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: MAP1LC3A

Gene summary for MAP1LC3A

Gene summary.

Gene information	Species	Human
	Gene symbol	MAP1LC3A
	Gene ID	84557
	Gene name	microtubule associated protein 1 light chain 3 alpha
	Gene Alias	ATG8E
	Cytomap	20q11.22
	Gene Type	protein-coding
	GO ID	GO:0000045
	UniProtAcc	Q9H492

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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
84557	MAP1LC3A	AEH-subject1	Human	Endometrium	AEH	4.03e-09	-3.54e-01	-0.3059
84557	MAP1LC3A	AEH-subject2	Human	Endometrium	AEH	2.16e-05	-3.33e-01	-0.2525
84557	MAP1LC3A	AEH-subject3	Human	Endometrium	AEH	1.15e-12	-3.35e-01	-0.2576
84557	MAP1LC3A	AEH-subject4	Human	Endometrium	AEH	2.11e-07	-4.01e-01	-0.2657
84557	MAP1LC3A	AEH-subject5	Human	Endometrium	AEH	1.19e-07	-3.47e-01	-0.2953
84557	MAP1LC3A	EEC-subject1	Human	Endometrium	EEC	4.73e-15	-4.04e-01	-0.2682
84557	MAP1LC3A	EEC-subject2	Human	Endometrium	EEC	8.41e-15	-3.50e-01	-0.2607
84557	MAP1LC3A	EEC-subject3	Human	Endometrium	EEC	9.29e-39	-4.83e-01	-0.2525
84557	MAP1LC3A	EEC-subject4	Human	Endometrium	EEC	2.68e-11	-3.95e-01	-0.2571
84557	MAP1LC3A	EEC-subject5	Human	Endometrium	EEC	4.89e-03	-2.71e-01	-0.249
84557	MAP1LC3A	GSM5276934	Human	Endometrium	EEC	4.33e-02	-1.48e-01	-0.0913
84557	MAP1LC3A	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	2.55e-28	-5.49e-01	-0.1869
84557	MAP1LC3A	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	2.06e-27	-5.08e-01	-0.1875
84557	MAP1LC3A	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	1.66e-28	-5.27e-01	-0.1883
84557	MAP1LC3A	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	5.58e-36	-5.27e-01	-0.1934
84557	MAP1LC3A	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	2.40e-39	-5.09e-01	-0.1917
84557	MAP1LC3A	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.47e-39	-5.31e-01	-0.1916
84557	MAP1LC3A	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	2.27e-05	-2.19e-01	-0.1269
84557	MAP1LC3A	LZE4T	Human	Esophagus	ESCC	1.41e-12	3.93e-01	0.0811
84557	MAP1LC3A	LZE20T	Human	Esophagus	ESCC	4.86e-02	2.26e-02	0.0662

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:000697916	Endometrium	AEH	response to oxidative stress	93/2100	446/18723	1.94e-09	1.64e-07	93
GO:000030216	Endometrium	AEH	response to reactive oxygen species	54/2100	222/18723	2.54e-08	1.49e-06	54
GO:006219716	Endometrium	AEH	cellular response to chemical stress	71/2100	337/18723	1.03e-07	5.05e-06	71
GO:004254215	Endometrium	AEH	response to hydrogen peroxide	38/2100	146/18723	4.70e-07	1.92e-05	38
GO:00004228	Endometrium	AEH	autophagy of mitochondrion	24/2100	81/18723	5.41e-06	1.36e-04	24
GO:00617268	Endometrium	AEH	mitochondrion disassembly	24/2100	81/18723	5.41e-06	1.36e-04	24
GO:003459916	Endometrium	AEH	cellular response to oxidative stress	58/2100	288/18723	6.49e-06	1.58e-04	58
GO:002241115	Endometrium	AEH	cellular component disassembly	80/2100	443/18723	1.07e-05	2.45e-04	80
GO:19030086	Endometrium	AEH	organelle disassembly	29/2100	114/18723	1.66e-05	3.43e-04	29
GO:00329848	Endometrium	AEH	protein-containing complex disassembly	45/2100	224/18723	7.16e-05	1.10e-03	45
GO:003461415	Endometrium	AEH	cellular response to reactive oxygen species	34/2100	155/18723	9.00e-05	1.30e-03	34
GO:001003816	Endometrium	AEH	response to metal ion	65/2100	373/18723	2.02e-04	2.54e-03	65
GO:007149616	Endometrium	AEH	cellular response to external stimulus	57/2100	320/18723	2.72e-04	3.14e-03	57
GO:003166716	Endometrium	AEH	response to nutrient levels	78/2100	474/18723	3.26e-04	3.64e-03	78
GO:00162368	Endometrium	AEH	macroautophagy	52/2100	291/18723	4.56e-04	4.80e-03	52
GO:00092679	Endometrium	AEH	cellular response to starvation	31/2100	156/18723	1.08e-03	9.46e-03	31
GO:00316699	Endometrium	AEH	cellular response to nutrient levels	39/2100	215/18723	1.66e-03	1.36e-02	39
GO:003166810	Endometrium	AEH	cellular response to extracellular stimulus	43/2100	246/18723	2.10e-03	1.63e-02	43
GO:00425949	Endometrium	AEH	response to starvation	36/2100	197/18723	2.15e-03	1.65e-02	36
GO:00703015	Endometrium	AEH	cellular response to hydrogen peroxide	20/2100	98/18723	5.64e-03	3.46e-02	20

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501420	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa0502220	Endometrium	AEH	Pathways of neurodegeneration - multiple diseases	137/1197	476/8465	9.27e-18	2.32e-16	1.70e-16	137
hsa0513126	Endometrium	AEH	Shigellosis	78/1197	247/8465	9.23e-13	2.00e-11	1.46e-11	78
hsa0421616	Endometrium	AEH	Ferroptosis	15/1197	41/8465	2.83e-04	2.30e-03	1.68e-03	15
hsa0413720	Endometrium	AEH	Mitophagy - animal	21/1197	72/8465	7.03e-04	4.86e-03	3.56e-03	21
hsa0516725	Endometrium	AEH	Kaposi sarcoma-associated herpesvirus infection	44/1197	194/8465	7.97e-04	5.28e-03	3.87e-03	44
hsa05014110	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa05022110	Endometrium	AEH	Pathways of neurodegeneration - multiple diseases	137/1197	476/8465	9.27e-18	2.32e-16	1.70e-16	137
hsa05131111	Endometrium	AEH	Shigellosis	78/1197	247/8465	9.23e-13	2.00e-11	1.46e-11	78
hsa0421617	Endometrium	AEH	Ferroptosis	15/1197	41/8465	2.83e-04	2.30e-03	1.68e-03	15
hsa04137110	Endometrium	AEH	Mitophagy - animal	21/1197	72/8465	7.03e-04	4.86e-03	3.56e-03	21
hsa05167111	Endometrium	AEH	Kaposi sarcoma-associated herpesvirus infection	44/1197	194/8465	7.97e-04	5.28e-03	3.87e-03	44
hsa0501425	Endometrium	EEC	Amyotrophic lateral sclerosis	128/1237	364/8465	9.83e-24	4.04e-22	3.01e-22	128
hsa0502225	Endometrium	EEC	Pathways of neurodegeneration - multiple diseases	140/1237	476/8465	9.49e-18	2.60e-16	1.94e-16	140
hsa0513127	Endometrium	EEC	Shigellosis	79/1237	247/8465	1.80e-12	3.95e-11	2.95e-11	79
hsa0421625	Endometrium	EEC	Ferroptosis	16/1237	41/8465	1.09e-04	1.08e-03	8.08e-04	16
hsa0413725	Endometrium	EEC	Mitophagy - animal	22/1237	72/8465	4.12e-04	3.30e-03	2.46e-03	22
hsa0516726	Endometrium	EEC	Kaposi sarcoma-associated herpesvirus infection	45/1237	194/8465	8.55e-04	5.86e-03	4.37e-03	45
hsa0501435	Endometrium	EEC	Amyotrophic lateral sclerosis	128/1237	364/8465	9.83e-24	4.04e-22	3.01e-22	128
hsa0502235	Endometrium	EEC	Pathways of neurodegeneration - multiple diseases	140/1237	476/8465	9.49e-18	2.60e-16	1.94e-16	140

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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

MAP1LC3A

SNV

Missense_Mutation

c.218N>A

p.Arg73His

p.R73H

Q9H492

protein_coding

deleterious(0.01)

probably_damaging(0.927)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

MAP1LC3A

SNV

Missense_Mutation

novel

c.9N>A

p.Met3Ile

p.M3I

Q9H492

protein_coding

tolerated_low_confidence(0.34)

benign(0)

TCGA-FU-A40J-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

carboplatin

MAP1LC3A

SNV

Missense_Mutation

c.218N>A

p.Arg73His

p.R73H

Q9H492

protein_coding

deleterious(0.01)

probably_damaging(0.927)

TCGA-MA-AA41-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

MAP1LC3A

SNV

Missense_Mutation

c.118N>A

p.Glu40Lys

p.E40K

Q9H492

protein_coding

deleterious(0.02)

probably_damaging(0.999)

TCGA-CA-6718-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

MAP1LC3A

SNV

Missense_Mutation

c.239N>T

p.Thr80Met

p.T80M

Q9H492

protein_coding

deleterious(0)

possibly_damaging(0.689)

TCGA-CK-4947-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Other, specify in notes

folinic

MAP1LC3A

SNV

Missense_Mutation

rs753652508

c.299N>T

p.Ala100Val

p.A100V

Q9H492

protein_coding

deleterious(0.02)

benign(0.044)

TCGA-CK-5914-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

MAP1LC3A

SNV

Missense_Mutation

c.196N>A

p.Glu66Lys

p.E66K

Q9H492

protein_coding

tolerated(0.07)

probably_damaging(0.973)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

MAP1LC3A

SNV

Missense_Mutation

novel

c.23N>A

p.Ser8Tyr

p.S8Y

Q9H492

protein_coding

tolerated_low_confidence(0.06)

benign(0.001)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

MAP1LC3A

SNV

Missense_Mutation

novel

c.367T>C

p.Phe123Leu

p.F123L

Q9H492

protein_coding

tolerated(0.05)

possibly_damaging(0.631)

TCGA-AX-A1C4-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MAP1LC3A

SNV

Missense_Mutation

novel

c.371G>A

p.Gly124Asp

p.G124D

Q9H492

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AX-A1CE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

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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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