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: CAMLG

Gene summary for CAMLG

Gene summary.

Gene information	Species	Human
	Gene symbol	CAMLG
	Gene ID	819
	Gene name	calcium modulating ligand
	Gene Alias	CAML
	Cytomap	5q31.1
	Gene Type	protein-coding
	GO ID	GO:0001776
	UniProtAcc	P49069

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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
819	CAMLG	HTA11_1938_2000001011	Human	Colorectum	AD	4.11e-03	3.08e-01	-0.0811
819	CAMLG	HTA11_347_2000001011	Human	Colorectum	AD	2.12e-05	2.73e-01	-0.1954
819	CAMLG	HTA11_866_3004761011	Human	Colorectum	AD	9.47e-07	3.17e-01	0.096
819	CAMLG	HTA11_7663_2000001011	Human	Colorectum	SER	4.88e-02	3.70e-01	0.0131
819	CAMLG	HTA11_7696_3000711011	Human	Colorectum	AD	2.86e-10	3.03e-01	0.0674
819	CAMLG	HTA11_99999970781_79442	Human	Colorectum	MSS	2.95e-10	4.06e-01	0.294
819	CAMLG	HTA11_99999965062_69753	Human	Colorectum	MSI-H	3.75e-03	5.49e-01	0.3487
819	CAMLG	HTA11_99999965104_69814	Human	Colorectum	MSS	8.63e-04	3.45e-01	0.281
819	CAMLG	HTA11_99999971662_82457	Human	Colorectum	MSS	1.24e-24	7.55e-01	0.3859
819	CAMLG	HTA11_99999974143_84620	Human	Colorectum	MSS	6.75e-07	2.88e-01	0.3005
819	CAMLG	AEH-subject1	Human	Endometrium	AEH	3.98e-10	-3.98e-01	-0.3059
819	CAMLG	AEH-subject2	Human	Endometrium	AEH	4.03e-14	-4.24e-01	-0.2525
819	CAMLG	AEH-subject3	Human	Endometrium	AEH	1.20e-25	-5.16e-01	-0.2576
819	CAMLG	AEH-subject4	Human	Endometrium	AEH	5.25e-09	-3.56e-01	-0.2657
819	CAMLG	AEH-subject5	Human	Endometrium	AEH	5.04e-12	-4.49e-01	-0.2953
819	CAMLG	EEC-subject1	Human	Endometrium	EEC	2.02e-13	-3.96e-01	-0.2682
819	CAMLG	EEC-subject2	Human	Endometrium	EEC	6.00e-22	-5.23e-01	-0.2607
819	CAMLG	EEC-subject3	Human	Endometrium	EEC	5.48e-37	-4.30e-01	-0.2525
819	CAMLG	EEC-subject4	Human	Endometrium	EEC	8.96e-07	-3.58e-01	-0.2571
819	CAMLG	EEC-subject5	Human	Endometrium	EEC	1.27e-09	-3.54e-01	-0.249

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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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid 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
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:0042176	Colorectum	AD	regulation of protein catabolic process	160/3918	391/18723	1.06e-19	7.34e-17	160
GO:1903362	Colorectum	AD	regulation of cellular protein catabolic process	109/3918	255/18723	2.14e-15	6.08e-13	109
GO:0010498	Colorectum	AD	proteasomal protein catabolic process	174/3918	490/18723	3.18e-14	7.66e-12	174
GO:0009895	Colorectum	AD	negative regulation of catabolic process	124/3918	320/18723	1.66e-13	3.35e-11	124
GO:1903050	Colorectum	AD	regulation of proteolysis involved in cellular protein catabolic process	92/3918	221/18723	2.04e-12	3.19e-10	92
GO:0031330	Colorectum	AD	negative regulation of cellular catabolic process	104/3918	262/18723	2.66e-12	3.96e-10	104
GO:0090150	Colorectum	AD	establishment of protein localization to membrane	100/3918	260/18723	6.01e-11	6.33e-09	100
GO:0043161	Colorectum	AD	proteasome-mediated ubiquitin-dependent protein catabolic process	141/3918	412/18723	1.77e-10	1.68e-08	141
GO:0031647	Colorectum	AD	regulation of protein stability	108/3918	298/18723	6.33e-10	5.08e-08	108
GO:0042177	Colorectum	AD	negative regulation of protein catabolic process	55/3918	121/18723	1.19e-09	8.85e-08	55
GO:0061136	Colorectum	AD	regulation of proteasomal protein catabolic process	75/3918	187/18723	1.65e-09	1.20e-07	75
GO:2000058	Colorectum	AD	regulation of ubiquitin-dependent protein catabolic process	68/3918	164/18723	1.82e-09	1.31e-07	68
GO:1903363	Colorectum	AD	negative regulation of cellular protein catabolic process	39/3918	75/18723	2.69e-09	1.87e-07	39
GO:0050821	Colorectum	AD	protein stabilization	73/3918	191/18723	3.02e-08	1.64e-06	73
GO:1903320	Colorectum	AD	regulation of protein modification by small protein conjugation or removal	86/3918	242/18723	9.43e-08	4.65e-06	86
GO:0032434	Colorectum	AD	regulation of proteasomal ubiquitin-dependent protein catabolic process	54/3918	134/18723	2.51e-07	1.02e-05	54
GO:1903051	Colorectum	AD	negative regulation of proteolysis involved in cellular protein catabolic process	31/3918	64/18723	8.71e-07	2.98e-05	31
GO:0031396	Colorectum	AD	regulation of protein ubiquitination	72/3918	210/18723	4.50e-06	1.21e-04	72
GO:2000059	Colorectum	AD	negative regulation of ubiquitin-dependent protein catabolic process	24/3918	48/18723	7.38e-06	1.81e-04	24
GO:0048872	Colorectum	AD	homeostasis of number of cells	87/3918	272/18723	1.16e-05	2.61e-04	87

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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

CAMLG

SNV

Missense_Mutation

rs143564828

c.310N>A

p.Glu104Lys

p.E104K

P49069

protein_coding

deleterious(0.01)

benign(0.266)

TCGA-HM-A3JK-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CAMLG

SNV

Missense_Mutation

novel

c.133N>C

p.Asn45His

p.N45H

P49069

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AA-3984-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

c.71C>T

p.Ala24Val

p.A24V

P49069

protein_coding

tolerated_low_confidence(0.07)

possibly_damaging(0.558)

TCGA-AD-5900-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

rs751766092

c.566N>A

p.Arg189Gln

p.R189Q

P49069

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.946)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

rs765331970

c.763N>A

p.Glu255Lys

p.E255K

P49069

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

novel

c.308N>T

p.Ala103Val

p.A103V

P49069

protein_coding

tolerated(0.2)

benign(0)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

CAMLG

SNV

Missense_Mutation

novel

c.204N>T

p.Gln68His

p.Q68H

P49069

protein_coding

tolerated(0.57)

benign(0)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

rs757373789

c.446N>A

p.Arg149His

p.R149H

P49069

protein_coding

tolerated_low_confidence(0.19)

benign(0.006)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CAMLG

SNV

Missense_Mutation

rs765331970

c.763N>A

p.Glu255Lys

p.E255K

P49069

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

CAMLG

SNV

Missense_Mutation

novel

c.868T>C

p.Tyr290His

p.Y290H

P49069

protein_coding

deleterious(0.02)

possibly_damaging(0.748)

TCGA-B5-A3FA-01

Endometrium

uterine corpus endometrioid 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
819	CAMLG	NA		CYCLOSPORINE A
819	CAMLG	NA		CYCLOSPORINE	CYCLOSPORINE

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