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: ERN1

Gene summary for ERN1

Gene summary.

Gene information	Species	Human
	Gene symbol	ERN1
	Gene ID	2081
	Gene name	endoplasmic reticulum to nucleus signaling 1
	Gene Alias	IRE1
	Cytomap	17q23.3
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	O75460

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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
2081	ERN1	AEH-subject1	Human	Endometrium	AEH	1.68e-09	4.40e-01	-0.3059
2081	ERN1	AEH-subject2	Human	Endometrium	AEH	3.15e-03	2.35e-01	-0.2525
2081	ERN1	AEH-subject3	Human	Endometrium	AEH	7.23e-05	2.55e-01	-0.2576
2081	ERN1	AEH-subject4	Human	Endometrium	AEH	7.38e-03	2.73e-01	-0.2657
2081	ERN1	AEH-subject5	Human	Endometrium	AEH	1.21e-03	3.06e-01	-0.2953
2081	ERN1	EEC-subject1	Human	Endometrium	EEC	1.01e-16	5.13e-01	-0.2682
2081	ERN1	EEC-subject2	Human	Endometrium	EEC	8.10e-03	1.70e-01	-0.2607
2081	ERN1	EEC-subject3	Human	Endometrium	EEC	1.34e-03	1.11e-01	-0.2525
2081	ERN1	EEC-subject4	Human	Endometrium	EEC	9.60e-04	3.31e-01	-0.2571
2081	ERN1	GSM5276934	Human	Endometrium	EEC	3.83e-04	2.38e-01	-0.0913
2081	ERN1	GSM5276937	Human	Endometrium	EEC	1.01e-14	5.09e-01	-0.0897
2081	ERN1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	7.28e-05	-1.23e-01	-0.1869
2081	ERN1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	6.52e-06	-1.45e-01	-0.1875
2081	ERN1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	9.10e-09	-8.05e-02	-0.1883
2081	ERN1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	4.43e-06	-3.25e-02	-0.1934
2081	ERN1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	3.94e-09	-2.11e-01	-0.1917
2081	ERN1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.04e-10	-1.75e-01	-0.1916
2081	ERN1	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	8.69e-06	-1.62e-01	-0.1269
2081	ERN1	LZE4T	Human	Esophagus	ESCC	4.64e-03	1.19e-01	0.0811
2081	ERN1	LZE22D1	Human	Esophagus	HGIN	8.52e-04	1.92e-01	0.0595

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma

∗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:000838016	Endometrium	AEH	RNA splicing	111/2100	434/18723	2.42e-17	1.12e-14	111
GO:004348416	Endometrium	AEH	regulation of RNA splicing	55/2100	148/18723	1.28e-16	5.49e-14	55
GO:009719316	Endometrium	AEH	intrinsic apoptotic signaling pathway	75/2100	288/18723	1.46e-12	2.83e-10	75
GO:000640210	Endometrium	AEH	mRNA catabolic process	59/2100	232/18723	9.51e-10	8.52e-08	59
GO:000974316	Endometrium	AEH	response to carbohydrate	62/2100	253/18723	1.76e-09	1.51e-07	62
GO:000697916	Endometrium	AEH	response to oxidative stress	93/2100	446/18723	1.94e-09	1.64e-07	93
GO:003428416	Endometrium	AEH	response to monosaccharide	57/2100	225/18723	2.13e-09	1.77e-07	57
GO:003497616	Endometrium	AEH	response to endoplasmic reticulum stress	62/2100	256/18723	2.88e-09	2.13e-07	62
GO:000974615	Endometrium	AEH	response to hexose	54/2100	219/18723	1.54e-08	9.72e-07	54
GO:000030216	Endometrium	AEH	response to reactive oxygen species	54/2100	222/18723	2.54e-08	1.49e-06	54
GO:000640110	Endometrium	AEH	RNA catabolic process	63/2100	278/18723	3.28e-08	1.87e-06	63
GO:000974910	Endometrium	AEH	response to glucose	52/2100	212/18723	3.40e-08	1.91e-06	52
GO:006219716	Endometrium	AEH	cellular response to chemical stress	71/2100	337/18723	1.03e-07	5.05e-06	71
GO:00016789	Endometrium	AEH	cellular glucose homeostasis	44/2100	172/18723	1.04e-07	5.07e-06	44
GO:00331209	Endometrium	AEH	positive regulation of RNA splicing	17/2100	37/18723	1.15e-07	5.49e-06	17
GO:007132210	Endometrium	AEH	cellular response to carbohydrate stimulus	41/2100	163/18723	4.55e-07	1.87e-05	41
GO:004254215	Endometrium	AEH	response to hydrogen peroxide	38/2100	146/18723	4.70e-07	1.92e-05	38
GO:00506738	Endometrium	AEH	epithelial cell proliferation	84/2100	437/18723	4.88e-07	1.94e-05	84
GO:00486604	Endometrium	AEH	regulation of smooth muscle cell proliferation	43/2100	180/18723	1.09e-06	3.68e-05	43
GO:00713339	Endometrium	AEH	cellular response to glucose stimulus	38/2100	151/18723	1.17e-06	3.82e-05	38

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501226	Endometrium	AEH	Parkinson disease	115/1197	266/8465	6.24e-32	1.01e-29	7.42e-30	115
hsa0501620	Endometrium	AEH	Huntington disease	118/1197	306/8465	3.00e-27	2.44e-25	1.78e-25	118
hsa0501420	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa0501020	Endometrium	AEH	Alzheimer disease	124/1197	384/8465	1.20e-20	3.91e-19	2.86e-19	124
hsa0493220	Endometrium	AEH	Non-alcoholic fatty liver disease	67/1197	155/8465	5.91e-19	1.75e-17	1.28e-17	67
hsa0502220	Endometrium	AEH	Pathways of neurodegeneration - multiple diseases	137/1197	476/8465	9.27e-18	2.32e-16	1.70e-16	137
hsa0414126	Endometrium	AEH	Protein processing in endoplasmic reticulum	62/1197	174/8465	5.97e-13	1.39e-11	1.01e-11	62
hsa0501718	Endometrium	AEH	Spinocerebellar ataxia	43/1197	143/8465	5.92e-07	7.69e-06	5.63e-06	43
hsa0541726	Endometrium	AEH	Lipid and atherosclerosis	47/1197	215/8465	1.24e-03	7.62e-03	5.58e-03	47
hsa0421010	Endometrium	AEH	Apoptosis	30/1197	136/8465	7.72e-03	4.05e-02	2.96e-02	30
hsa05012111	Endometrium	AEH	Parkinson disease	115/1197	266/8465	6.24e-32	1.01e-29	7.42e-30	115
hsa05016110	Endometrium	AEH	Huntington disease	118/1197	306/8465	3.00e-27	2.44e-25	1.78e-25	118
hsa05014110	Endometrium	AEH	Amyotrophic lateral sclerosis	123/1197	364/8465	2.17e-22	7.82e-21	5.72e-21	123
hsa05010110	Endometrium	AEH	Alzheimer disease	124/1197	384/8465	1.20e-20	3.91e-19	2.86e-19	124
hsa04932110	Endometrium	AEH	Non-alcoholic fatty liver disease	67/1197	155/8465	5.91e-19	1.75e-17	1.28e-17	67
hsa05022110	Endometrium	AEH	Pathways of neurodegeneration - multiple diseases	137/1197	476/8465	9.27e-18	2.32e-16	1.70e-16	137
hsa04141111	Endometrium	AEH	Protein processing in endoplasmic reticulum	62/1197	174/8465	5.97e-13	1.39e-11	1.01e-11	62
hsa0501719	Endometrium	AEH	Spinocerebellar ataxia	43/1197	143/8465	5.92e-07	7.69e-06	5.63e-06	43
hsa05417111	Endometrium	AEH	Lipid and atherosclerosis	47/1197	215/8465	1.24e-03	7.62e-03	5.58e-03	47
hsa0421015	Endometrium	AEH	Apoptosis	30/1197	136/8465	7.72e-03	4.05e-02	2.96e-02	30

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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

ERN1

SNV

Missense_Mutation

c.2251N>A

p.Pro751Thr

p.P751T

O75460

protein_coding

tolerated(0.25)

benign(0.055)

TCGA-A2-A04Q-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

ERN1

SNV

Missense_Mutation

rs372670758

c.2021C>T

p.Ser674Leu

p.S674L

O75460

protein_coding

deleterious(0.02)

benign(0.286)

TCGA-A2-A0YT-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

arimidex

ERN1

SNV

Missense_Mutation

rs780870849

c.2468N>T

p.Ala823Val

p.A823V

O75460

protein_coding

deleterious(0)

possibly_damaging(0.576)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ERN1

SNV

Missense_Mutation

novel

c.1786G>A

p.Val596Met

p.V596M

O75460

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-BH-A0B4-01

Breast

breast invasive carcinoma

Male

>=65

III/IV

Hormone Therapy

tamoxiphen

ERN1

SNV

Missense_Mutation

c.2108N>A

p.Gly703Asp

p.G703D

O75460

protein_coding

deleterious(0)

benign(0.272)

TCGA-BH-A0C7-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

ERN1

SNV

Missense_Mutation

c.731N>G

p.Asn244Ser

p.N244S

O75460

protein_coding

tolerated(0.61)

probably_damaging(0.956)

TCGA-BH-A18U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

ERN1

insertion

Nonsense_Mutation

novel

c.700_701insTTCAGAGTTCTTAAATATTACATAAAAATCATGGAT

p.Arg234delinsLeuGlnSerSerTerIleLeuHisLysAsnHisGlyTrp

p.R234delinsLQSS*ILHKNHGW

O75460

protein_coding

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ERN1

insertion

Nonsense_Mutation

novel

c.2432_2433insAACGCCCAGAAAAGCACAGAAAGAATGAAGCAAC

p.Met812ThrfsTer9

p.M812Tfs*9

O75460

protein_coding

TCGA-A8-A08S-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

ERN1

insertion

Frame_Shift_Ins

novel

c.1854_1855insATTAAAATAAAGTT

p.Ser619IlefsTer12

p.S619Ifs*12

O75460

protein_coding

TCGA-A8-A0A7-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ERN1

insertion

Nonsense_Mutation

novel

c.1784_1785insTTATAGAAAACACAGATTAGCATAAAGGCCCATATATTCCCATTATA

p.Val596TyrfsTer8

p.V596Yfs*8

O75460

protein_coding

TCGA-BH-A0B4-01

Breast

breast invasive carcinoma

Male

>=65

III/IV

Hormone Therapy

tamoxiphen

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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
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE	inhibitor	249565809
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		BB 0223767
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		879325-11-8
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		AC1LE05K
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		US8614253, 32-5
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		T8361
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		US9241942, 32-12
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		US9040714, 155
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		US8614253, 29-19
2081	ERN1	DRUGGABLE GENOME, ENZYME, SERINE THREONINE KINASE, TRANSCRIPTION FACTOR, KINASE		US8614253, 29-1

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