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: UBE2Q1

Gene summary for UBE2Q1

Gene summary.

Gene information	Species	Human
	Gene symbol	UBE2Q1
	Gene ID	55585
	Gene name	ubiquitin conjugating enzyme E2 Q1
	Gene Alias	GTAP
	Cytomap	1q21.3
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	Q7Z7E8

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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
55585	UBE2Q1	HTA11_3410_2000001011	Human	Colorectum	AD	3.10e-05	1.54e-01	0.0155
55585	UBE2Q1	HTA11_2487_2000001011	Human	Colorectum	SER	6.91e-03	2.22e-01	-0.1808
55585	UBE2Q1	HTA11_1938_2000001011	Human	Colorectum	AD	3.40e-06	3.24e-01	-0.0811
55585	UBE2Q1	HTA11_78_2000001011	Human	Colorectum	AD	1.53e-04	2.13e-01	-0.1088
55585	UBE2Q1	HTA11_347_2000001011	Human	Colorectum	AD	9.32e-10	2.79e-01	-0.1954
55585	UBE2Q1	HTA11_696_2000001011	Human	Colorectum	AD	1.59e-03	2.27e-01	-0.1464
55585	UBE2Q1	HTA11_1391_2000001011	Human	Colorectum	AD	2.50e-13	4.76e-01	-0.059
55585	UBE2Q1	HTA11_5212_2000001011	Human	Colorectum	AD	1.08e-04	3.82e-01	-0.2061
55585	UBE2Q1	HTA11_7862_2000001011	Human	Colorectum	AD	5.47e-04	2.78e-01	-0.0179
55585	UBE2Q1	HTA11_866_3004761011	Human	Colorectum	AD	2.32e-15	4.27e-01	0.096
55585	UBE2Q1	HTA11_7663_2000001011	Human	Colorectum	SER	2.47e-04	3.99e-01	0.0131
55585	UBE2Q1	HTA11_10711_2000001011	Human	Colorectum	AD	2.54e-04	1.98e-01	0.0338
55585	UBE2Q1	HTA11_7696_3000711011	Human	Colorectum	AD	1.12e-06	3.05e-01	0.0674
55585	UBE2Q1	HTA11_99999970781_79442	Human	Colorectum	MSS	1.96e-05	3.39e-01	0.294
55585	UBE2Q1	HTA11_99999971662_82457	Human	Colorectum	MSS	1.39e-25	6.68e-01	0.3859
55585	UBE2Q1	HTA11_99999974143_84620	Human	Colorectum	MSS	2.77e-02	1.85e-01	0.3005
55585	UBE2Q1	LZE2T	Human	Esophagus	ESCC	8.46e-03	4.72e-01	0.082
55585	UBE2Q1	LZE4T	Human	Esophagus	ESCC	7.52e-06	2.64e-02	0.0811
55585	UBE2Q1	LZE24T	Human	Esophagus	ESCC	1.52e-05	1.69e-01	0.0596
55585	UBE2Q1	LZE6T	Human	Esophagus	ESCC	8.88e-03	6.82e-02	0.0845

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:0000209	Colorectum	AD	protein polyubiquitination	78/3918	236/18723	8.71e-06	2.06e-04	78
GO:0009306	Colorectum	AD	protein secretion	105/3918	359/18723	1.05e-04	1.57e-03	105
GO:0035592	Colorectum	AD	establishment of protein localization to extracellular region	105/3918	360/18723	1.18e-04	1.73e-03	105
GO:0071692	Colorectum	AD	protein localization to extracellular region	106/3918	368/18723	1.86e-04	2.49e-03	106
GO:0015833	Colorectum	AD	peptide transport	77/3918	264/18723	8.90e-04	8.60e-03	77
GO:0061458	Colorectum	AD	reproductive system development	116/3918	427/18723	1.11e-03	1.01e-02	116
GO:0030072	Colorectum	AD	peptide hormone secretion	68/3918	236/18723	2.39e-03	1.85e-02	68
GO:0002790	Colorectum	AD	peptide secretion	69/3918	242/18723	2.97e-03	2.22e-02	69
GO:0042886	Colorectum	AD	amide transport	83/3918	301/18723	3.37e-03	2.46e-02	83
GO:00002091	Colorectum	SER	protein polyubiquitination	58/2897	236/18723	1.69e-04	3.18e-03	58
GO:00093061	Colorectum	SER	protein secretion	79/2897	359/18723	5.99e-04	8.19e-03	79
GO:00355921	Colorectum	SER	establishment of protein localization to extracellular region	79/2897	360/18723	6.54e-04	8.77e-03	79
GO:00716921	Colorectum	SER	protein localization to extracellular region	80/2897	368/18723	8.13e-04	1.01e-02	80
GO:00158331	Colorectum	SER	peptide transport	58/2897	264/18723	3.08e-03	2.70e-02	58
GO:00614581	Colorectum	SER	reproductive system development	87/2897	427/18723	3.69e-03	3.07e-02	87
GO:00002092	Colorectum	MSS	protein polyubiquitination	72/3467	236/18723	5.19e-06	1.42e-04	72
GO:00614582	Colorectum	MSS	reproductive system development	115/3467	427/18723	9.86e-06	2.39e-04	115
GO:00093062	Colorectum	MSS	protein secretion	98/3467	359/18723	2.43e-05	5.09e-04	98
GO:00355922	Colorectum	MSS	establishment of protein localization to extracellular region	98/3467	360/18723	2.75e-05	5.58e-04	98
GO:00716922	Colorectum	MSS	protein localization to extracellular region	99/3467	368/18723	4.17e-05	7.83e-04	99

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04120	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041201	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041202	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041203	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041204	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa041205	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa0412027	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122
hsa0412036	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122
hsa0412041	Liver	HCC	Ubiquitin mediated proteolysis	110/4020	142/8465	1.67e-13	3.74e-12	2.08e-12	110
hsa0412051	Liver	HCC	Ubiquitin mediated proteolysis	110/4020	142/8465	1.67e-13	3.74e-12	2.08e-12	110
hsa0412020	Oral cavity	OSCC	Ubiquitin mediated proteolysis	105/3704	142/8465	1.83e-13	4.37e-12	2.23e-12	105
hsa04120110	Oral cavity	OSCC	Ubiquitin mediated proteolysis	105/3704	142/8465	1.83e-13	4.37e-12	2.23e-12	105
hsa0412025	Oral cavity	LP	Ubiquitin mediated proteolysis	66/2418	142/8465	3.74e-06	3.46e-05	2.23e-05	66
hsa0412035	Oral cavity	LP	Ubiquitin mediated proteolysis	66/2418	142/8465	3.74e-06	3.46e-05	2.23e-05	66
hsa0412018	Prostate	BPH	Ubiquitin mediated proteolysis	61/1718	142/8465	5.50e-10	9.07e-09	5.61e-09	61
hsa0412019	Prostate	BPH	Ubiquitin mediated proteolysis	61/1718	142/8465	5.50e-10	9.07e-09	5.61e-09	61
hsa0412024	Prostate	Tumor	Ubiquitin mediated proteolysis	61/1791	142/8465	3.08e-09	5.09e-08	3.16e-08	61
hsa0412034	Prostate	Tumor	Ubiquitin mediated proteolysis	61/1791	142/8465	3.08e-09	5.09e-08	3.16e-08	61

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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

UBE2Q1

SNV

Missense_Mutation

rs760511660

c.280N>T

p.Arg94Trp

p.R94W

Q7Z7E8

protein_coding

deleterious(0)

possibly_damaging(0.522)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

UBE2Q1

SNV

Missense_Mutation

novel

c.458N>C

p.Ile153Thr

p.I153T

Q7Z7E8

protein_coding

deleterious(0)

possibly_damaging(0.601)

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

UBE2Q1

SNV

Missense_Mutation

c.829G>A

p.Glu277Lys

p.E277K

Q7Z7E8

protein_coding

deleterious(0)

possibly_damaging(0.581)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UBE2Q1

SNV

Missense_Mutation

c.746N>T

p.Ser249Leu

p.S249L

Q7Z7E8

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-C8-A134-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

UBE2Q1

SNV

Missense_Mutation

c.337N>A

p.Pro113Thr

p.P113T

Q7Z7E8

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

UBE2Q1

insertion

Frame_Shift_Ins

novel

c.455_456insTCCTTTTCTTTTCACTCCCACCCCA

p.Ile153ProfsTer14

p.I153Pfs*14

Q7Z7E8

protein_coding

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

UBE2Q1

SNV

Missense_Mutation

novel

c.1186A>T

p.Thr396Ser

p.T396S

Q7Z7E8

protein_coding

tolerated(0.17)

benign(0.003)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

UBE2Q1

SNV

Missense_Mutation

novel

c.624G>T

p.Glu208Asp

p.E208D

Q7Z7E8

protein_coding

tolerated(0.13)

benign(0.11)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

UBE2Q1

SNV

Missense_Mutation

rs754369992

c.1228N>A

p.Glu410Lys

p.E410K

Q7Z7E8

protein_coding

tolerated(0.07)

benign(0.234)

TCGA-EK-A3GK-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

UBE2Q1

SNV

Missense_Mutation

c.478T>G

p.Tyr160Asp

p.Y160D

Q7Z7E8

protein_coding

deleterious(0)

probably_damaging(0.943)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

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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