TISIDB

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Mitochondrion
Domain	PF10037 Mitochondrial 28S ribosomal protein S27
Function	Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function.

> Gene Ontology [ TOP ]
Biological Process	GO:0001655 urogenital system development GO:0001822 kidney development GO:0001889 liver development GO:0003007 heart morphogenesis GO:0003205 cardiac chamber development GO:0003206 cardiac chamber morphogenesis GO:0003208 cardiac ventricle morphogenesis GO:0003229 ventricular cardiac muscle tissue development GO:0003231 cardiac ventricle development GO:0006397 mRNA processing GO:0007507 heart development GO:0007517 muscle organ development GO:0014706 striated muscle tissue development GO:0042692 muscle cell differentiation GO:0048644 muscle organ morphogenesis GO:0048732 gland development GO:0048738 cardiac muscle tissue development GO:0048747 muscle fiber development GO:0050684 regulation of mRNA processing GO:0051146 striated muscle cell differentiation GO:0055001 muscle cell development GO:0055002 striated muscle cell development GO:0055008 cardiac muscle tissue morphogenesis GO:0055010 ventricular cardiac muscle tissue morphogenesis GO:0060415 muscle tissue morphogenesis GO:0060537 muscle tissue development GO:0061008 hepaticobiliary system development GO:0072001 renal system development GO:1903311 regulation of mRNA metabolic process
Molecular Function	-
Cellular Component	-

> KEGG and Reactome Pathway [ TOP ]
KEGG	-
Reactome	-

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between PTCD2 and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining

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Literatures describing the relation between PTCD2 and anti-tumor immunity in human cancer.

PMID	Cancer type	Relation to immunity	Evidence sentences
28783722	Melanoma	Promote immunity (T cell function)	We targeted each gene in NY-ESO-1+ melanoma cells, Mel624 and A375, with four sgRNAs and individually measured resistance against ESO-T cells. Fifteen genes showed significant resistance to T cell-mediated cytolysis with at least 1 sgRNA in these cells.

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

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Statistical results of PTCD2 in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

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Points in the above scatter plot represent the expression difference of PTCD2 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	0.354	0.0739
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.243	0.801
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	0.432	0.564
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.004	0.989
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0.237	0.828
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	-0.295	0.811
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.044	0.876
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.156	0.876
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	0.095	0.93
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.631	0.407
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	1.396	0.2
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	-0.063	0.316

> Mutation difference between responders and non-responders

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Points in the above scatter plot represent the mutation difference of PTCD2 in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	7.4	7.4	0.0709
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	7.4	7.4	0.096
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	0	0	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	0	0	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	2.6	2.6	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	4.5	4.5	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	1

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of PTCD2. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of PTCD2. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by PTCD2. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of PTCD2. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of PTCD2 expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between PTCD2 and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	PTCD2
Name	pentatricopeptide repeat domain 2
Aliases	FLJ12598; CTC-365E16.1; Pentatricopeptide repeat-containing protein 2, mitochondrial
Chromosomal Location	5q13.2
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting PTCD2 collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

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