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: CD40

Gene summary for CD40

Gene summary.

Gene information	Species	Human
	Gene symbol	CD40
	Gene ID	958
	Gene name	CD40 molecule
	Gene Alias	Bp50
	Cytomap	20q13.12
	Gene Type	protein-coding
	GO ID	GO:0000018
	UniProtAcc	A0A0S2Z3C7

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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
958	CD40	LZE4T	Human	Esophagus	ESCC	3.11e-05	2.81e-01	0.0811
958	CD40	LZE8T	Human	Esophagus	ESCC	2.55e-04	1.24e-01	0.067
958	CD40	LZE22T	Human	Esophagus	ESCC	2.10e-02	3.67e-01	0.068
958	CD40	LZE24T	Human	Esophagus	ESCC	1.81e-21	5.80e-01	0.0596
958	CD40	LZE6T	Human	Esophagus	ESCC	3.22e-03	2.12e-01	0.0845
958	CD40	P1T-E	Human	Esophagus	ESCC	1.46e-12	8.11e-01	0.0875
958	CD40	P2T-E	Human	Esophagus	ESCC	3.87e-34	7.29e-01	0.1177
958	CD40	P4T-E	Human	Esophagus	ESCC	1.07e-32	8.28e-01	0.1323
958	CD40	P5T-E	Human	Esophagus	ESCC	2.00e-04	4.77e-03	0.1327
958	CD40	P8T-E	Human	Esophagus	ESCC	4.98e-42	9.19e-01	0.0889
958	CD40	P9T-E	Human	Esophagus	ESCC	2.48e-04	2.86e-01	0.1131
958	CD40	P10T-E	Human	Esophagus	ESCC	1.39e-26	5.64e-01	0.116
958	CD40	P11T-E	Human	Esophagus	ESCC	5.21e-23	1.12e+00	0.1426
958	CD40	P12T-E	Human	Esophagus	ESCC	6.40e-56	1.06e+00	0.1122
958	CD40	P15T-E	Human	Esophagus	ESCC	4.67e-10	2.62e-01	0.1149
958	CD40	P17T-E	Human	Esophagus	ESCC	7.41e-10	5.82e-01	0.1278
958	CD40	P20T-E	Human	Esophagus	ESCC	5.27e-39	9.25e-01	0.1124
958	CD40	P21T-E	Human	Esophagus	ESCC	2.66e-53	1.17e+00	0.1617
958	CD40	P22T-E	Human	Esophagus	ESCC	2.51e-25	4.25e-01	0.1236
958	CD40	P23T-E	Human	Esophagus	ESCC	1.12e-50	1.24e+00	0.108

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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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:19013427	Thyroid	ATC	regulation of vasculature development	143/6293	348/18723	1.95e-03	9.44e-03	143
GO:00181086	Thyroid	ATC	peptidyl-tyrosine phosphorylation	153/6293	375/18723	1.96e-03	9.48e-03	153
GO:000759618	Thyroid	ATC	blood coagulation	93/6293	217/18723	2.69e-03	1.23e-02	93
GO:000759918	Thyroid	ATC	hemostasis	94/6293	222/18723	3.92e-03	1.70e-02	94
GO:005081718	Thyroid	ATC	coagulation	94/6293	222/18723	3.92e-03	1.70e-02	94
GO:004354715	Thyroid	ATC	positive regulation of GTPase activity	106/6293	255/18723	4.58e-03	1.89e-02	106
GO:004340611	Thyroid	ATC	positive regulation of MAP kinase activity	51/6293	112/18723	5.68e-03	2.30e-02	51
GO:007055513	Thyroid	ATC	response to interleukin-1	63/6293	143/18723	5.82e-03	2.35e-02	63
GO:00507305	Thyroid	ATC	regulation of peptidyl-tyrosine phosphorylation	108/6293	264/18723	7.50e-03	2.93e-02	108
GO:003434116	Thyroid	ATC	response to interferon-gamma	61/6293	141/18723	1.04e-02	3.79e-02	61
GO:0050878112	Thyroid	ATC	regulation of body fluid levels	149/6293	379/18723	1.08e-02	3.90e-02	149
GO:003016813	Thyroid	ATC	platelet activation	54/6293	123/18723	1.10e-02	3.95e-02	54
GO:004349116	Thyroid	ATC	protein kinase B signaling	87/6293	211/18723	1.20e-02	4.27e-02	87

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05166211	Esophagus	ESCC	Human T-cell leukemia virus 1 infection	164/4205	222/8465	8.13e-14	2.09e-12	1.07e-12	164
hsa05169210	Esophagus	ESCC	Epstein-Barr virus infection	151/4205	202/8465	1.55e-13	3.45e-12	1.77e-12	151
hsa05417211	Esophagus	ESCC	Lipid and atherosclerosis	143/4205	215/8465	3.30e-07	2.45e-06	1.26e-06	143
hsa0514525	Esophagus	ESCC	Toxoplasmosis	76/4205	112/8465	6.83e-05	2.90e-04	1.48e-04	76
hsa040645	Esophagus	ESCC	NF-kappa B signaling pathway	67/4205	104/8465	1.62e-03	4.89e-03	2.50e-03	67
hsa052028	Esophagus	ESCC	Transcriptional misregulation in cancer	116/4205	193/8465	2.08e-03	5.95e-03	3.05e-03	116
hsa0541630	Esophagus	ESCC	Viral myocarditis	41/4205	60/8465	2.59e-03	7.05e-03	3.61e-03	41
hsa05166310	Esophagus	ESCC	Human T-cell leukemia virus 1 infection	164/4205	222/8465	8.13e-14	2.09e-12	1.07e-12	164
hsa0516937	Esophagus	ESCC	Epstein-Barr virus infection	151/4205	202/8465	1.55e-13	3.45e-12	1.77e-12	151
hsa05417310	Esophagus	ESCC	Lipid and atherosclerosis	143/4205	215/8465	3.30e-07	2.45e-06	1.26e-06	143
hsa05145111	Esophagus	ESCC	Toxoplasmosis	76/4205	112/8465	6.83e-05	2.90e-04	1.48e-04	76
hsa0406412	Esophagus	ESCC	NF-kappa B signaling pathway	67/4205	104/8465	1.62e-03	4.89e-03	2.50e-03	67
hsa0520213	Esophagus	ESCC	Transcriptional misregulation in cancer	116/4205	193/8465	2.08e-03	5.95e-03	3.05e-03	116
hsa05416114	Esophagus	ESCC	Viral myocarditis	41/4205	60/8465	2.59e-03	7.05e-03	3.61e-03	41
hsa0516928	Oral cavity	OSCC	Epstein-Barr virus infection	144/3704	202/8465	1.08e-15	3.60e-14	1.83e-14	144
hsa0516630	Oral cavity	OSCC	Human T-cell leukemia virus 1 infection	150/3704	222/8465	3.68e-13	7.26e-12	3.70e-12	150
hsa0541730	Oral cavity	OSCC	Lipid and atherosclerosis	131/3704	215/8465	2.20e-07	1.45e-06	7.37e-07	131
hsa0514520	Oral cavity	OSCC	Toxoplasmosis	75/3704	112/8465	5.28e-07	3.16e-06	1.61e-06	75
hsa040644	Oral cavity	OSCC	NF-kappa B signaling pathway	67/3704	104/8465	1.57e-05	6.75e-05	3.44e-05	67
hsa0541629	Oral cavity	OSCC	Viral myocarditis	39/3704	60/8465	7.13e-04	2.09e-03	1.07e-03	39

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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
CD40LG	CD40	CD40LG_CD40	CD40	Breast	DCIS
CD40LG	CD40	CD40LG_CD40	CD40	Breast	Healthy
CD40LG	CD40	CD40LG_CD40	CD40	Cervix	Healthy
CD40LG	CD40	CD40LG_CD40	CD40	Cervix	Precancer
CD40LG	CD40	CD40LG_CD40	CD40	Endometrium	ADJ
CD40LG	CD40	CD40LG_CD40	CD40	Endometrium	AEH
CD40LG	CD40	CD40LG_CD40	CD40	Endometrium	EEC
CD40LG	CD40	CD40LG_CD40	CD40	Endometrium	Healthy
CD40LG	CD40	CD40LG_CD40	CD40	HNSCC	ADJ
CD40LG	CD40	CD40LG_CD40	CD40	HNSCC	Healthy
CD40LG	CD40	CD40LG_CD40	CD40	Liver	Healthy
CD40LG	CD40	CD40LG_CD40	CD40	Liver	Precancer
CD40LG	CD40	CD40LG_CD40	CD40	Skin	ADJ
CD40LG	CD40	CD40LG_CD40	CD40	Skin	AK
CD40LG	CD40	CD40LG_CD40	CD40	Skin	cSCC
CD40LG	CD40	CD40LG_CD40	CD40	THCA	ADJ

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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

CD40

SNV

Missense_Mutation

c.316G>A

p.Glu106Lys

p.E106K

P25942

protein_coding

tolerated(1)

benign(0)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

CD40

SNV

Missense_Mutation

novel

c.808N>T

p.Arg270Cys

p.R270C

P25942

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-LL-A8F5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

CD40

insertion

In_Frame_Ins

novel

c.241_242insGTGTGGGAGCTCCACGTTCACAGGATGGTGTCTTGC

p.Lys81delinsSerValGlyAlaProArgSerGlnAspGlyValLeuGln

p.K81delinsSVGAPRSQDGVLQ

P25942

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CD40

insertion

In_Frame_Ins

novel

c.643_644insAAGGGGAGGGGAGGCAGTTTGGGGGTGTGGTATCACAGC

p.Ile215delinsLysGlyGluGlyArgGlnPheGlyGlyValValSerGlnLeu

p.I215delinsKGEGRQFGGVVSQL

P25942

protein_coding

TCGA-A2-A0CT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

CD40

SNV

Missense_Mutation

c.570N>A

p.Asp190Glu

p.D190E

P25942

protein_coding

tolerated(0.26)

benign(0.01)

TCGA-AY-6197-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

CD40

SNV

Missense_Mutation

c.131N>T

p.Gly44Val

p.G44V

P25942

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-CM-5348-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

CD40

SNV

Missense_Mutation

c.8G>A

p.Arg3His

p.R3H

P25942

protein_coding

tolerated(0.06)

possibly_damaging(0.642)

TCGA-G4-6303-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Chemotherapy

5-fu

CD40

SNV

Missense_Mutation

c.475G>A

p.Glu159Lys

p.E159K

P25942

protein_coding

deleterious(0.02)

possibly_damaging(0.866)

TCGA-AG-A002-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

CD40

SNV

Missense_Mutation

novel

c.505A>C

p.Thr169Pro

p.T169P

P25942

protein_coding

tolerated(0.15)

benign(0.184)

TCGA-EI-6917-01

Colorectum

rectum adenocarcinoma

Male

<65

III/IV

Chemotherapy

5fluorouracil+oxaciplatina+l-folinian

CD40

SNV

Missense_Mutation

novel

c.662A>C

p.Lys221Thr

p.K221T

P25942

protein_coding

tolerated(0.07)

benign(0.15)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<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
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		LUCATUMUMAB	LUCATUMUMAB
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		APX005M	APX-005M
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		BI 655064
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		ABBV-323	RAVAGALIMAB
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		RECOMBINANT HUMAN IL-2		10383947
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		KINASE INHIBITOR		17307797
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR	partial agonist	CHEMBL2108144	TENELIXIMAB
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		CFZ533	ISCALIMAB
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		SGN-14		10866315
958	CD40	CLINICALLY ACTIONABLE, CELL SURFACE, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR		HYDROQUINONE	HYDROQUINONE	17118622

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