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

Home

Download

Statistics

Help

Contact

	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: TPT1

Gene summary for TPT1

Gene summary.

Gene information	Species	Human
	Gene symbol	TPT1
	Gene ID	7178
	Gene name	tumor protein, translationally-controlled 1
	Gene Alias	HRF
	Cytomap	13q14.13
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	A0A0B4J2C3

Top

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
7178	TPT1	GSM4909281	Human	Breast	IDC	5.16e-125	-8.75e-01	0.21
7178	TPT1	GSM4909282	Human	Breast	IDC	1.19e-60	-4.08e-01	-0.0288
7178	TPT1	GSM4909286	Human	Breast	IDC	7.13e-46	-3.06e-01	0.1081
7178	TPT1	GSM4909288	Human	Breast	IDC	4.78e-13	2.64e-01	0.0988
7178	TPT1	GSM4909289	Human	Breast	IDC	5.55e-07	-3.46e-01	0.1064
7178	TPT1	GSM4909290	Human	Breast	IDC	8.59e-42	-4.49e-01	0.2096
7178	TPT1	GSM4909291	Human	Breast	IDC	7.36e-44	-5.09e-01	0.1753
7178	TPT1	GSM4909293	Human	Breast	IDC	1.94e-21	-1.73e-01	0.1581
7178	TPT1	GSM4909294	Human	Breast	IDC	6.02e-03	7.88e-02	0.2022
7178	TPT1	GSM4909295	Human	Breast	IDC	9.53e-22	-4.24e-01	0.0898
7178	TPT1	GSM4909296	Human	Breast	IDC	6.18e-50	-4.81e-01	0.1524
7178	TPT1	GSM4909297	Human	Breast	IDC	1.23e-61	-8.09e-01	0.1517
7178	TPT1	GSM4909298	Human	Breast	IDC	2.36e-07	1.23e-01	0.1551
7178	TPT1	GSM4909299	Human	Breast	IDC	3.01e-02	-8.62e-02	0.035
7178	TPT1	GSM4909300	Human	Breast	IDC	1.43e-02	-1.67e-01	0.0334
7178	TPT1	GSM4909301	Human	Breast	IDC	1.93e-105	-7.56e-01	0.1577
7178	TPT1	GSM4909302	Human	Breast	IDC	4.56e-31	-3.69e-01	0.1545
7178	TPT1	GSM4909304	Human	Breast	IDC	2.94e-43	-2.93e-01	0.1636
7178	TPT1	GSM4909305	Human	Breast	IDC	1.82e-18	-2.21e-01	0.0436
7178	TPT1	GSM4909306	Human	Breast	IDC	1.21e-57	-3.66e-01	0.1564

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

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
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
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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.

Top

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).

Page: 1 2 3 4 5 6 7 8 9

Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:00971939	Breast	Precancer	intrinsic apoptotic signaling pathway	59/1080	288/18723	8.07e-18	3.60e-15	59
GO:20012339	Breast	Precancer	regulation of apoptotic signaling pathway	65/1080	356/18723	7.70e-17	3.17e-14	65
GO:20012429	Breast	Precancer	regulation of intrinsic apoptotic signaling pathway	41/1080	164/18723	6.48e-16	2.31e-13	41
GO:20012349	Breast	Precancer	negative regulation of apoptotic signaling pathway	39/1080	224/18723	5.35e-10	4.77e-08	39
GO:20012439	Breast	Precancer	negative regulation of intrinsic apoptotic signaling pathway	23/1080	98/18723	5.82e-09	4.45e-07	23
GO:00086308	Breast	Precancer	intrinsic apoptotic signaling pathway in response to DNA damage	16/1080	99/18723	1.65e-04	2.74e-03	16
GO:19022293	Breast	Precancer	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	8/1080	36/18723	8.49e-04	9.82e-03	8
GO:20010208	Breast	Precancer	regulation of response to DNA damage stimulus	24/1080	219/18723	1.93e-03	1.87e-02	24
GO:0072503	Breast	Precancer	cellular divalent inorganic cation homeostasis	42/1080	486/18723	5.91e-03	4.21e-02	42
GO:200123314	Breast	IDC	regulation of apoptotic signaling pathway	82/1434	356/18723	6.27e-20	5.93e-17	82
GO:009719314	Breast	IDC	intrinsic apoptotic signaling pathway	69/1434	288/18723	6.32e-18	2.99e-15	69
GO:200124214	Breast	IDC	regulation of intrinsic apoptotic signaling pathway	47/1434	164/18723	8.25e-16	2.93e-13	47
GO:200123414	Breast	IDC	negative regulation of apoptotic signaling pathway	49/1434	224/18723	1.45e-11	2.58e-09	49
GO:200124314	Breast	IDC	negative regulation of intrinsic apoptotic signaling pathway	27/1434	98/18723	2.91e-09	2.50e-07	27
GO:000863013	Breast	IDC	intrinsic apoptotic signaling pathway in response to DNA damage	21/1434	99/18723	1.57e-05	3.94e-04	21
GO:00096157	Breast	IDC	response to virus	47/1434	367/18723	3.53e-04	5.16e-03	47
GO:190222912	Breast	IDC	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	9/1434	36/18723	1.25e-03	1.33e-02	9
GO:200102013	Breast	IDC	regulation of response to DNA damage stimulus	30/1434	219/18723	1.36e-03	1.40e-02	30
GO:200123324	Breast	DCIS	regulation of apoptotic signaling pathway	81/1390	356/18723	3.51e-20	3.31e-17	81
GO:009719324	Breast	DCIS	intrinsic apoptotic signaling pathway	68/1390	288/18723	4.93e-18	2.33e-15	68

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

Page: 1

Top

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

Page: 1

Top

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.

Page: 1

Top

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

TPT1

SNV

Missense_Mutation

novel

c.320N>C

p.Arg107Thr

p.R107T

protein_coding

tolerated(0.09)

benign(0.418)

TCGA-AC-A3W5-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

docetaxel

TPT1

deletion

Frame_Shift_Del

c.513delA

p.Lys171AsnfsTer21

p.K171Nfs*21

protein_coding

TCGA-AA-3710-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

TPT1

insertion

Frame_Shift_Ins

novel

c.513dupA

p.Cys172MetfsTer2

p.C172Mfs*2

protein_coding

TCGA-AA-3864-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

TPT1

SNV

Missense_Mutation

novel

c.548N>A

p.Cys183Tyr

p.C183Y

protein_coding

deleterious_low_confidence(0.03)

benign(0.003)

TCGA-AP-A05P-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

TPT1

SNV

Missense_Mutation

novel

c.481N>T

p.Ile161Phe

p.I161F

protein_coding

deleterious(0)

benign(0.387)

TCGA-AX-A1CE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

TPT1

SNV

Missense_Mutation

rs771758941

c.562N>T

p.Arg188Trp

p.R188W

protein_coding

deleterious_low_confidence(0.03)

benign(0.067)

TCGA-AX-A2HC-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

TPT1

SNV

Missense_Mutation

c.110N>T

p.Ser37Ile

p.S37I

protein_coding

deleterious(0.03)

benign(0.217)

TCGA-BG-A0VV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

TPT1

SNV

Missense_Mutation

novel

c.29N>T

p.His10Leu

p.H10L

protein_coding

tolerated(0.14)

benign(0.007)

TCGA-ZP-A9D0-01

Liver

liver hepatocellular carcinoma

Female

>=65

I/II

Unknown

TPT1

SNV

Missense_Mutation

novel

c.322N>T

p.Pro108Ser

p.P108S

protein_coding

tolerated(0.06)

benign(0.171)

TCGA-XK-AAIW-01

Prostate

prostate adenocarcinoma

Male

>=65

Unknown

TPT1

SNV

Missense_Mutation

novel

c.529A>G

p.Arg177Gly

p.R177G

protein_coding

deleterious_low_confidence(0.01)

benign(0.007)

TCGA-BR-4257-01

Stomach

stomach adenocarcinoma

Female

>=65

I/II

Unknown

Page: 1 2

Top

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
7178	TPT1	DRUGGABLE GENOME		5-FLUOROURACIL	FLUOROURACIL	15262975

Page: 1