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: EPB41L2

Gene summary for EPB41L2

Gene summary.

Gene information	Species	Human
	Gene symbol	EPB41L2
	Gene ID	2037
	Gene name	erythrocyte membrane protein band 4.1 like 2
	Gene Alias	4.1-G
	Cytomap	6q23.1-q23.2
	Gene Type	protein-coding
	GO ID	GO:0006996
	UniProtAcc	I6L9B1

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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
2037	EPB41L2	HTA11_3410_2000001011	Human	Colorectum	AD	8.19e-03	3.80e-01	0.0155
2037	EPB41L2	HTA11_2487_2000001011	Human	Colorectum	SER	6.96e-03	5.36e-01	-0.1808
2037	EPB41L2	HTA11_1938_2000001011	Human	Colorectum	AD	1.97e-37	1.81e+00	-0.0811
2037	EPB41L2	HTA11_78_2000001011	Human	Colorectum	AD	1.32e-14	9.13e-01	-0.1088
2037	EPB41L2	HTA11_1391_2000001011	Human	Colorectum	AD	1.54e-16	1.74e+00	-0.059
2037	EPB41L2	HTA11_866_3004761011	Human	Colorectum	AD	6.41e-05	5.20e-01	0.096
2037	EPB41L2	HTA11_6801_2000001011	Human	Colorectum	SER	1.37e-02	6.98e-01	0.0171
2037	EPB41L2	HTA11_10711_2000001011	Human	Colorectum	AD	5.82e-04	6.96e-01	0.0338
2037	EPB41L2	HTA11_7696_3000711011	Human	Colorectum	AD	3.85e-15	9.39e-01	0.0674
2037	EPB41L2	HTA11_6818_2000001021	Human	Colorectum	AD	2.01e-27	1.42e+00	0.0588
2037	EPB41L2	HTA11_99999970781_79442	Human	Colorectum	MSS	7.92e-63	2.04e+00	0.294
2037	EPB41L2	HTA11_99999965104_69814	Human	Colorectum	MSS	1.66e-16	1.13e+00	0.281
2037	EPB41L2	HTA11_99999973899_84307	Human	Colorectum	MSS	3.98e-02	4.21e-01	0.2585
2037	EPB41L2	HTA11_99999974143_84620	Human	Colorectum	MSS	3.20e-07	-3.67e-01	0.3005
2037	EPB41L2	A002-C-010	Human	Colorectum	FAP	1.45e-03	4.29e-01	0.242
2037	EPB41L2	A001-C-207	Human	Colorectum	FAP	1.03e-20	8.09e-01	0.1278
2037	EPB41L2	A015-C-203	Human	Colorectum	FAP	6.53e-09	3.14e-02	-0.1294
2037	EPB41L2	A015-C-204	Human	Colorectum	FAP	1.50e-10	5.37e-01	-0.0228
2037	EPB41L2	A002-C-201	Human	Colorectum	FAP	6.71e-09	3.74e-01	0.0324
2037	EPB41L2	A002-C-203	Human	Colorectum	FAP	9.01e-26	7.84e-01	0.2786

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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
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:1990778	Colorectum	AD	protein localization to cell periphery	129/3918	333/18723	5.51e-14	1.15e-11	129
GO:1903829	Colorectum	AD	positive regulation of cellular protein localization	110/3918	276/18723	4.58e-13	8.44e-11	110
GO:1904375	Colorectum	AD	regulation of protein localization to cell periphery	54/3918	125/18723	1.52e-08	9.00e-07	54
GO:1904377	Colorectum	AD	positive regulation of protein localization to cell periphery	30/3918	69/18723	1.98e-05	4.05e-04	30
GO:0031032	Colorectum	AD	actomyosin structure organization	65/3918	196/18723	4.17e-05	7.37e-04	65
GO:0030866	Colorectum	AD	cortical actin cytoskeleton organization	19/3918	40/18723	1.58e-04	2.20e-03	19
GO:0030865	Colorectum	AD	cortical cytoskeleton organization	25/3918	61/18723	2.96e-04	3.60e-03	25
GO:19038291	Colorectum	SER	positive regulation of cellular protein localization	86/2897	276/18723	3.61e-11	6.11e-09	86
GO:19907781	Colorectum	SER	protein localization to cell periphery	98/2897	333/18723	6.09e-11	9.57e-09	98
GO:19043751	Colorectum	SER	regulation of protein localization to cell periphery	40/2897	125/18723	2.85e-06	1.16e-04	40
GO:19043771	Colorectum	SER	positive regulation of protein localization to cell periphery	23/2897	69/18723	1.78e-04	3.30e-03	23
GO:00308651	Colorectum	SER	cortical cytoskeleton organization	19/2897	61/18723	1.59e-03	1.69e-02	19
GO:00308661	Colorectum	SER	cortical actin cytoskeleton organization	14/2897	40/18723	1.88e-03	1.90e-02	14
GO:00310321	Colorectum	SER	actomyosin structure organization	45/2897	196/18723	3.60e-03	3.03e-02	45
GO:19907782	Colorectum	MSS	protein localization to cell periphery	120/3467	333/18723	2.02e-14	5.47e-12	120
GO:19038292	Colorectum	MSS	positive regulation of cellular protein localization	103/3467	276/18723	1.12e-13	2.67e-11	103
GO:19043752	Colorectum	MSS	regulation of protein localization to cell periphery	51/3467	125/18723	5.46e-09	3.55e-07	51
GO:19043772	Colorectum	MSS	positive regulation of protein localization to cell periphery	28/3467	69/18723	1.65e-05	3.64e-04	28
GO:00308652	Colorectum	MSS	cortical cytoskeleton organization	24/3467	61/18723	1.16e-04	1.81e-03	24
GO:00308662	Colorectum	MSS	cortical actin cytoskeleton organization	17/3467	40/18723	3.87e-04	4.86e-03	17

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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

EPB41L2

SNV

Missense_Mutation

c.2881A>C

p.Thr961Pro

p.T961P

O43491

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A09M-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

paclitaxel

EPB41L2

SNV

Missense_Mutation

rs140419333

c.1987C>T

p.Arg663Cys

p.R663C

O43491

protein_coding

deleterious(0)

probably_damaging(0.938)

TCGA-AC-A5XU-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

letrozole

EPB41L2

SNV

Missense_Mutation

rs765521376

c.1354N>T

p.Arg452Cys

p.R452C

O43491

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AC-A62Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPB41L2

SNV

Missense_Mutation

c.2851N>A

p.Glu951Lys

p.E951K

O43491

protein_coding

deleterious(0)

possibly_damaging(0.848)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPB41L2

SNV

Missense_Mutation

rs778911472

c.1061N>A

p.Gly354Asp

p.G354D

O43491

protein_coding

tolerated(0.15)

benign(0.003)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

EPB41L2

SNV

Missense_Mutation

c.1114N>A

p.Glu372Lys

p.E372K

O43491

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-E2-A153-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

EPB41L2

SNV

Missense_Mutation

c.2907N>G

p.Asp969Glu

p.D969E

O43491

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-E9-A22B-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

EPB41L2

SNV

Missense_Mutation

c.2723C>G

p.Ser908Cys

p.S908C

O43491

protein_coding

deleterious(0)

possibly_damaging(0.894)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

EPB41L2

insertion

Frame_Shift_Ins

novel

c.2634_2635insTTATTAATCGATGAATTATATCAGATAAACTTTGCAAG

p.Thr879LeufsTer58

p.T879Lfs*58

O43491

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EPB41L2

deletion

Frame_Shift_Del

novel

c.847delN

p.Leu283Ter

p.L283*

O43491

protein_coding

TCGA-EW-A2FV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

docetaxel

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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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