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:00329331	Colorectum	SER	SREBP signaling pathway	7/2897	15/18723	4.30e-03	3.45e-02	7
GO:00316691	Colorectum	SER	cellular response to nutrient levels	48/2897	215/18723	4.82e-03	3.78e-02	48
GO:1903955	Colorectum	SER	positive regulation of protein targeting to mitochondrion	11/2897	32/18723	6.58e-03	4.68e-02	11
GO:00715011	Colorectum	SER	cellular response to sterol depletion	7/2897	16/18723	6.63e-03	4.69e-02	7
GO:19038292	Colorectum	MSS	positive regulation of cellular protein localization	103/3467	276/18723	1.12e-13	2.67e-11	103
GO:00725942	Colorectum	MSS	establishment of protein localization to organelle	139/3467	422/18723	5.75e-13	1.12e-10	139
GO:00068392	Colorectum	MSS	mitochondrial transport	93/3467	254/18723	6.14e-12	9.82e-10	93
GO:19049512	Colorectum	MSS	positive regulation of establishment of protein localization	110/3467	319/18723	6.30e-12	9.83e-10	110
GO:00512222	Colorectum	MSS	positive regulation of protein transport	104/3467	303/18723	3.23e-11	4.11e-09	104
GO:00903162	Colorectum	MSS	positive regulation of intracellular protein transport	60/3467	160/18723	1.18e-08	7.08e-07	60
GO:00224112	Colorectum	MSS	cellular component disassembly	130/3467	443/18723	1.44e-08	8.46e-07	130
GO:00323882	Colorectum	MSS	positive regulation of intracellular transport	70/3467	202/18723	3.32e-08	1.82e-06	70
GO:00066052	Colorectum	MSS	protein targeting	97/3467	314/18723	6.76e-08	3.46e-06	97
GO:00331572	Colorectum	MSS	regulation of intracellular protein transport	76/3467	229/18723	7.03e-08	3.56e-06	76
GO:00323862	Colorectum	MSS	regulation of intracellular transport	102/3467	337/18723	9.73e-08	4.71e-06	102
GO:00108212	Colorectum	MSS	regulation of mitochondrion organization	53/3467	144/18723	1.67e-07	7.55e-06	53
GO:00705852	Colorectum	MSS	protein localization to mitochondrion	47/3467	125/18723	3.98e-07	1.58e-05	47
GO:00105062	Colorectum	MSS	regulation of autophagy	95/3467	317/18723	4.36e-07	1.71e-05	95
GO:19031462	Colorectum	MSS	regulation of autophagy of mitochondrion	19/3467	33/18723	6.51e-07	2.39e-05	19
GO:00726552	Colorectum	MSS	establishment of protein localization to mitochondrion	44/3467	120/18723	2.03e-06	6.28e-05	44

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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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