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: TRIM29

Gene summary for TRIM29

Gene summary.

Gene information	Species	Human
	Gene symbol	TRIM29
	Gene ID	23650
	Gene name	tripartite motif containing 29
	Gene Alias	ATDC
	Cytomap	11q23.3
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	B7Z5V5

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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
23650	TRIM29	CA_HPV_1	Human	Cervix	CC	1.42e-12	-3.19e-01	0.0264
23650	TRIM29	CA_HPV_3	Human	Cervix	CC	2.05e-08	3.39e-01	0.0414
23650	TRIM29	Tumor	Human	Cervix	CC	5.02e-38	7.91e-01	0.1241
23650	TRIM29	sample3	Human	Cervix	CC	5.07e-47	8.08e-01	0.1387
23650	TRIM29	L1	Human	Cervix	CC	3.73e-03	3.65e-01	0.0802
23650	TRIM29	T3	Human	Cervix	CC	1.34e-46	8.25e-01	0.1389
23650	TRIM29	HTA11_2487_2000001011	Human	Colorectum	SER	1.05e-03	2.11e-01	-0.1808
23650	TRIM29	HTA11_2951_2000001011	Human	Colorectum	AD	2.35e-03	2.95e-01	0.0216
23650	TRIM29	HTA11_411_2000001011	Human	Colorectum	SER	1.94e-04	5.25e-01	-0.2602
23650	TRIM29	HTA11_8622_2000001021	Human	Colorectum	SER	2.29e-06	3.14e-01	0.0528
23650	TRIM29	HTA11_7696_3000711011	Human	Colorectum	AD	4.86e-04	9.76e-02	0.0674
23650	TRIM29	HTA11_99999970781_79442	Human	Colorectum	MSS	3.10e-11	2.58e-01	0.294
23650	TRIM29	HTA11_99999965104_69814	Human	Colorectum	MSS	2.42e-04	1.89e-01	0.281
23650	TRIM29	HTA11_99999971662_82457	Human	Colorectum	MSS	2.09e-25	6.04e-01	0.3859
23650	TRIM29	HTA11_99999974143_84620	Human	Colorectum	MSS	3.78e-18	4.40e-01	0.3005
23650	TRIM29	LZE4T	Human	Esophagus	ESCC	7.93e-08	6.00e-01	0.0811
23650	TRIM29	LZE8T	Human	Esophagus	ESCC	2.62e-03	6.90e-02	0.067
23650	TRIM29	LZE24T	Human	Esophagus	ESCC	9.99e-21	1.27e+00	0.0596
23650	TRIM29	LZE22D3	Human	Esophagus	HGIN	1.83e-05	1.80e-01	0.0653
23650	TRIM29	LZE6T	Human	Esophagus	ESCC	1.47e-06	-4.32e-01	0.0845

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
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

∗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:00345048	Cervix	CC	protein localization to nucleus	68/2311	290/18723	9.91e-08	5.25e-06	68
GO:19001808	Cervix	CC	regulation of protein localization to nucleus	31/2311	136/18723	4.76e-04	4.69e-03	31
GO:19038286	Cervix	CC	negative regulation of cellular protein localization	24/2311	117/18723	8.10e-03	4.23e-02	24
GO:1900180	Colorectum	AD	regulation of protein localization to nucleus	55/3918	136/18723	1.70e-07	7.34e-06	55
GO:0034504	Colorectum	AD	protein localization to nucleus	94/3918	290/18723	2.83e-06	8.09e-05	94
GO:1903828	Colorectum	AD	negative regulation of cellular protein localization	39/3918	117/18723	1.18e-03	1.06e-02	39
GO:19001801	Colorectum	SER	regulation of protein localization to nucleus	46/2897	136/18723	8.50e-08	5.27e-06	46
GO:00345041	Colorectum	SER	protein localization to nucleus	74/2897	290/18723	5.74e-06	2.05e-04	74
GO:19038281	Colorectum	SER	negative regulation of cellular protein localization	30/2897	117/18723	2.96e-03	2.62e-02	30
GO:19001802	Colorectum	MSS	regulation of protein localization to nucleus	54/3467	136/18723	6.20e-09	3.95e-07	54
GO:00345042	Colorectum	MSS	protein localization to nucleus	92/3467	290/18723	3.66e-08	1.98e-06	92
GO:19038282	Colorectum	MSS	negative regulation of cellular protein localization	36/3467	117/18723	9.19e-04	9.34e-03	36
GO:003450417	Esophagus	HGIN	protein localization to nucleus	84/2587	290/18723	1.06e-11	1.24e-09	84
GO:190018017	Esophagus	HGIN	regulation of protein localization to nucleus	40/2587	136/18723	1.69e-06	6.31e-05	40
GO:003450418	Esophagus	ESCC	protein localization to nucleus	211/8552	290/18723	4.06e-21	6.60e-19	211
GO:190018018	Esophagus	ESCC	regulation of protein localization to nucleus	102/8552	136/18723	2.84e-12	1.13e-10	102
GO:19038289	Esophagus	ESCC	negative regulation of cellular protein localization	76/8552	117/18723	1.97e-05	1.72e-04	76
GO:003450415	Oral cavity	OSCC	protein localization to nucleus	193/7305	290/18723	1.22e-21	2.35e-19	193
GO:190018015	Oral cavity	OSCC	regulation of protein localization to nucleus	93/7305	136/18723	3.46e-12	1.35e-10	93
GO:19038288	Oral cavity	OSCC	negative regulation of cellular protein localization	65/7305	117/18723	2.05e-04	1.36e-03	65

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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

TRIM29

SNV

Missense_Mutation

c.704N>G

p.Phe235Cys

p.F235C

Q14134

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A09A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

TRIM29

SNV

Missense_Mutation

rs185266068

c.1562C>T

p.Ser521Phe

p.S521F

Q14134

protein_coding

deleterious(0)

probably_damaging(0.95)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

TRIM29

SNV

Missense_Mutation

novel

c.1118N>T

p.Ser373Phe

p.S373F

Q14134

protein_coding

deleterious(0.01)

probably_damaging(0.942)

TCGA-BH-A209-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

TRIM29

SNV

Missense_Mutation

c.1420T>C

p.Tyr474His

p.Y474H

Q14134

protein_coding

tolerated(0.05)

benign(0.003)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

TRIM29

insertion

Frame_Shift_Ins

novel

c.855dupT

p.Glu286Ter

p.E286*

Q14134

protein_coding

TCGA-B6-A400-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

TRIM29

SNV

Missense_Mutation

novel

c.715N>A

p.Asp239Asn

p.D239N

Q14134

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

TRIM29

SNV

Missense_Mutation

novel

c.267N>C

p.Lys89Asn

p.K89N

Q14134

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.994)

TCGA-C5-A2LZ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Unknown

TRIM29

SNV

Missense_Mutation

rs557844201

c.893G>A

p.Arg298His

p.R298H

Q14134

protein_coding

deleterious(0.01)

probably_damaging(0.997)

TCGA-A6-5661-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

TRIM29

SNV

Missense_Mutation

novel

c.1500N>T

p.Lys500Asn

p.K500N

Q14134

protein_coding

tolerated(0.07)

benign(0.034)

TCGA-AA-A010-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Chemotherapy

folinic

TRIM29

SNV

Missense_Mutation

c.260A>C

p.Asp87Ala

p.D87A

Q14134

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.996)

TCGA-AD-6890-01

Colorectum

colon adenocarcinoma

Male

>=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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