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: SORL1

Gene summary for SORL1

Gene summary.

Gene information	Species	Human
	Gene symbol	SORL1
	Gene ID	6653
	Gene name	sortilin related receptor 1
	Gene Alias	C11orf32
	Cytomap	11q24.1
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A0A024R3H2

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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
6653	SORL1	CA_HPV_2	Human	Cervix	CC	4.09e-02	-3.72e-01	0.0391
6653	SORL1	CA_HPV_3	Human	Cervix	CC	1.42e-09	-3.26e-01	0.0414
6653	SORL1	N_HPV_1	Human	Cervix	N_HPV	6.72e-06	-4.26e-01	0.0079
6653	SORL1	N_HPV_2	Human	Cervix	N_HPV	1.84e-02	-1.68e-01	-0.0131
6653	SORL1	CCI_1	Human	Cervix	CC	1.15e-03	-5.73e-01	0.528
6653	SORL1	CCII_1	Human	Cervix	CC	4.24e-11	-6.02e-01	0.3249
6653	SORL1	Tumor	Human	Cervix	CC	1.54e-07	-4.53e-01	0.1241
6653	SORL1	sample1	Human	Cervix	CC	2.76e-11	-6.14e-01	0.0959
6653	SORL1	sample3	Human	Cervix	CC	6.79e-09	-4.11e-01	0.1387
6653	SORL1	L1	Human	Cervix	CC	7.48e-07	-5.13e-01	0.0802
6653	SORL1	T1	Human	Cervix	CC	5.26e-19	-5.89e-01	0.0918
6653	SORL1	T3	Human	Cervix	CC	1.17e-06	-3.97e-01	0.1389
6653	SORL1	HTA11_1938_2000001011	Human	Colorectum	AD	1.38e-11	8.42e-01	-0.0811
6653	SORL1	HTA11_78_2000001011	Human	Colorectum	AD	1.85e-02	4.46e-01	-0.1088
6653	SORL1	HTA11_347_2000001011	Human	Colorectum	AD	1.62e-23	9.15e-01	-0.1954
6653	SORL1	HTA11_411_2000001011	Human	Colorectum	SER	1.41e-03	9.47e-01	-0.2602
6653	SORL1	HTA11_5212_2000001011	Human	Colorectum	AD	1.43e-03	6.84e-01	-0.2061
6653	SORL1	HTA11_6818_2000001021	Human	Colorectum	AD	4.15e-07	6.49e-01	0.0588
6653	SORL1	HTA11_99999965104_69814	Human	Colorectum	MSS	2.42e-04	5.47e-01	0.281
6653	SORL1	HTA11_99999971662_82457	Human	Colorectum	MSS	7.31e-07	6.56e-01	0.3859

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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
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
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ

∗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:009031610	Oral cavity	OSCC	positive regulation of intracellular protein transport	110/7305	160/18723	2.10e-14	1.19e-12	110
GO:005109820	Oral cavity	OSCC	regulation of binding	212/7305	363/18723	3.88e-14	2.15e-12	212
GO:005134820	Oral cavity	OSCC	negative regulation of transferase activity	165/7305	268/18723	5.02e-14	2.74e-12	165
GO:005254720	Oral cavity	OSCC	regulation of peptidase activity	255/7305	461/18723	5.78e-13	2.75e-11	255
GO:001056320	Oral cavity	OSCC	negative regulation of phosphorus metabolic process	246/7305	442/18723	6.12e-13	2.89e-11	246
GO:004593620	Oral cavity	OSCC	negative regulation of phosphate metabolic process	245/7305	441/18723	8.85e-13	4.09e-11	245
GO:00161979	Oral cavity	OSCC	endosomal transport	141/7305	230/18723	5.40e-12	2.06e-10	141
GO:000703410	Oral cavity	OSCC	vacuolar transport	103/7305	157/18723	1.25e-11	4.44e-10	103
GO:004232619	Oral cavity	OSCC	negative regulation of phosphorylation	214/7305	385/18723	2.30e-11	7.74e-10	214
GO:007099720	Oral cavity	OSCC	neuron death	202/7305	361/18723	3.75e-11	1.23e-09	202
GO:007190010	Oral cavity	OSCC	regulation of protein serine/threonine kinase activity	201/7305	359/18723	3.90e-11	1.27e-09	201
GO:005160410	Oral cavity	OSCC	protein maturation	170/7305	294/18723	3.97e-11	1.28e-09	170
GO:005254820	Oral cavity	OSCC	regulation of endopeptidase activity	235/7305	432/18723	4.35e-11	1.40e-09	235
GO:004339318	Oral cavity	OSCC	regulation of protein binding	121/7305	196/18723	8.92e-11	2.73e-09	121
GO:000193319	Oral cavity	OSCC	negative regulation of protein phosphorylation	191/7305	342/18723	1.58e-10	4.62e-09	191
GO:00164829	Oral cavity	OSCC	cytosolic transport	106/7305	168/18723	2.08e-10	5.90e-09	106
GO:000989519	Oral cavity	OSCC	negative regulation of catabolic process	180/7305	320/18723	2.44e-10	6.86e-09	180
GO:003367317	Oral cavity	OSCC	negative regulation of kinase activity	140/7305	237/18723	2.74e-10	7.57e-09	140
GO:003133020	Oral cavity	OSCC	negative regulation of cellular catabolic process	152/7305	262/18723	3.04e-10	8.28e-09	152
GO:000646918	Oral cavity	OSCC	negative regulation of protein kinase activity	127/7305	212/18723	5.21e-10	1.37e-08	127

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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

SORL1

SNV

Missense_Mutation

novel

c.1999N>A

p.Asp667Asn

p.D667N

Q92673

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SORL1

SNV

Missense_Mutation

c.883N>A

p.Glu295Lys

p.E295K

Q92673

protein_coding

deleterious(0.02)

probably_damaging(0.989)

TCGA-AO-A0JC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

SORL1

SNV

Missense_Mutation

novel

c.3388A>T

p.Thr1130Ser

p.T1130S

Q92673

protein_coding

tolerated(0.71)

benign(0.007)

TCGA-BH-A0E2-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

SORL1

SNV

Missense_Mutation

novel

c.529N>C

p.Tyr177His

p.Y177H

Q92673

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SORL1

SNV

Missense_Mutation

c.1426C>T

p.His476Tyr

p.H476Y

Q92673

protein_coding

deleterious(0)

possibly_damaging(0.852)

TCGA-D8-A1XM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SORL1

SNV

Missense_Mutation

rs149445303

c.5627N>T

p.Thr1876Met

p.T1876M

Q92673

protein_coding

deleterious(0.01)

probably_damaging(0.997)

TCGA-E9-A243-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SORL1

insertion

Frame_Shift_Ins

novel

c.4917_4918insATTGTTGGGATTCATCTCATTGTTATTTCTGTTACTCAAACCA

p.Asp1640IlefsTer60

p.D1640Ifs*60

Q92673

protein_coding

TCGA-A8-A07R-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Ancillary

zoledronic

SORL1

insertion

Frame_Shift_Ins

novel

c.2838_2839insTATTA

p.Thr947TyrfsTer2

p.T947Yfs*2

Q92673

protein_coding

TCGA-A8-A07U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

SORL1

insertion

In_Frame_Ins

novel

c.4008_4009insCTGTATCAGATGGCACTCCCAGCGTGCCGTAGCCCCTTACCC

p.Val1336_Cys1337insLeuTyrGlnMetAlaLeuProAlaCysArgSerProLeuPro

p.V1336_C1337insLYQMALPACRSPLP

Q92673

protein_coding

TCGA-A8-A097-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

SORL1

insertion

Frame_Shift_Ins

novel

c.5847_5848insTTTTGCAAATGTTCCGGTGCCCCTGCTGCTCTTGGAT

p.Ile1950PhefsTer20

p.I1950Ffs*20

Q92673

protein_coding

TCGA-B6-A0IM-01

Breast

breast invasive 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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