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: RER1

Gene summary for RER1

Gene summary.

Gene information	Species	Human
	Gene symbol	RER1
	Gene ID	11079
	Gene name	retention in endoplasmic reticulum sorting receptor 1
	Gene Alias	RER1
	Cytomap	1p36.32
	Gene Type	protein-coding
	GO ID	GO:0001941
	UniProtAcc	O15258

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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
11079	RER1	HTA11_347_2000001011	Human	Colorectum	AD	7.49e-10	3.51e-01	-0.1954
11079	RER1	HTA11_2112_2000001011	Human	Colorectum	SER	2.26e-02	7.22e-01	-0.2196
11079	RER1	HTA11_1391_2000001011	Human	Colorectum	AD	3.11e-05	5.16e-01	-0.059
11079	RER1	HTA11_7696_3000711011	Human	Colorectum	AD	1.96e-03	2.69e-01	0.0674
11079	RER1	HTA11_99999970781_79442	Human	Colorectum	MSS	5.84e-06	3.66e-01	0.294
11079	RER1	HTA11_99999971662_82457	Human	Colorectum	MSS	4.54e-06	3.58e-01	0.3859
11079	RER1	A002-C-116	Human	Colorectum	FAP	1.36e-04	-1.43e-01	-0.0452
11079	RER1	AEH-subject1	Human	Endometrium	AEH	1.53e-08	-3.18e-01	-0.3059
11079	RER1	AEH-subject2	Human	Endometrium	AEH	6.13e-09	-2.85e-01	-0.2525
11079	RER1	AEH-subject3	Human	Endometrium	AEH	3.89e-08	-2.81e-01	-0.2576
11079	RER1	AEH-subject4	Human	Endometrium	AEH	3.07e-05	-3.03e-01	-0.2657
11079	RER1	AEH-subject5	Human	Endometrium	AEH	1.18e-02	-2.60e-01	-0.2953
11079	RER1	EEC-subject1	Human	Endometrium	EEC	2.06e-12	-3.96e-01	-0.2682
11079	RER1	EEC-subject2	Human	Endometrium	EEC	3.72e-09	-3.05e-01	-0.2607
11079	RER1	EEC-subject3	Human	Endometrium	EEC	5.33e-36	-4.91e-01	-0.2525
11079	RER1	EEC-subject4	Human	Endometrium	EEC	1.81e-03	-1.88e-01	-0.2571
11079	RER1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	1.40e-30	-2.67e-01	-0.1869
11079	RER1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	8.91e-41	-1.92e-01	-0.1875
11079	RER1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	2.80e-37	-2.89e-01	-0.1883
11079	RER1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	2.19e-24	-3.03e-01	-0.1934

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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
Prostate		BPH: Benign Prostatic Hyperplasia
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:00481931	Colorectum	SER	Golgi vesicle transport	79/2897	296/18723	4.20e-07	2.15e-05	79
GO:19030761	Colorectum	SER	regulation of protein localization to plasma membrane	36/2897	104/18723	1.12e-06	5.18e-05	36
GO:19054751	Colorectum	SER	regulation of protein localization to membrane	52/2897	175/18723	1.31e-06	6.04e-05	52
GO:19043751	Colorectum	SER	regulation of protein localization to cell periphery	40/2897	125/18723	2.85e-06	1.16e-04	40
GO:19054771	Colorectum	SER	positive regulation of protein localization to membrane	33/2897	106/18723	3.83e-05	9.82e-04	33
GO:00068901	Colorectum	SER	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	20/2897	52/18723	4.80e-05	1.18e-03	20
GO:00991731	Colorectum	SER	postsynapse organization	46/2897	168/18723	5.20e-05	1.25e-03	46
GO:19030781	Colorectum	SER	positive regulation of protein localization to plasma membrane	22/2897	62/18723	8.58e-05	1.88e-03	22
GO:19043771	Colorectum	SER	positive regulation of protein localization to cell periphery	23/2897	69/18723	1.78e-04	3.30e-03	23
GO:00325071	Colorectum	SER	maintenance of protein location in cell	21/2897	65/18723	5.39e-04	7.57e-03	21
GO:00451851	Colorectum	SER	maintenance of protein location	26/2897	94/18723	1.76e-03	1.81e-02	26
GO:00508081	Colorectum	SER	synapse organization	85/2897	426/18723	7.17e-03	4.99e-02	85
GO:00516511	Colorectum	SER	maintenance of location in cell	47/2897	214/18723	7.20e-03	4.99e-02	47
GO:00726592	Colorectum	MSS	protein localization to plasma membrane	113/3467	284/18723	3.23e-17	1.55e-14	113
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:00481932	Colorectum	MSS	Golgi vesicle transport	101/3467	296/18723	9.09e-11	9.77e-09	101
GO:19054752	Colorectum	MSS	regulation of protein localization to membrane	68/3467	175/18723	2.16e-10	2.09e-08	68
GO:19030762	Colorectum	MSS	regulation of protein localization to plasma membrane	45/3467	104/18723	4.82e-09	3.17e-07	45
GO:19043752	Colorectum	MSS	regulation of protein localization to cell periphery	51/3467	125/18723	5.46e-09	3.55e-07	51

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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

RER1

SNV

Missense_Mutation

novel

c.58A>G

p.Arg20Gly

p.R20G

O15258

protein_coding

deleterious(0.04)

benign(0.122)

TCGA-AC-A23C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

chemo

RER1

insertion

Nonsense_Mutation

novel

c.359_360insCTG

p.Lys120delinsAsnTer

p.K120delinsN*

O15258

protein_coding

TCGA-AN-A0FJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

RER1

insertion

Frame_Shift_Ins

novel

c.361_362insGGTTGCTCTGCCTTACAGATGACGGTCC

p.Phe121TrpfsTer60

p.F121Wfs*60

O15258

protein_coding

TCGA-AN-A0FJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

RER1

deletion

Frame_Shift_Del

novel

c.348_349delNN

p.Pro117ArgfsTer3

p.P117Rfs*3

O15258

protein_coding

TCGA-D8-A147-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine

RER1

SNV

Missense_Mutation

novel

c.464T>C

p.Ile155Thr

p.I155T

O15258

protein_coding

deleterious(0)

probably_damaging(0.915)

TCGA-CK-5913-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

RER1

SNV

Missense_Mutation

rs746542852

c.47C>T

p.Ser16Leu

p.S16L

O15258

protein_coding

tolerated(0.2)

probably_damaging(0.915)

TCGA-G4-6304-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Chemotherapy

fluorouracil

RER1

SNV

Missense_Mutation

novel

c.434N>C

p.Val145Ala

p.V145A

O15258

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

RER1

SNV

Missense_Mutation

novel

c.520T>C

p.Tyr174His

p.Y174H

O15258

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RER1

SNV

Missense_Mutation

rs567205815

c.583G>A

p.Ala195Thr

p.A195T

O15258

protein_coding

tolerated(0.15)

benign(0.001)

TCGA-AJ-A3BH-01

Endometrium

uterine corpus endometrioid carcinoma

Female

Unknown

I/II

Unknown

RER1

SNV

Missense_Mutation

c.418G>A

p.Ala140Thr

p.A140T

O15258

protein_coding

deleterious(0.05)

benign(0.196)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=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

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