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: PSEN1

Gene summary for PSEN1

Gene summary.

Gene information	Species	Human
	Gene symbol	PSEN1
	Gene ID	5663
	Gene name	presenilin 1
	Gene Alias	ACNINV3
	Cytomap	14q24.2
	Gene Type	protein-coding
	GO ID	GO:0000045
	UniProtAcc	A0A024R6A3

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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
5663	PSEN1	N_HPV_2	Human	Cervix	N_HPV	2.15e-02	1.32e-01	-0.0131
5663	PSEN1	CCI_1	Human	Cervix	CC	2.07e-03	4.85e-01	0.528
5663	PSEN1	CCI_2	Human	Cervix	CC	3.92e-05	6.31e-01	0.5249
5663	PSEN1	CCI_3	Human	Cervix	CC	2.71e-09	6.33e-01	0.516
5663	PSEN1	sample3	Human	Cervix	CC	1.18e-06	2.79e-01	0.1387
5663	PSEN1	T3	Human	Cervix	CC	3.71e-08	2.86e-01	0.1389
5663	PSEN1	HTA11_3410_2000001011	Human	Colorectum	AD	5.32e-06	-4.62e-01	0.0155
5663	PSEN1	HTA11_347_2000001011	Human	Colorectum	AD	3.06e-09	4.55e-01	-0.1954
5663	PSEN1	HTA11_866_3004761011	Human	Colorectum	AD	8.33e-03	-4.02e-01	0.096
5663	PSEN1	HTA11_7696_3000711011	Human	Colorectum	AD	1.19e-04	-3.40e-01	0.0674
5663	PSEN1	HTA11_99999970781_79442	Human	Colorectum	MSS	1.65e-11	-4.61e-01	0.294
5663	PSEN1	HTA11_99999971662_82457	Human	Colorectum	MSS	1.58e-07	-4.50e-01	0.3859
5663	PSEN1	HTA11_99999974143_84620	Human	Colorectum	MSS	1.57e-10	-4.63e-01	0.3005
5663	PSEN1	F007	Human	Colorectum	FAP	2.13e-03	-5.00e-01	0.1176
5663	PSEN1	A002-C-010	Human	Colorectum	FAP	1.45e-05	-3.18e-01	0.242
5663	PSEN1	A015-C-203	Human	Colorectum	FAP	1.17e-28	-4.47e-01	-0.1294
5663	PSEN1	A015-C-204	Human	Colorectum	FAP	3.95e-06	-4.05e-01	-0.0228
5663	PSEN1	A014-C-040	Human	Colorectum	FAP	1.35e-03	-4.62e-01	-0.1184
5663	PSEN1	A002-C-201	Human	Colorectum	FAP	1.94e-12	-4.41e-01	0.0324
5663	PSEN1	A002-C-203	Human	Colorectum	FAP	1.08e-05	-2.65e-01	0.2786

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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
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
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:0006096	Colorectum	AD	glycolytic process	38/3918	81/18723	1.52e-07	6.78e-06	38
GO:1900180	Colorectum	AD	regulation of protein localization to nucleus	55/3918	136/18723	1.70e-07	7.34e-06	55
GO:0090316	Colorectum	AD	positive regulation of intracellular protein transport	62/3918	160/18723	1.82e-07	7.79e-06	62
GO:0032388	Colorectum	AD	positive regulation of intracellular transport	74/3918	202/18723	1.83e-07	7.80e-06	74
GO:0006757	Colorectum	AD	ATP generation from ADP	38/3918	82/18723	2.26e-07	9.37e-06	38
GO:0032434	Colorectum	AD	regulation of proteasomal ubiquitin-dependent protein catabolic process	54/3918	134/18723	2.51e-07	1.02e-05	54
GO:1903052	Colorectum	AD	positive regulation of proteolysis involved in cellular protein catabolic process	53/3918	133/18723	4.93e-07	1.85e-05	53
GO:0032386	Colorectum	AD	regulation of intracellular transport	109/3918	337/18723	5.33e-07	1.95e-05	109
GO:0033157	Colorectum	AD	regulation of intracellular protein transport	80/3918	229/18723	5.81e-07	2.09e-05	80
GO:0043112	Colorectum	AD	receptor metabolic process	62/3918	166/18723	8.18e-07	2.85e-05	62
GO:1901653	Colorectum	AD	cellular response to peptide	114/3918	359/18723	8.32e-07	2.88e-05	114
GO:1903051	Colorectum	AD	negative regulation of proteolysis involved in cellular protein catabolic process	31/3918	64/18723	8.71e-07	2.98e-05	31
GO:0070997	Colorectum	AD	neuron death	114/3918	361/18723	1.13e-06	3.72e-05	114
GO:0030099	Colorectum	AD	myeloid cell differentiation	119/3918	381/18723	1.24e-06	4.01e-05	119
GO:1900182	Colorectum	AD	positive regulation of protein localization to nucleus	38/3918	87/18723	1.43e-06	4.52e-05	38
GO:2000060	Colorectum	AD	positive regulation of ubiquitin-dependent protein catabolic process	44/3918	107/18723	1.65e-06	5.03e-05	44
GO:0009132	Colorectum	AD	nucleoside diphosphate metabolic process	49/3918	124/18723	1.75e-06	5.31e-05	49
GO:0046939	Colorectum	AD	nucleotide phosphorylation	42/3918	101/18723	1.99e-06	5.92e-05	42
GO:1901185	Colorectum	AD	negative regulation of ERBB signaling pathway	19/3918	32/18723	2.39e-06	6.98e-05	19
GO:0034504	Colorectum	AD	protein localization to nucleus	94/3918	290/18723	2.83e-06	8.09e-05	94

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501018	Cervix	CC	Alzheimer disease	113/1267	384/8465	9.67e-14	3.92e-12	2.32e-12	113
hsa0502218	Cervix	CC	Pathways of neurodegeneration - multiple diseases	128/1267	476/8465	2.87e-12	9.29e-11	5.50e-11	128
hsa051657	Cervix	CC	Human papillomavirus infection	74/1267	331/8465	1.70e-04	1.02e-03	6.03e-04	74
hsa043109	Cervix	CC	Wnt signaling pathway	43/1267	171/8465	3.03e-04	1.64e-03	9.68e-04	43
hsa0472214	Cervix	CC	Neurotrophin signaling pathway	32/1267	119/8465	5.01e-04	2.42e-03	1.43e-03	32
hsa04330	Cervix	CC	Notch signaling pathway	17/1267	62/8465	7.99e-03	2.56e-02	1.51e-02	17
hsa0501019	Cervix	CC	Alzheimer disease	113/1267	384/8465	9.67e-14	3.92e-12	2.32e-12	113
hsa0502219	Cervix	CC	Pathways of neurodegeneration - multiple diseases	128/1267	476/8465	2.87e-12	9.29e-11	5.50e-11	128
hsa0516512	Cervix	CC	Human papillomavirus infection	74/1267	331/8465	1.70e-04	1.02e-03	6.03e-04	74
hsa0431012	Cervix	CC	Wnt signaling pathway	43/1267	171/8465	3.03e-04	1.64e-03	9.68e-04	43
hsa0472215	Cervix	CC	Neurotrophin signaling pathway	32/1267	119/8465	5.01e-04	2.42e-03	1.43e-03	32
hsa043301	Cervix	CC	Notch signaling pathway	17/1267	62/8465	7.99e-03	2.56e-02	1.51e-02	17
hsa0502244	Cervix	N_HPV	Pathways of neurodegeneration - multiple diseases	47/349	476/8465	1.48e-08	3.13e-07	2.45e-07	47
hsa0501044	Cervix	N_HPV	Alzheimer disease	41/349	384/8465	1.50e-08	3.13e-07	2.45e-07	41
hsa0502254	Cervix	N_HPV	Pathways of neurodegeneration - multiple diseases	47/349	476/8465	1.48e-08	3.13e-07	2.45e-07	47
hsa0501054	Cervix	N_HPV	Alzheimer disease	41/349	384/8465	1.50e-08	3.13e-07	2.45e-07	41
hsa05010	Colorectum	AD	Alzheimer disease	174/2092	384/8465	1.82e-19	9.26e-18	5.91e-18	174
hsa05022	Colorectum	AD	Pathways of neurodegeneration - multiple diseases	201/2092	476/8465	4.54e-18	1.27e-16	8.09e-17	201
hsa04722	Colorectum	AD	Neurotrophin signaling pathway	50/2092	119/8465	2.28e-05	2.24e-04	1.43e-04	50
hsa04310	Colorectum	AD	Wnt signaling pathway	56/2092	171/8465	1.03e-02	3.93e-02	2.51e-02	56

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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

PSEN1

SNV

Missense_Mutation

c.211G>A

p.Glu71Lys

p.E71K

P49768

protein_coding

deleterious(0.01)

probably_damaging(0.996)

TCGA-BH-A18P-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PSEN1

insertion

Nonsense_Mutation

novel

c.254_255insTCATTTTCAGTGAACTACAAATCTCTGAAACCCAAAA

p.Phe86HisfsTer4

p.F86Hfs*4

P49768

protein_coding

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

PSEN1

insertion

Frame_Shift_Ins

novel

c.277_278insTGGTGGTGGTCGTGGCATGG

p.Thr99TrpfsTer22

p.T99Wfs*22

P49768

protein_coding

TCGA-AR-A2LK-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

anastrozole

PSEN1

SNV

Missense_Mutation

rs756764981

c.1037N>A

p.Ser346Asn

p.S346N

P49768

protein_coding

tolerated(0.45)

benign(0)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

c.151N>C

p.Ser51Pro

p.S51P

P49768

protein_coding

tolerated(0.14)

benign(0)

TCGA-C5-A1M9-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

c.961G>A

p.Glu321Lys

p.E321K

P49768

protein_coding

tolerated(0.6)

benign(0.015)

TCGA-FU-A23L-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

c.630G>T

p.Met210Ile

p.M210I

P49768

protein_coding

deleterious(0.03)

probably_damaging(0.989)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

c.1321T>G

p.Phe441Val

p.F441V

P49768

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

novel

c.908N>A

p.Pro303Gln

p.P303Q

P49768

protein_coding

deleterious(0.03)

possibly_damaging(0.573)

TCGA-RA-A741-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PSEN1

SNV

Missense_Mutation

c.407N>T

p.Ala136Val

p.A136V

P49768

protein_coding

deleterious(0.04)

possibly_damaging(0.704)

TCGA-AA-3821-01

Colorectum

colon adenocarcinoma

Female

>=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
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE	inhibitor	MK0752
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE		BMS-708163	AVAGACESTAT
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE		E2012
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE	inhibitor	MK0752
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE		R-flurbiprofen
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE	inhibitor	CHEMBL1090771	AVAGACESTAT
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE		LY-411575	CHEMBL392068	23181502,19443228
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE		BMS-299897	CHEMBL247471
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE	inhibitor	178103911
5663	PSEN1	ENZYME, TRANSPORTER, PROTEASE, DRUGGABLE GENOME, CELL SURFACE	inhibitor	178103557	SEMAGACESTAT

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