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: CORO1C

Gene summary for CORO1C

Gene summary.

Gene information	Species	Human
	Gene symbol	CORO1C
	Gene ID	23603
	Gene name	coronin 1C
	Gene Alias	HCRNN4
	Cytomap	12q24.11
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	Q9ULV4

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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
23603	CORO1C	LZE2T	Human	Esophagus	ESCC	3.22e-02	3.21e-01	0.082
23603	CORO1C	LZE4T	Human	Esophagus	ESCC	5.24e-14	4.73e-01	0.0811
23603	CORO1C	LZE5T	Human	Esophagus	ESCC	1.88e-04	-1.09e-01	0.0514
23603	CORO1C	LZE8T	Human	Esophagus	ESCC	3.77e-03	2.02e-01	0.067
23603	CORO1C	LZE22T	Human	Esophagus	ESCC	2.61e-09	2.54e-01	0.068
23603	CORO1C	LZE24T	Human	Esophagus	ESCC	4.27e-12	3.33e-01	0.0596
23603	CORO1C	LZE6T	Human	Esophagus	ESCC	1.37e-06	-3.52e-02	0.0845
23603	CORO1C	P1T-E	Human	Esophagus	ESCC	2.94e-02	1.16e-01	0.0875
23603	CORO1C	P2T-E	Human	Esophagus	ESCC	3.50e-17	4.27e-01	0.1177
23603	CORO1C	P4T-E	Human	Esophagus	ESCC	8.33e-15	5.51e-01	0.1323
23603	CORO1C	P5T-E	Human	Esophagus	ESCC	5.02e-24	4.94e-01	0.1327
23603	CORO1C	P8T-E	Human	Esophagus	ESCC	2.85e-11	1.84e-01	0.0889
23603	CORO1C	P9T-E	Human	Esophagus	ESCC	2.66e-12	2.21e-01	0.1131
23603	CORO1C	P10T-E	Human	Esophagus	ESCC	2.51e-13	-1.47e-02	0.116
23603	CORO1C	P11T-E	Human	Esophagus	ESCC	4.91e-16	4.76e-01	0.1426
23603	CORO1C	P12T-E	Human	Esophagus	ESCC	2.11e-19	4.40e-01	0.1122
23603	CORO1C	P15T-E	Human	Esophagus	ESCC	4.28e-20	5.45e-01	0.1149
23603	CORO1C	P16T-E	Human	Esophagus	ESCC	1.30e-10	2.41e-01	0.1153
23603	CORO1C	P17T-E	Human	Esophagus	ESCC	3.52e-02	4.49e-01	0.1278
23603	CORO1C	P20T-E	Human	Esophagus	ESCC	6.63e-23	6.58e-01	0.1124

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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
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:00064697	Liver	Cirrhotic	negative regulation of protein kinase activity	68/4634	212/18723	9.35e-03	4.29e-02	68
GO:0010771	Liver	Cirrhotic	negative regulation of cell morphogenesis involved in differentiation	8/4634	14/18723	9.65e-03	4.35e-02	8
GO:1900025	Liver	Cirrhotic	negative regulation of substrate adhesion-dependent cell spreading	8/4634	14/18723	9.65e-03	4.35e-02	8
GO:00071624	Liver	Cirrhotic	negative regulation of cell adhesion	93/4634	303/18723	1.06e-02	4.66e-02	93
GO:004886311	Liver	Cirrhotic	stem cell differentiation	66/4634	206/18723	1.06e-02	4.68e-02	66
GO:001605021	Liver	HCC	vesicle organization	194/7958	300/18723	5.58e-15	3.97e-13	194
GO:001619721	Liver	HCC	endosomal transport	154/7958	230/18723	4.74e-14	2.95e-12	154
GO:001056322	Liver	HCC	negative regulation of phosphorus metabolic process	259/7958	442/18723	4.29e-12	1.92e-10	259
GO:004593622	Liver	HCC	negative regulation of phosphate metabolic process	258/7958	441/18723	6.00e-12	2.60e-10	258
GO:004232622	Liver	HCC	negative regulation of phosphorylation	227/7958	385/18723	3.98e-11	1.52e-09	227
GO:002260422	Liver	HCC	regulation of cell morphogenesis	188/7958	309/18723	4.84e-11	1.82e-09	188
GO:005134822	Liver	HCC	negative regulation of transferase activity	166/7958	268/18723	8.97e-11	3.18e-09	166
GO:000701522	Liver	HCC	actin filament organization	252/7958	442/18723	3.83e-10	1.25e-08	252
GO:000703211	Liver	HCC	endosome organization	61/7958	82/18723	4.36e-09	1.15e-07	61
GO:003367322	Liver	HCC	negative regulation of kinase activity	144/7958	237/18723	9.76e-09	2.45e-07	144
GO:000193322	Liver	HCC	negative regulation of protein phosphorylation	196/7958	342/18723	1.95e-08	4.63e-07	196
GO:015011522	Liver	HCC	cell-substrate junction organization	69/7958	101/18723	1.36e-07	2.57e-06	69
GO:000646912	Liver	HCC	negative regulation of protein kinase activity	126/7958	212/18723	4.55e-07	7.49e-06	126
GO:001076922	Liver	HCC	regulation of cell morphogenesis involved in differentiation	65/7958	96/18723	5.17e-07	8.37e-06	65
GO:000704422	Liver	HCC	cell-substrate junction assembly	64/7958	95/18723	8.33e-07	1.28e-05	64

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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

CORO1C

SNV

Missense_Mutation

c.803C>T

p.Ala268Val

p.A268V

Q9ULV4

protein_coding

tolerated(0.08)

benign(0.052)

TCGA-A7-A0CE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CORO1C

SNV

Missense_Mutation

c.374N>G

p.Ser125Cys

p.S125C

Q9ULV4

protein_coding

deleterious(0.03)

benign(0.049)

TCGA-A8-A06Q-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

CORO1C

SNV

Missense_Mutation

c.1531N>G

p.Gln511Glu

p.Q511E

Q9ULV4

protein_coding

deleterious(0.04)

benign(0.127)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CORO1C

SNV

Missense_Mutation

c.1323N>G

p.Ile441Met

p.I441M

Q9ULV4

protein_coding

tolerated(0.54)

benign(0.092)

TCGA-AO-A0J9-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

CORO1C

SNV

Missense_Mutation

novel

c.106N>A

p.His36Asn

p.H36N

Q9ULV4

protein_coding

tolerated_low_confidence(0.17)

benign(0)

TCGA-E9-A5UO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CORO1C

insertion

In_Frame_Ins

novel

c.938_939insCAGACTTGTCTCTGGTTTCTTACAGGGTGACAGCAGTAT

p.His313_Glu314insArgLeuValSerGlyPheLeuGlnGlyAspSerSerIle

p.H313_E314insRLVSGFLQGDSSI

Q9ULV4

protein_coding

TCGA-A2-A0D2-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CORO1C

insertion

Nonsense_Mutation

novel

c.1256_1257insTAAATGAAGATAAGATATTTATTCCATCCATGTAT

p.Gly420LysfsTer2

p.G420Kfs*2

Q9ULV4

protein_coding

TCGA-BH-A0EE-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

CORO1C

SNV

Missense_Mutation

novel

c.59N>A

p.Arg20His

p.R20H

Q9ULV4

protein_coding

deleterious_low_confidence(0.01)

benign(0)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CORO1C

SNV

Missense_Mutation

rs762661543

c.1270N>A

p.Ala424Thr

p.A424T

Q9ULV4

protein_coding

deleterious(0.01)

possibly_damaging(0.742)

TCGA-EA-A410-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CORO1C

SNV

Missense_Mutation

c.790N>A

p.Glu264Lys

p.E264K

Q9ULV4

protein_coding

deleterious(0.01)

possibly_damaging(0.479)

TCGA-EK-A2RJ-01

Cervix

cervical & endocervical cancer

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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