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: AIMP1

Gene summary for AIMP1

Gene summary.

Gene information	Species	Human
	Gene symbol	AIMP1
	Gene ID	9255
	Gene name	aminoacyl tRNA synthetase complex interacting multifunctional protein 1
	Gene Alias	EMAP2
	Cytomap	4q24
	Gene Type	protein-coding
	GO ID	GO:0001525
	UniProtAcc	B4DNK3

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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
9255	AIMP1	LZE2T	Human	Esophagus	ESCC	7.50e-03	7.77e-01	0.082
9255	AIMP1	LZE4T	Human	Esophagus	ESCC	8.24e-16	4.73e-01	0.0811
9255	AIMP1	LZE5T	Human	Esophagus	ESCC	2.69e-03	5.60e-01	0.0514
9255	AIMP1	LZE7T	Human	Esophagus	ESCC	3.83e-05	5.54e-01	0.0667
9255	AIMP1	LZE8T	Human	Esophagus	ESCC	3.67e-06	2.77e-01	0.067
9255	AIMP1	LZE20T	Human	Esophagus	ESCC	5.05e-09	2.43e-01	0.0662
9255	AIMP1	LZE24T	Human	Esophagus	ESCC	9.85e-16	6.11e-01	0.0596
9255	AIMP1	LZE21T	Human	Esophagus	ESCC	2.98e-06	6.28e-01	0.0655
9255	AIMP1	P1T-E	Human	Esophagus	ESCC	1.17e-13	6.76e-01	0.0875
9255	AIMP1	P2T-E	Human	Esophagus	ESCC	4.72e-32	7.39e-01	0.1177
9255	AIMP1	P4T-E	Human	Esophagus	ESCC	2.04e-38	1.03e+00	0.1323
9255	AIMP1	P5T-E	Human	Esophagus	ESCC	4.89e-33	7.80e-01	0.1327
9255	AIMP1	P8T-E	Human	Esophagus	ESCC	3.33e-36	7.76e-01	0.0889
9255	AIMP1	P9T-E	Human	Esophagus	ESCC	2.76e-23	6.51e-01	0.1131
9255	AIMP1	P10T-E	Human	Esophagus	ESCC	4.51e-30	4.94e-01	0.116
9255	AIMP1	P11T-E	Human	Esophagus	ESCC	5.05e-12	6.36e-01	0.1426
9255	AIMP1	P12T-E	Human	Esophagus	ESCC	4.70e-31	6.22e-01	0.1122
9255	AIMP1	P15T-E	Human	Esophagus	ESCC	6.06e-34	8.18e-01	0.1149
9255	AIMP1	P16T-E	Human	Esophagus	ESCC	1.62e-33	6.59e-01	0.1153
9255	AIMP1	P17T-E	Human	Esophagus	ESCC	2.35e-12	8.76e-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
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:000961518	Esophagus	ESCC	response to virus	238/8552	367/18723	6.65e-14	3.32e-12	238
GO:00516075	Esophagus	ESCC	defense response to virus	171/8552	265/18723	3.91e-10	1.05e-08	171
GO:01405465	Esophagus	ESCC	defense response to symbiont	171/8552	265/18723	3.91e-10	1.05e-08	171
GO:005067318	Esophagus	ESCC	epithelial cell proliferation	238/8552	437/18723	1.19e-04	8.20e-04	238
GO:005067817	Esophagus	ESCC	regulation of epithelial cell proliferation	206/8552	381/18723	5.51e-04	3.02e-03	206
GO:00096155	Liver	Cirrhotic	response to virus	126/4634	367/18723	2.10e-05	2.77e-04	126
GO:0051607	Liver	Cirrhotic	defense response to virus	84/4634	265/18723	6.02e-03	3.00e-02	84
GO:0140546	Liver	Cirrhotic	defense response to symbiont	84/4634	265/18723	6.02e-03	3.00e-02	84
GO:000961511	Liver	HCC	response to virus	210/7958	367/18723	7.32e-09	1.86e-07	210
GO:00516071	Liver	HCC	defense response to virus	151/7958	265/18723	1.27e-06	1.85e-05	151
GO:01405461	Liver	HCC	defense response to symbiont	151/7958	265/18723	1.27e-06	1.85e-05	151
GO:000961515	Oral cavity	OSCC	response to virus	215/7305	367/18723	1.63e-14	9.41e-13	215
GO:00516074	Oral cavity	OSCC	defense response to virus	154/7305	265/18723	1.96e-10	5.63e-09	154
GO:01405464	Oral cavity	OSCC	defense response to symbiont	154/7305	265/18723	1.96e-10	5.63e-09	154
GO:005067310	Oral cavity	OSCC	epithelial cell proliferation	212/7305	437/18723	2.82e-05	2.61e-04	212
GO:005090010	Oral cavity	OSCC	leukocyte migration	176/7305	369/18723	3.80e-04	2.31e-03	176
GO:005067810	Oral cavity	OSCC	regulation of epithelial cell proliferation	180/7305	381/18723	5.88e-04	3.35e-03	180
GO:000961516	Oral cavity	LP	response to virus	143/4623	367/18723	7.42e-10	3.52e-08	143
GO:005160711	Oral cavity	LP	defense response to virus	97/4623	265/18723	9.31e-06	1.74e-04	97
GO:014054611	Oral cavity	LP	defense response to symbiont	97/4623	265/18723	9.31e-06	1.74e-04	97

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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

AIMP1

SNV

Missense_Mutation

rs770399051

c.343N>G

p.Met115Val

p.M115V

Q12904

protein_coding

tolerated(0.36)

benign(0)

TCGA-A2-A1FW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

AIMP1

insertion

Nonsense_Mutation

novel

c.836_837insCTACATGTTAGTTGCATGATGCATGATGCTGAAATTGTTAAATGA

p.Ala279_Phe280insTyrMetLeuValAlaTerCysMetMetLeuLysLeuLeuAsnAsp

p.A279_F280insYMLVA*CMMLKLLND

Q12904

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

AIMP1

SNV

Missense_Mutation

rs564105201

c.989T>C

p.Met330Thr

p.M330T

Q12904

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

AIMP1

SNV

Missense_Mutation

c.385N>A

p.Val129Ile

p.V129I

Q12904

protein_coding

tolerated(0.27)

benign(0.001)

TCGA-WS-AB45-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

AIMP1

SNV

Missense_Mutation

novel

c.821G>T

p.Arg274Ile

p.R274I

Q12904

protein_coding

deleterious(0.04)

possibly_damaging(0.724)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

AIMP1

SNV

Missense_Mutation

novel

c.193N>C

p.Thr65Pro

p.T65P

Q12904

protein_coding

tolerated(0.09)

probably_damaging(0.984)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

AIMP1

SNV

Missense_Mutation

rs747675209

c.218N>A

p.Arg73Gln

p.R73Q

Q12904

protein_coding

tolerated(0.44)

benign(0.261)

TCGA-AP-A056-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

AIMP1

SNV

Missense_Mutation

novel

c.685N>T

p.Arg229Trp

p.R229W

Q12904

protein_coding

deleterious(0.02)

probably_damaging(1)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

AIMP1

SNV

Missense_Mutation

rs143219988

c.590C>A

p.Ser197Tyr

p.S197Y

Q12904

protein_coding

deleterious(0)

possibly_damaging(0.789)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

AIMP1

SNV

Missense_Mutation

novel

c.980C>A

p.Ala327Asp

p.A327D

Q12904

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

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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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