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: SEC24B

Gene summary for SEC24B

Gene summary.

Gene information	Species	Human
	Gene symbol	SEC24B
	Gene ID	10427
	Gene name	SEC24 homolog B, COPII coat complex component
	Gene Alias	SEC24
	Cytomap	4q25
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	O95487

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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
10427	SEC24B	CCI_1	Human	Cervix	CC	1.78e-06	8.01e-01	0.528
10427	SEC24B	CCI_2	Human	Cervix	CC	6.13e-06	6.83e-01	0.5249
10427	SEC24B	CCI_3	Human	Cervix	CC	1.62e-03	4.97e-01	0.516
10427	SEC24B	HTA11_3410_2000001011	Human	Colorectum	AD	2.93e-19	-6.20e-01	0.0155
10427	SEC24B	HTA11_3361_2000001011	Human	Colorectum	AD	1.30e-07	-5.24e-01	-0.1207
10427	SEC24B	HTA11_83_2000001011	Human	Colorectum	SER	8.81e-03	-4.39e-01	-0.1526
10427	SEC24B	HTA11_696_2000001011	Human	Colorectum	AD	3.34e-04	-3.69e-01	-0.1464
10427	SEC24B	HTA11_866_2000001011	Human	Colorectum	AD	4.62e-06	-3.47e-01	-0.1001
10427	SEC24B	HTA11_5212_2000001011	Human	Colorectum	AD	9.11e-03	-5.86e-01	-0.2061
10427	SEC24B	HTA11_866_3004761011	Human	Colorectum	AD	5.74e-08	-4.83e-01	0.096
10427	SEC24B	HTA11_7696_3000711011	Human	Colorectum	AD	1.25e-14	-4.91e-01	0.0674
10427	SEC24B	HTA11_6818_2000001021	Human	Colorectum	AD	1.31e-04	-5.34e-01	0.0588
10427	SEC24B	HTA11_99999970781_79442	Human	Colorectum	MSS	1.72e-05	-3.31e-01	0.294
10427	SEC24B	HTA11_99999971662_82457	Human	Colorectum	MSS	6.10e-04	-3.22e-01	0.3859
10427	SEC24B	HTA11_99999973899_84307	Human	Colorectum	MSS	4.43e-05	-5.96e-01	0.2585
10427	SEC24B	HTA11_99999974143_84620	Human	Colorectum	MSS	4.02e-17	-5.04e-01	0.3005
10427	SEC24B	F007	Human	Colorectum	FAP	1.66e-02	-3.82e-01	0.1176
10427	SEC24B	A002-C-010	Human	Colorectum	FAP	8.00e-03	-2.71e-01	0.242
10427	SEC24B	A001-C-207	Human	Colorectum	FAP	8.39e-06	-4.12e-01	0.1278
10427	SEC24B	A015-C-203	Human	Colorectum	FAP	7.62e-34	-5.84e-01	-0.1294

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
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
Prostate		BPH: Benign Prostatic Hyperplasia

∗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:00085446	Cervix	CC	epidermis development	83/2311	324/18723	3.91e-11	8.54e-09	83
GO:00099137	Cervix	CC	epidermal cell differentiation	53/2311	202/18723	5.48e-08	3.25e-06	53
GO:00323868	Cervix	CC	regulation of intracellular transport	71/2311	337/18723	3.70e-06	9.74e-05	71
GO:000690010	Cervix	CC	vesicle budding from membrane	20/2311	61/18723	2.50e-05	4.28e-04	20
GO:00481938	Cervix	CC	Golgi vesicle transport	58/2311	296/18723	2.24e-04	2.54e-03	58
GO:000206410	Cervix	CC	epithelial cell development	45/2311	220/18723	4.14e-04	4.21e-03	45
GO:00488579	Cervix	CC	neural nucleus development	18/2311	64/18723	5.42e-04	5.23e-03	18
GO:00604253	Cervix	CC	lung morphogenesis	15/2311	50/18723	7.36e-04	6.60e-03	15
GO:00303245	Cervix	CC	lung development	36/2311	177/18723	1.64e-03	1.26e-02	36
GO:00351487	Cervix	CC	tube formation	31/2311	148/18723	2.07e-03	1.51e-02	31
GO:00017384	Cervix	CC	morphogenesis of a polarized epithelium	22/2311	94/18723	2.09e-03	1.52e-02	22
GO:00303235	Cervix	CC	respiratory tube development	36/2311	181/18723	2.46e-03	1.71e-02	36
GO:00160506	Cervix	CC	vesicle organization	54/2311	300/18723	2.71e-03	1.85e-02	54
GO:00018417	Cervix	CC	neural tube formation	23/2311	102/18723	2.80e-03	1.87e-02	23
GO:00605413	Cervix	CC	respiratory system development	39/2311	203/18723	3.18e-03	2.07e-02	39
GO:00605626	Cervix	CC	epithelial tube morphogenesis	57/2311	325/18723	3.79e-03	2.41e-02	57
GO:00140206	Cervix	CC	primary neural tube formation	21/2311	94/18723	4.68e-03	2.82e-02	21
GO:00219156	Cervix	CC	neural tube development	30/2311	152/18723	6.00e-03	3.43e-02	30
GO:00901752	Cervix	CC	regulation of establishment of planar polarity	14/2311	56/18723	6.93e-03	3.74e-02	14
GO:00018435	Cervix	CC	neural tube closure	19/2311	88/18723	1.01e-02	4.91e-02	19

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513020	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa0414120	Cervix	CC	Protein processing in endoplasmic reticulum	55/1267	174/8465	1.74e-08	2.68e-07	1.58e-07	55
hsa05130110	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa04141110	Cervix	CC	Protein processing in endoplasmic reticulum	55/1267	174/8465	1.74e-08	2.68e-07	1.58e-07	55
hsa04141	Colorectum	AD	Protein processing in endoplasmic reticulum	80/2092	174/8465	5.96e-10	1.25e-08	7.96e-09	80
hsa05130	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa041411	Colorectum	AD	Protein processing in endoplasmic reticulum	80/2092	174/8465	5.96e-10	1.25e-08	7.96e-09	80
hsa051301	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa041412	Colorectum	SER	Protein processing in endoplasmic reticulum	60/1580	174/8465	4.20e-07	7.33e-06	5.32e-06	60
hsa051302	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa041413	Colorectum	SER	Protein processing in endoplasmic reticulum	60/1580	174/8465	4.20e-07	7.33e-06	5.32e-06	60
hsa051303	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa041414	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa051304	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa041415	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa051305	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa051308	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa041418	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50
hsa051309	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa041419	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50

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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

SEC24B

SNV

Missense_Mutation

c.774N>A

p.Phe258Leu

p.F258L

O95487

protein_coding

tolerated_low_confidence(0.28)

benign(0.079)

TCGA-A7-A26F-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

SEC24B

SNV

Missense_Mutation

novel

c.1234N>C

p.Glu412Gln

p.E412Q

O95487

protein_coding

deleterious_low_confidence(0.02)

benign(0.036)

TCGA-A8-A08R-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SEC24B

SNV

Missense_Mutation

novel

c.3604N>T

p.Gly1202Trp

p.G1202W

O95487

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AC-A3W5-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

SEC24B

SNV

Missense_Mutation

novel

c.3530A>C

p.Lys1177Thr

p.K1177T

O95487

protein_coding

tolerated(0.06)

benign(0.19)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SEC24B

SNV

Missense_Mutation

c.2509N>G

p.Arg837Gly

p.R837G

O95487

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0B1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

adriamycin

SEC24B

SNV

Missense_Mutation

c.982N>G

p.Leu328Val

p.L328V

O95487

protein_coding

tolerated_low_confidence(0.55)

benign(0.023)

TCGA-BH-A0H7-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

doxorubicin

SEC24B

SNV

Missense_Mutation

c.2378N>G

p.Tyr793Cys

p.Y793C

O95487

protein_coding

tolerated(0.08)

possibly_damaging(0.779)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SEC24B

insertion

Nonsense_Mutation

novel

c.1460_1461insCTGCCACGATGCCTGGGTAGTTTTTTTGTATTTTTAG

p.Lys488CysfsTer12

p.K488Cfs*12

O95487

protein_coding

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

SEC24B

insertion

Frame_Shift_Ins

novel

c.668_669insAT

p.Tyr224CysfsTer69

p.Y224Cfs*69

O95487

protein_coding

TCGA-BH-A0AY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

SEC24B

insertion

Nonsense_Mutation

novel

c.670_671insAATGGAATACTATTCAGACATTAAAAATAATGATGGAAAG

p.Tyr224Ter

p.Y224*

O95487

protein_coding

TCGA-BH-A0AY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

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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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