esophagus	ESCC	negative regulation of cellular protein localization	76/8552	117/18723	1.97e-05	1.72e-04	76
GO:005122013	Esophagus	ESCC	cytoplasmic sequestering of protein	18/8552	22/18723	5.69e-04	3.10e-03	18
GO:00512244	Esophagus	ESCC	negative regulation of protein transport	74/8552	127/18723	2.86e-03	1.21e-02	74
GO:19049505	Esophagus	ESCC	negative regulation of establishment of protein localization	76/8552	131/18723	2.96e-03	1.24e-02	76
GO:19030778	Esophagus	ESCC	negative regulation of protein localization to plasma membrane	17/8552	24/18723	1.13e-02	3.81e-02	17

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

GOPC

SNV

Missense_Mutation

c.853N>A

p.Pro285Thr

p.P285T

Q9HD26

protein_coding

tolerated(0.37)

benign(0.428)

TCGA-BH-A209-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GOPC

SNV

Missense_Mutation

c.684N>A

p.Met228Ile

p.M228I

Q9HD26

protein_coding

tolerated(0.08)

benign(0.085)

TCGA-D8-A1JC-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

GOPC

SNV

Missense_Mutation

c.294N>C

p.Leu98Phe

p.L98F

Q9HD26

protein_coding

tolerated(0.06)

probably_damaging(0.94)

TCGA-D8-A1XQ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GOPC

insertion

In_Frame_Ins

novel

c.625_626insCAT

p.Lys208_Tyr209insSer

p.K208_Y209insS

Q9HD26

protein_coding

TCGA-AN-A0AJ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GOPC

insertion

Nonsense_Mutation

novel

c.623_624insATTCCCGTATTTTTCTAAAGAAAATTAAACCTGAGGCCCCT

p.Tyr209PhefsTer9

p.Y209Ffs*9

Q9HD26

protein_coding

TCGA-AN-A0AJ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GOPC

insertion

Frame_Shift_Ins

novel

c.1192_1193insA

p.Leu398TyrfsTer6

p.L398Yfs*6

Q9HD26

protein_coding

TCGA-AR-A0TU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Doxorubicin

GOPC

SNV

Missense_Mutation

novel

c.112N>C

p.Glu38Gln

p.E38Q

Q9HD26

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-VS-A8EI-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

GOPC

insertion

Frame_Shift_Ins

novel

c.501dupA

p.Glu168ArgfsTer9

p.E168Rfs*9

Q9HD26

protein_coding

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

GOPC

SNV

Missense_Mutation

novel

c.1044N>T

p.Lys348Asn

p.K348N

Q9HD26

protein_coding

deleterious(0.01)

probably_damaging(0.978)

TCGA-AA-3947-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

GOPC

SNV

Missense_Mutation

c.608C>T

p.Ala203Val

p.A203V

Q9HD26

protein_coding

deleterious(0.01)

probably_damaging(0.999)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=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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