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: PDCD2

Gene summary for PDCD2

Gene summary.

Gene information	Species	Human
	Gene symbol	PDCD2
	Gene ID	5134
	Gene name	programmed cell death 2
	Gene Alias	RP8
	Cytomap	6q27
	Gene Type	protein-coding
	GO ID	GO:0002244
	UniProtAcc	A0A087WYJ3

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
5134	PDCD2	LZE2T	Human	Esophagus	ESCC	1.58e-04	5.04e-01	0.082
5134	PDCD2	LZE7T	Human	Esophagus	ESCC	2.95e-02	1.04e-02	0.0667
5134	PDCD2	LZE20T	Human	Esophagus	ESCC	9.88e-03	1.74e-01	0.0662
5134	PDCD2	LZE22D1	Human	Esophagus	HGIN	8.31e-09	2.29e-01	0.0595
5134	PDCD2	LZE22T	Human	Esophagus	ESCC	1.99e-06	6.69e-01	0.068
5134	PDCD2	LZE24T	Human	Esophagus	ESCC	2.12e-39	1.08e+00	0.0596
5134	PDCD2	LZE21T	Human	Esophagus	ESCC	7.63e-10	2.60e-01	0.0655
5134	PDCD2	P1T-E	Human	Esophagus	ESCC	1.44e-10	5.36e-01	0.0875
5134	PDCD2	P2T-E	Human	Esophagus	ESCC	3.77e-33	6.81e-01	0.1177
5134	PDCD2	P4T-E	Human	Esophagus	ESCC	4.50e-46	1.29e+00	0.1323
5134	PDCD2	P5T-E	Human	Esophagus	ESCC	6.80e-31	7.86e-01	0.1327
5134	PDCD2	P8T-E	Human	Esophagus	ESCC	2.71e-29	6.15e-01	0.0889
5134	PDCD2	P9T-E	Human	Esophagus	ESCC	8.60e-19	5.26e-01	0.1131
5134	PDCD2	P10T-E	Human	Esophagus	ESCC	5.20e-42	8.56e-01	0.116
5134	PDCD2	P11T-E	Human	Esophagus	ESCC	3.28e-15	7.82e-01	0.1426
5134	PDCD2	P12T-E	Human	Esophagus	ESCC	6.25e-19	4.89e-01	0.1122
5134	PDCD2	P15T-E	Human	Esophagus	ESCC	9.46e-44	1.02e+00	0.1149
5134	PDCD2	P16T-E	Human	Esophagus	ESCC	1.20e-41	9.25e-01	0.1153
5134	PDCD2	P17T-E	Human	Esophagus	ESCC	1.17e-14	9.15e-01	0.1278
5134	PDCD2	P19T-E	Human	Esophagus	ESCC	3.95e-16	1.65e+00	0.1662

Page: 1 2 3 4 5 6 7

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:004586227	Esophagus	HGIN	positive regulation of proteolysis	107/2587	372/18723	2.61e-14	4.60e-12	107
GO:004328126	Esophagus	HGIN	regulation of cysteine-type endopeptidase activity involved in apoptotic process	59/2587	209/18723	3.39e-08	1.97e-06	59
GO:200011626	Esophagus	HGIN	regulation of cysteine-type endopeptidase activity	63/2587	235/18723	9.71e-08	5.02e-06	63
GO:005254726	Esophagus	HGIN	regulation of peptidase activity	102/2587	461/18723	6.29e-07	2.72e-05	102
GO:001095225	Esophagus	HGIN	positive regulation of peptidase activity	53/2587	197/18723	8.70e-07	3.59e-05	53
GO:005254826	Esophagus	HGIN	regulation of endopeptidase activity	96/2587	432/18723	1.09e-06	4.30e-05	96
GO:004328020	Esophagus	HGIN	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	38/2587	129/18723	2.92e-06	1.01e-04	38
GO:200105620	Esophagus	HGIN	positive regulation of cysteine-type endopeptidase activity	41/2587	148/18723	6.65e-06	2.07e-04	41
GO:001095020	Esophagus	HGIN	positive regulation of endopeptidase activity	47/2587	179/18723	7.23e-06	2.20e-04	47
GO:00069197	Esophagus	HGIN	activation of cysteine-type endopeptidase activity involved in apoptotic process	21/2587	78/18723	1.65e-03	1.82e-02	21
GO:0045862111	Esophagus	ESCC	positive regulation of proteolysis	256/8552	372/18723	7.88e-20	9.43e-18	256
GO:2000116111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity	158/8552	235/18723	1.67e-11	5.90e-10	158
GO:0043281111	Esophagus	ESCC	regulation of cysteine-type endopeptidase activity involved in apoptotic process	143/8552	209/18723	2.12e-11	7.31e-10	143
GO:0010952111	Esophagus	ESCC	positive regulation of peptidase activity	133/8552	197/18723	4.31e-10	1.14e-08	133
GO:0052547111	Esophagus	ESCC	regulation of peptidase activity	275/8552	461/18723	7.54e-10	1.88e-08	275
GO:0052548111	Esophagus	ESCC	regulation of endopeptidase activity	253/8552	432/18723	3.68e-08	6.78e-07	253
GO:0010950111	Esophagus	ESCC	positive regulation of endopeptidase activity	116/8552	179/18723	1.77e-07	2.79e-06	116
GO:0043280110	Esophagus	ESCC	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	84/8552	129/18723	6.38e-06	6.55e-05	84
GO:2001056110	Esophagus	ESCC	positive regulation of cysteine-type endopeptidase activity	94/8552	148/18723	8.87e-06	8.59e-05	94
GO:000691915	Esophagus	ESCC	activation of cysteine-type endopeptidase activity involved in apoptotic process	54/8552	78/18723	2.17e-05	1.87e-04	54

Page: 1 2 3 4 5

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

PDCD2

SNV

Missense_Mutation

novel

c.335N>A

p.Pro112His

p.P112H

Q16342

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PDCD2

SNV

Missense_Mutation

novel

c.416N>A

p.Gly139Asp

p.G139D

Q16342

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-S3-AA0Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Ancillary

neulasta

PDCD2

insertion

Frame_Shift_Ins

novel

c.363_364insTCTGTTTCTCGGGTCGG

p.Glu122SerfsTer26

p.E122Sfs*26

Q16342

protein_coding

TCGA-A8-A06P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

PDCD2

insertion

Frame_Shift_Ins

novel

c.362_363insTAAGTTCCTCTGGGTCGCAG

p.Glu122LysfsTer27

p.E122Kfs*27

Q16342

protein_coding

TCGA-A8-A06P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

PDCD2

insertion

Frame_Shift_Ins

novel

c.445_446insATATTTT

p.Cys149TyrfsTer23

p.C149Yfs*23

Q16342

protein_coding

TCGA-B6-A0IK-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

PDCD2

SNV

Missense_Mutation

novel

c.724C>G

p.Gln242Glu

p.Q242E

Q16342

protein_coding

tolerated(0.06)

benign(0.068)

TCGA-EA-A1QS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PDCD2

SNV

Missense_Mutation

novel

c.635A>G

p.Tyr212Cys

p.Y212C

Q16342

protein_coding

tolerated(0.11)

benign(0.202)

TCGA-VS-A9U6-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PDCD2

SNV

Missense_Mutation

c.1027N>G

p.Thr343Ala

p.T343A

Q16342

protein_coding

tolerated(0.16)

benign(0.006)

TCGA-AA-3811-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

PDCD2

SNV

Missense_Mutation

c.394N>A

p.Ala132Thr

p.A132T

Q16342

protein_coding

tolerated(0.2)

benign(0.018)

TCGA-AD-A5EJ-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

PDCD2

SNV

Missense_Mutation

novel

c.389N>T

p.Ser130Phe

p.S130F

Q16342

protein_coding

deleterious(0.04)

benign(0.052)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

Page: 1 2 3

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

Page: 1