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: FAIM

Gene summary for FAIM

Gene summary.

Gene information	Species	Human
	Gene symbol	FAIM
	Gene ID	55179
	Gene name	Fas apoptotic inhibitory molecule
	Gene Alias	FAIM1
	Cytomap	3q22.3
	Gene Type	protein-coding
	GO ID	GO:0006915
	UniProtAcc	Q9NVQ4

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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
55179	FAIM	LZE2T	Human	Esophagus	ESCC	4.26e-04	5.77e-01	0.082
55179	FAIM	LZE4T	Human	Esophagus	ESCC	6.77e-08	2.97e-01	0.0811
55179	FAIM	LZE5T	Human	Esophagus	ESCC	3.72e-02	2.33e-01	0.0514
55179	FAIM	LZE7T	Human	Esophagus	ESCC	1.22e-03	4.31e-01	0.0667
55179	FAIM	LZE8T	Human	Esophagus	ESCC	1.33e-08	2.01e-01	0.067
55179	FAIM	LZE20T	Human	Esophagus	ESCC	5.60e-06	1.12e-01	0.0662
55179	FAIM	LZE22D1	Human	Esophagus	HGIN	2.51e-02	1.26e-01	0.0595
55179	FAIM	LZE22T	Human	Esophagus	ESCC	7.55e-05	3.40e-01	0.068
55179	FAIM	LZE24T	Human	Esophagus	ESCC	1.21e-21	6.76e-01	0.0596
55179	FAIM	LZE6T	Human	Esophagus	ESCC	6.11e-07	4.54e-01	0.0845
55179	FAIM	P1T-E	Human	Esophagus	ESCC	2.09e-04	2.56e-01	0.0875
55179	FAIM	P2T-E	Human	Esophagus	ESCC	1.98e-39	8.09e-01	0.1177
55179	FAIM	P4T-E	Human	Esophagus	ESCC	2.42e-27	8.64e-01	0.1323
55179	FAIM	P5T-E	Human	Esophagus	ESCC	7.37e-13	2.73e-01	0.1327
55179	FAIM	P8T-E	Human	Esophagus	ESCC	3.56e-33	6.95e-01	0.0889
55179	FAIM	P9T-E	Human	Esophagus	ESCC	9.75e-14	3.44e-01	0.1131
55179	FAIM	P10T-E	Human	Esophagus	ESCC	2.31e-43	8.13e-01	0.116
55179	FAIM	P11T-E	Human	Esophagus	ESCC	1.72e-15	7.52e-01	0.1426
55179	FAIM	P12T-E	Human	Esophagus	ESCC	2.51e-40	7.65e-01	0.1122
55179	FAIM	P15T-E	Human	Esophagus	ESCC	2.49e-20	5.38e-01	0.1149

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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:190204123	Skin	cSCC	regulation of extrinsic apoptotic signaling pathway via death domain receptors	25/4864	49/18723	1.53e-04	1.35e-03	25
GO:001072016	Skin	cSCC	positive regulation of cell development	105/4864	298/18723	2.30e-04	1.89e-03	105
GO:000862522	Skin	cSCC	extrinsic apoptotic signaling pathway via death domain receptors	36/4864	82/18723	3.22e-04	2.57e-03	36
GO:005076913	Skin	cSCC	positive regulation of neurogenesis	80/4864	225/18723	8.85e-04	6.07e-03	80
GO:200123727	Skin	cSCC	negative regulation of extrinsic apoptotic signaling pathway	38/4864	97/18723	2.95e-03	1.64e-02	38
GO:005076722	Skin	cSCC	regulation of neurogenesis	118/4864	364/18723	3.32e-03	1.81e-02	118
GO:005196213	Skin	cSCC	positive regulation of nervous system development	88/4864	272/18723	1.07e-02	4.66e-02	88
GO:2001233113	Thyroid	PTC	regulation of apoptotic signaling pathway	197/5968	356/18723	2.58e-20	3.69e-18	197
GO:2001234113	Thyroid	PTC	negative regulation of apoptotic signaling pathway	124/5968	224/18723	2.57e-13	1.32e-11	124
GO:0097191113	Thyroid	PTC	extrinsic apoptotic signaling pathway	117/5968	219/18723	2.73e-11	1.03e-09	117
GO:2001236113	Thyroid	PTC	regulation of extrinsic apoptotic signaling pathway	82/5968	151/18723	9.01e-09	2.18e-07	82
GO:001072018	Thyroid	PTC	positive regulation of cell development	138/5968	298/18723	1.13e-07	2.22e-06	138
GO:000724926	Thyroid	PTC	I-kappaB kinase/NF-kappaB signaling	130/5968	281/18723	2.78e-07	4.80e-06	130
GO:000862523	Thyroid	PTC	extrinsic apoptotic signaling pathway via death domain receptors	47/5968	82/18723	1.70e-06	2.38e-05	47
GO:005076914	Thyroid	PTC	positive regulation of neurogenesis	105/5968	225/18723	2.28e-06	3.05e-05	105
GO:005076716	Thyroid	PTC	regulation of neurogenesis	156/5968	364/18723	5.86e-06	7.05e-05	156
GO:2001237113	Thyroid	PTC	negative regulation of extrinsic apoptotic signaling pathway	51/5968	97/18723	1.83e-05	1.88e-04	51
GO:005196214	Thyroid	PTC	positive regulation of nervous system development	117/5968	272/18723	6.72e-05	5.89e-04	117
GO:190204120	Thyroid	PTC	regulation of extrinsic apoptotic signaling pathway via death domain receptors	29/5968	49/18723	7.32e-05	6.31e-04	29
GO:00519608	Thyroid	PTC	regulation of nervous system development	177/5968	443/18723	1.72e-04	1.32e-03	177

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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

FAIM

SNV

Missense_Mutation

novel

c.191G>A

p.Arg64Gln

p.R64Q

Q9NVQ4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-5L-AAT0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

FAIM

SNV

Missense_Mutation

novel

c.172N>T

p.Gly58Trp

p.G58W

Q9NVQ4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-E2-A14N-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

FAIM

insertion

Nonsense_Mutation

novel

c.586_587insAGGCTTAGA

p.Gly196delinsGluAlaTerArg

p.G196delinsEA*R

Q9NVQ4

protein_coding

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

FAIM

SNV

Missense_Mutation

c.217N>A

p.Glu73Lys

p.E73K

Q9NVQ4

protein_coding

deleterious(0.03)

benign(0.006)

TCGA-C5-A1M7-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

FAIM

SNV

Missense_Mutation

novel

c.76N>G

p.Leu26Val

p.L26V

Q9NVQ4

protein_coding

tolerated_low_confidence(0.19)

benign(0.02)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

FAIM

SNV

Missense_Mutation

c.569N>A

p.Ser190Asn

p.S190N

Q9NVQ4

protein_coding

deleterious(0)

probably_damaging(0.973)

TCGA-DM-A28K-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

FAIM

SNV

Missense_Mutation

rs767931243

c.260C>T

p.Thr87Ile

p.T87I

Q9NVQ4

protein_coding

tolerated(0.12)

benign(0.222)

TCGA-DY-A1DD-01

Colorectum

rectum adenocarcinoma

Female

>=65

III/IV

Unknown

FAIM

SNV

Missense_Mutation

novel

c.106N>G

p.Thr36Ala

p.T36A

Q9NVQ4

protein_coding

tolerated(0.42)

benign(0.015)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

FAIM

SNV

Missense_Mutation

novel

c.48N>G

p.His16Gln

p.H16Q

Q9NVQ4

protein_coding

tolerated_low_confidence(0.47)

benign(0.018)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

FAIM

SNV

Missense_Mutation

novel

c.635N>T

p.Ala212Val

p.A212V

Q9NVQ4

protein_coding

deleterious(0.02)

benign(0.015)

TCGA-A5-A2K3-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

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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