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: EIF3D

Gene summary for EIF3D

Gene summary.

Gene information	Species	Human
	Gene symbol	EIF3D
	Gene ID	8664
	Gene name	eukaryotic translation initiation factor 3 subunit D
	Gene Alias	EIF3S7
	Cytomap	22q12.3
	Gene Type	protein-coding
	GO ID	GO:0001732
	UniProtAcc	O15371

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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
8664	EIF3D	GSM4909281	Human	Breast	IDC	1.97e-04	-2.89e-01	0.21
8664	EIF3D	GSM4909287	Human	Breast	IDC	3.42e-10	-4.63e-01	0.2057
8664	EIF3D	GSM4909291	Human	Breast	IDC	8.11e-10	-5.41e-01	0.1753
8664	EIF3D	GSM4909293	Human	Breast	IDC	4.05e-16	-4.76e-01	0.1581
8664	EIF3D	GSM4909294	Human	Breast	IDC	2.30e-14	-4.28e-01	0.2022
8664	EIF3D	GSM4909296	Human	Breast	IDC	6.43e-34	-6.15e-01	0.1524
8664	EIF3D	GSM4909297	Human	Breast	IDC	6.96e-23	-3.08e-01	0.1517
8664	EIF3D	GSM4909298	Human	Breast	IDC	5.84e-04	-3.02e-01	0.1551
8664	EIF3D	GSM4909301	Human	Breast	IDC	5.77e-35	-7.09e-01	0.1577
8664	EIF3D	GSM4909302	Human	Breast	IDC	3.63e-11	-4.72e-01	0.1545
8664	EIF3D	GSM4909304	Human	Breast	IDC	8.46e-13	-4.31e-01	0.1636
8664	EIF3D	GSM4909305	Human	Breast	IDC	3.42e-03	2.95e-01	0.0436
8664	EIF3D	GSM4909307	Human	Breast	IDC	5.24e-05	-3.38e-01	0.1569
8664	EIF3D	GSM4909309	Human	Breast	IDC	4.25e-04	-2.85e-01	0.0483
8664	EIF3D	GSM4909311	Human	Breast	IDC	1.29e-46	-4.00e-01	0.1534
8664	EIF3D	GSM4909312	Human	Breast	IDC	1.28e-19	-5.57e-02	0.1552
8664	EIF3D	GSM4909313	Human	Breast	IDC	9.84e-07	1.20e-02	0.0391
8664	EIF3D	GSM4909315	Human	Breast	IDC	1.87e-09	-4.25e-01	0.21
8664	EIF3D	GSM4909316	Human	Breast	IDC	8.62e-05	-5.22e-01	0.21
8664	EIF3D	GSM4909317	Human	Breast	IDC	1.77e-02	-2.84e-01	0.1355

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid 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:00021819	Breast	Precancer	cytoplasmic translation	80/1080	148/18723	1.59e-59	8.54e-56	80
GO:00226139	Breast	Precancer	ribonucleoprotein complex biogenesis	79/1080	463/18723	2.11e-18	1.03e-15	79
GO:00718269	Breast	Precancer	ribonucleoprotein complex subunit organization	48/1080	227/18723	2.68e-15	8.45e-13	48
GO:00226189	Breast	Precancer	ribonucleoprotein complex assembly	47/1080	220/18723	3.47e-15	1.03e-12	47
GO:00064138	Breast	Precancer	translational initiation	30/1080	118/18723	3.23e-12	5.58e-10	30
GO:00064179	Breast	Precancer	regulation of translation	67/1080	468/18723	4.71e-12	7.64e-10	67
GO:00457279	Breast	Precancer	positive regulation of translation	32/1080	136/18723	5.89e-12	9.27e-10	32
GO:00342509	Breast	Precancer	positive regulation of cellular amide metabolic process	33/1080	162/18723	1.72e-10	1.77e-08	33
GO:00160329	Breast	Precancer	viral process	58/1080	415/18723	3.42e-10	3.16e-08	58
GO:00021838	Breast	Precancer	cytoplasmic translational initiation	11/1080	34/18723	1.87e-06	6.63e-05	11
GO:00510989	Breast	Precancer	regulation of binding	44/1080	363/18723	2.59e-06	8.65e-05	44
GO:00017328	Breast	Precancer	formation of cytoplasmic translation initiation complex	7/1080	16/18723	1.50e-05	3.71e-04	7
GO:00510999	Breast	Precancer	positive regulation of binding	23/1080	173/18723	1.58e-04	2.68e-03	23
GO:000218114	Breast	IDC	cytoplasmic translation	82/1434	148/18723	2.60e-52	1.48e-48	82
GO:002261314	Breast	IDC	ribonucleoprotein complex biogenesis	83/1434	463/18723	2.01e-13	5.20e-11	83
GO:007182614	Breast	IDC	ribonucleoprotein complex subunit organization	52/1434	227/18723	5.18e-13	1.21e-10	52
GO:002261814	Breast	IDC	ribonucleoprotein complex assembly	51/1434	220/18723	5.32e-13	1.21e-10	51
GO:001603214	Breast	IDC	viral process	75/1434	415/18723	1.98e-12	4.02e-10	75
GO:000641313	Breast	IDC	translational initiation	31/1434	118/18723	7.29e-10	7.52e-08	31
GO:000641714	Breast	IDC	regulation of translation	74/1434	468/18723	1.67e-09	1.53e-07	74

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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

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-A2-A0CS-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

EIF3D

SNV

Missense_Mutation

rs761711093

c.89A>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-A2-A1FW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-A2-A1G0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-A2-A1G4-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

adriamycin

EIF3D

SNV

Missense_Mutation

novel

c.892N>A

p.Pro298Thr

p.P298T

O15371

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-BH-A0HU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-D8-A1JD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-D8-A1JK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-D8-A1X6-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

EIF3D

SNV

Missense_Mutation

rs761711093

c.89N>C

p.Tyr30Ser

p.Y30S

O15371

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-D8-A1XG-01

Breast

breast invasive carcinoma

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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