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: CAPRIN1

Gene summary for CAPRIN1

Gene summary.

Gene information	Species	Human
	Gene symbol	CAPRIN1
	Gene ID	4076
	Gene name	cell cycle associated protein 1
	Gene Alias	GPIAP1
	Cytomap	11p13
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	Q14444

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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
4076	CAPRIN1	HTA11_99999970781_79442	Human	Colorectum	MSS	8.85e-04	4.44e-01	0.294
4076	CAPRIN1	A015-C-203	Human	Colorectum	FAP	5.32e-29	-4.15e-01	-0.1294
4076	CAPRIN1	A015-C-204	Human	Colorectum	FAP	7.39e-05	-3.09e-01	-0.0228
4076	CAPRIN1	A014-C-040	Human	Colorectum	FAP	9.86e-05	-5.67e-01	-0.1184
4076	CAPRIN1	A002-C-201	Human	Colorectum	FAP	7.27e-09	-2.87e-01	0.0324
4076	CAPRIN1	A002-C-203	Human	Colorectum	FAP	2.36e-04	-1.41e-01	0.2786
4076	CAPRIN1	A001-C-119	Human	Colorectum	FAP	4.03e-04	-2.64e-01	-0.1557
4076	CAPRIN1	A001-C-108	Human	Colorectum	FAP	1.45e-11	-2.39e-01	-0.0272
4076	CAPRIN1	A002-C-205	Human	Colorectum	FAP	9.68e-15	-3.12e-01	-0.1236
4076	CAPRIN1	A001-C-104	Human	Colorectum	FAP	1.01e-02	-1.10e-01	0.0184
4076	CAPRIN1	A015-C-006	Human	Colorectum	FAP	1.17e-08	-3.55e-01	-0.0994
4076	CAPRIN1	A015-C-106	Human	Colorectum	FAP	1.26e-09	-2.52e-01	-0.0511
4076	CAPRIN1	A002-C-114	Human	Colorectum	FAP	1.12e-11	-3.20e-01	-0.1561
4076	CAPRIN1	A015-C-104	Human	Colorectum	FAP	7.26e-27	-3.13e-01	-0.1899
4076	CAPRIN1	A001-C-014	Human	Colorectum	FAP	7.92e-15	-3.12e-01	0.0135
4076	CAPRIN1	A002-C-016	Human	Colorectum	FAP	6.21e-19	-2.80e-01	0.0521
4076	CAPRIN1	A015-C-002	Human	Colorectum	FAP	2.14e-07	-2.60e-01	-0.0763
4076	CAPRIN1	A001-C-203	Human	Colorectum	FAP	8.20e-07	-1.77e-01	-0.0481
4076	CAPRIN1	A002-C-116	Human	Colorectum	FAP	2.14e-26	-3.24e-01	-0.0452
4076	CAPRIN1	A014-C-008	Human	Colorectum	FAP	5.82e-08	-3.75e-01	-0.191

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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
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:00226042	Colorectum	MSS	regulation of cell morphogenesis	103/3467	309/18723	2.70e-10	2.56e-08	103
GO:00064172	Colorectum	MSS	regulation of translation	134/3467	468/18723	4.43e-08	2.38e-06	134
GO:01060272	Colorectum	MSS	neuron projection organization	34/3467	93/18723	3.04e-05	6.14e-04	34
GO:00313462	Colorectum	MSS	positive regulation of cell projection organization	96/3467	353/18723	3.44e-05	6.70e-04	96
GO:00107692	Colorectum	MSS	regulation of cell morphogenesis involved in differentiation	34/3467	96/18723	6.43e-05	1.12e-03	34
GO:00109752	Colorectum	MSS	regulation of neuron projection development	115/3467	445/18723	6.91e-05	1.20e-03	115
GO:00107702	Colorectum	MSS	positive regulation of cell morphogenesis involved in differentiation	29/3467	79/18723	1.04e-04	1.63e-03	29
GO:00107202	Colorectum	MSS	positive regulation of cell development	81/3467	298/18723	1.38e-04	2.06e-03	81
GO:00507671	Colorectum	MSS	regulation of neurogenesis	94/3467	364/18723	3.12e-04	4.06e-03	94
GO:00970612	Colorectum	MSS	dendritic spine organization	29/3467	84/18723	3.54e-04	4.50e-03	29
GO:00991732	Colorectum	MSS	postsynapse organization	48/3467	168/18723	9.32e-04	9.44e-03	48
GO:00163582	Colorectum	MSS	dendrite development	65/3467	243/18723	9.41e-04	9.50e-03	65
GO:0017148	Colorectum	MSS	negative regulation of translation	64/3467	245/18723	1.94e-03	1.67e-02	64
GO:0034249	Colorectum	MSS	negative regulation of cellular amide metabolic process	70/3467	273/18723	2.07e-03	1.76e-02	70
GO:00508082	Colorectum	MSS	synapse organization	101/3467	426/18723	3.96e-03	2.89e-02	101
GO:0050769	Colorectum	MSS	positive regulation of neurogenesis	57/3467	225/18723	6.60e-03	4.38e-02	57
GO:0051960	Colorectum	MSS	regulation of nervous system development	103/3467	443/18723	6.68e-03	4.38e-02	103
GO:00226044	Colorectum	FAP	regulation of cell morphogenesis	87/2622	309/18723	4.89e-11	1.87e-08	87
GO:00064174	Colorectum	FAP	regulation of translation	111/2622	468/18723	8.47e-09	1.13e-06	111
GO:00109753	Colorectum	FAP	regulation of neuron projection development	102/2622	445/18723	2.04e-07	1.24e-05	102

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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

CAPRIN1

SNV

Missense_Mutation

rs772325651

c.1624C>G

p.Gln542Glu

p.Q542E

Q14444

protein_coding

tolerated(0.23)

possibly_damaging(0.814)

TCGA-AO-A12H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

CAPRIN1

SNV

Missense_Mutation

novel

c.233A>G

p.Tyr78Cys

p.Y78C

Q14444

protein_coding

deleterious(0.01)

benign(0.014)

TCGA-BH-A0HW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

CAPRIN1

SNV

Missense_Mutation

novel

c.253N>A

p.Gly85Arg

p.G85R

Q14444

protein_coding

deleterious(0)

probably_damaging(0.963)

TCGA-LL-A5YP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CAPRIN1

SNV

Missense_Mutation

novel

c.1141N>A

p.Glu381Lys

p.E381K

Q14444

protein_coding

deleterious(0)

possibly_damaging(0.828)

TCGA-PE-A5DE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

CAPRIN1

SNV

Missense_Mutation

rs148571717

c.1744N>G

p.Gln582Glu

p.Q582E

Q14444

protein_coding

tolerated(0.44)

possibly_damaging(0.498)

TCGA-S3-AA17-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

CAPRIN1

SNV

Missense_Mutation

novel

c.395N>T

p.Arg132Leu

p.R132L

Q14444

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-C5-A8YR-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CAPRIN1

SNV

Missense_Mutation

c.370C>G

p.Gln124Glu

p.Q124E

Q14444

protein_coding

tolerated(0.14)

probably_damaging(0.98)

TCGA-EK-A2RC-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CAPRIN1

SNV

Missense_Mutation

c.418N>C

p.Glu140Gln

p.E140Q

Q14444

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CAPRIN1

SNV

Missense_Mutation

c.2054N>A

p.Gly685Glu

p.G685E

Q14444

protein_coding

deleterious(0)

possibly_damaging(0.617)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CAPRIN1

SNV

Missense_Mutation

novel

c.1244C>G

p.Ser415Cys

p.S415C

Q14444

protein_coding

deleterious(0)

probably_damaging(0.911)

TCGA-VS-A8Q8-01

Cervix

cervical & endocervical cancer

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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