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: CPEB2

Gene summary for CPEB2

Gene summary.

Gene information	Species	Human
	Gene symbol	CPEB2
	Gene ID	132864
	Gene name	cytoplasmic polyadenylation element binding protein 2
	Gene Alias	CPE-BP2
	Cytomap	4p15.32
	Gene Type	protein-coding
	GO ID	GO:0001666
	UniProtAcc	Q7Z5Q1

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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
132864	CPEB2	RNA-P25T1-P25T1-1	Human	Lung	AIS	6.51e-09	5.10e-01	-0.2116
132864	CPEB2	RNA-P25T1-P25T1-3	Human	Lung	AIS	1.49e-02	4.99e-01	-0.2107
132864	CPEB2	RNA-P25T1-P25T1-4	Human	Lung	AIS	6.86e-06	5.06e-01	-0.2119

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma

∗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:000218113	Lung	AIS	cytoplasmic translation	85/1849	148/18723	5.48e-47	3.19e-43	85
GO:004308711	Lung	AIS	regulation of GTPase activity	65/1849	348/18723	3.35e-07	2.83e-05	65
GO:003286812	Lung	AIS	response to insulin	52/1849	264/18723	9.51e-07	6.69e-05	52
GO:190165312	Lung	AIS	cellular response to peptide	65/1849	359/18723	1.05e-06	7.27e-05	65
GO:007137512	Lung	AIS	cellular response to peptide hormone stimulus	55/1849	290/18723	1.62e-06	9.91e-05	55
GO:000641713	Lung	AIS	regulation of translation	78/1849	468/18723	2.68e-06	1.49e-04	78
GO:003286912	Lung	AIS	cellular response to insulin stimulus	42/1849	203/18723	2.80e-06	1.52e-04	42
GO:000697913	Lung	AIS	response to oxidative stress	75/1849	446/18723	2.97e-06	1.60e-04	75
GO:004343413	Lung	AIS	response to peptide hormone	70/1849	414/18723	5.19e-06	2.48e-04	70
GO:006219713	Lung	AIS	cellular response to chemical stress	58/1849	337/18723	1.91e-05	6.62e-04	58
GO:003459913	Lung	AIS	cellular response to oxidative stress	49/1849	288/18723	1.10e-04	2.57e-03	49
GO:003629313	Lung	AIS	response to decreased oxygen levels	53/1849	322/18723	1.42e-04	3.09e-03	53
GO:003629412	Lung	AIS	cellular response to decreased oxygen levels	31/1849	161/18723	2.15e-04	4.36e-03	31
GO:007145312	Lung	AIS	cellular response to oxygen levels	33/1849	177/18723	2.56e-04	4.96e-03	33
GO:000166613	Lung	AIS	response to hypoxia	50/1849	307/18723	2.79e-04	5.26e-03	50
GO:007145612	Lung	AIS	cellular response to hypoxia	29/1849	151/18723	3.54e-04	6.32e-03	29
GO:20007651	Lung	AIS	regulation of cytoplasmic translation	7/1849	16/18723	4.64e-04	7.78e-03	7
GO:007048213	Lung	AIS	response to oxygen levels	54/1849	347/18723	5.15e-04	8.38e-03	54

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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

CPEB2

SNV

Missense_Mutation

c.3044A>G

p.His1015Arg

p.H1015R

Q7Z5Q1

protein_coding

deleterious_low_confidence(0)

probably_damaging(1)

TCGA-A1-A0SD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CPEB2

SNV

Missense_Mutation

c.2452N>T

p.Pro818Ser

p.P818S

Q7Z5Q1

protein_coding

deleterious_low_confidence(0.02)

probably_damaging(0.996)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

CPEB2

SNV

Missense_Mutation

c.2316A>G

p.Ile772Met

p.I772M

Q7Z5Q1

protein_coding

tolerated_low_confidence(0.1)

benign(0.113)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CPEB2

SNV

Missense_Mutation

rs781736943

c.2932N>A

p.Ala978Thr

p.A978T

Q7Z5Q1

protein_coding

tolerated_low_confidence(0.26)

benign(0.249)

TCGA-BH-A1FC-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CPEB2

SNV

Missense_Mutation

c.2465N>G

p.Tyr822Cys

p.Y822C

Q7Z5Q1

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.997)

TCGA-C8-A132-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CPEB2

SNV

Missense_Mutation

c.2203N>T

p.Arg735Cys

p.R735C

Q7Z5Q1

protein_coding

deleterious_low_confidence(0.01)

benign(0.106)

TCGA-S3-AA14-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CPEB2

SNV

Missense_Mutation

c.2761N>A

p.Pro921Thr

p.P921T

Q7Z5Q1

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.945)

TCGA-UU-A93S-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

CPEB2

SNV

Missense_Mutation

c.1753C>T

p.His585Tyr

p.H585Y

Q7Z5Q1

protein_coding

tolerated_low_confidence(0.16)

benign(0.051)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

CPEB2

SNV

Missense_Mutation

c.2233T>A

p.Leu745Met

p.L745M

Q7Z5Q1

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.946)

TCGA-AA-3488-01

Colorectum

colon adenocarcinoma

Male

<65

III/IV

Unknown

CPEB2

SNV

Missense_Mutation

c.1693C>A

p.His565Asn

p.H565N

Q7Z5Q1

protein_coding

tolerated_low_confidence(0.07)

possibly_damaging(0.626)

TCGA-AA-3811-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

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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