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: EBF2

Gene summary for EBF2

Gene summary.

Gene information	Species	Human
	Gene symbol	EBF2
	Gene ID	64641
	Gene name	EBF transcription factor 2
	Gene Alias	COE2
	Cytomap	8p21.2
	Gene Type	protein-coding
	GO ID	GO:0001659
	UniProtAcc	B2RNT0

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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
64641	EBF2	ATC12	Human	Thyroid	ATC	4.23e-28	5.17e-01	0.34
64641	EBF2	ATC13	Human	Thyroid	ATC	1.88e-57	9.99e-01	0.34
64641	EBF2	ATC4	Human	Thyroid	ATC	2.45e-37	6.47e-01	0.34
64641	EBF2	ATC5	Human	Thyroid	ATC	1.85e-55	1.08e+00	0.34

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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:00725949	Cervix	CC	establishment of protein localization to organelle	99/2311	422/18723	1.23e-10	2.11e-08	99
GO:190382910	Cervix	CC	positive regulation of cellular protein localization	72/2311	276/18723	3.20e-10	4.46e-08	72
GO:007149610	Cervix	CC	cellular response to external stimulus	78/2311	320/18723	1.82e-09	1.98e-07	78
GO:00512359	Cervix	CC	maintenance of location	78/2311	327/18723	5.18e-09	4.92e-07	78
GO:005122210	Cervix	CC	positive regulation of protein transport	72/2311	303/18723	2.36e-08	1.70e-06	72
GO:190495110	Cervix	CC	positive regulation of establishment of protein localization	73/2311	319/18723	9.69e-08	5.25e-06	73
GO:00316689	Cervix	CC	cellular response to extracellular stimulus	59/2311	246/18723	3.03e-07	1.24e-05	59
GO:00068399	Cervix	CC	mitochondrial transport	60/2311	254/18723	4.21e-07	1.67e-05	60
GO:000660510	Cervix	CC	protein targeting	68/2311	314/18723	2.17e-06	6.55e-05	68
GO:00903167	Cervix	CC	positive regulation of intracellular protein transport	41/2311	160/18723	3.24e-06	8.80e-05	41
GO:00323868	Cervix	CC	regulation of intracellular transport	71/2311	337/18723	3.70e-06	9.74e-05	71
GO:00616148	Cervix	CC	pri-miRNA transcription by RNA polymerase II	20/2311	55/18723	4.22e-06	1.09e-04	20
GO:003166710	Cervix	CC	response to nutrient levels	92/2311	474/18723	5.80e-06	1.42e-04	92
GO:00331579	Cervix	CC	regulation of intracellular protein transport	52/2311	229/18723	8.16e-06	1.88e-04	52
GO:00092678	Cervix	CC	cellular response to starvation	39/2311	156/18723	1.04e-05	2.32e-04	39
GO:00425948	Cervix	CC	response to starvation	46/2311	197/18723	1.24e-05	2.59e-04	46
GO:19028938	Cervix	CC	regulation of pri-miRNA transcription by RNA polymerase II	19/2311	54/18723	1.27e-05	2.60e-04	19
GO:00316698	Cervix	CC	cellular response to nutrient levels	49/2311	215/18723	1.32e-05	2.68e-04	49
GO:00705859	Cervix	CC	protein localization to mitochondrion	33/2311	125/18723	1.46e-05	2.90e-04	33
GO:00323889	Cervix	CC	positive regulation of intracellular transport	46/2311	202/18723	2.45e-05	4.24e-04	46

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
EBF2	ECM	Oral cavity	ADJ	PLAC9,EFHD1,MFAP5, etc.	7.18e-01
EBF2	ECM	Oral cavity	OSCC	PLAC9,EFHD1,MFAP5, etc.	1.13e-01

∗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

EBF2

SNV

Missense_Mutation

c.1373C>T

p.Pro458Leu

p.P458L

Q9HAK2

protein_coding

deleterious_low_confidence(0.04)

possibly_damaging(0.593)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

EBF2

SNV

Missense_Mutation

novel

c.202N>T

p.His68Tyr

p.H68Y

Q9HAK2

protein_coding

deleterious(0)

probably_damaging(0.911)

TCGA-AC-A2QI-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cytoxan

EBF2

SNV

Missense_Mutation

c.469N>A

p.Glu157Lys

p.E157K

Q9HAK2

protein_coding

deleterious(0)

possibly_damaging(0.6)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EBF2

SNV

Missense_Mutation

c.1468N>G

p.Leu490Val

p.L490V

Q9HAK2

protein_coding

deleterious_low_confidence(0.02)

possibly_damaging(0.816)

TCGA-BH-A0AW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

EBF2

SNV

Missense_Mutation

c.421N>A

p.Glu141Lys

p.E141K

Q9HAK2

protein_coding

deleterious(0.02)

probably_damaging(0.997)

TCGA-BH-A0DP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

EBF2

SNV

Missense_Mutation

novel

c.1204N>G

p.Leu402Val

p.L402V

Q9HAK2

protein_coding

deleterious_low_confidence(0.03)

probably_damaging(0.911)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

EBF2

SNV

Missense_Mutation

novel

c.599C>G

p.Thr200Arg

p.T200R

Q9HAK2

protein_coding

deleterious(0)

benign(0.142)

TCGA-D8-A1JP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

EBF2

SNV

Missense_Mutation

novel

c.725N>C

p.Arg242Thr

p.R242T

Q9HAK2

protein_coding

deleterious(0)

possibly_damaging(0.491)

TCGA-EW-A423-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

EBF2

SNV

Missense_Mutation

novel

c.8N>A

p.Gly3Glu

p.G3E

Q9HAK2

protein_coding

deleterious_low_confidence(0.04)

benign(0.018)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

EBF2

SNV

Missense_Mutation

c.1138C>G

p.Leu380Val

p.L380V

Q9HAK2

protein_coding

tolerated(0.06)

benign(0.148)

TCGA-VS-A954-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

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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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