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Gene: PTCD3 |
Gene summary for PTCD3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTCD3 | Gene ID | 55037 |
| Gene name | pentatricopeptide repeat domain 3 | |
| Gene Alias | COXPD51 | |
| Cytomap | 2p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0006412 | UniProtAcc | Q96EY7 |
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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 |
| 55037 | PTCD3 | LZE4T | Human | Esophagus | ESCC | 3.69e-10 | 2.15e-01 | 0.0811 |
| 55037 | PTCD3 | LZE7T | Human | Esophagus | ESCC | 1.09e-13 | 5.48e-01 | 0.0667 |
| 55037 | PTCD3 | LZE8T | Human | Esophagus | ESCC | 9.82e-05 | 7.33e-02 | 0.067 |
| 55037 | PTCD3 | LZE20T | Human | Esophagus | ESCC | 4.10e-02 | 1.23e-01 | 0.0662 |
| 55037 | PTCD3 | LZE24T | Human | Esophagus | ESCC | 4.02e-09 | 2.77e-01 | 0.0596 |
| 55037 | PTCD3 | LZE21T | Human | Esophagus | ESCC | 2.18e-04 | 4.09e-01 | 0.0655 |
| 55037 | PTCD3 | LZE6T | Human | Esophagus | ESCC | 6.60e-06 | 1.13e-01 | 0.0845 |
| 55037 | PTCD3 | P1T-E | Human | Esophagus | ESCC | 3.91e-05 | 3.25e-01 | 0.0875 |
| 55037 | PTCD3 | P2T-E | Human | Esophagus | ESCC | 1.67e-28 | 5.17e-01 | 0.1177 |
| 55037 | PTCD3 | P4T-E | Human | Esophagus | ESCC | 1.18e-21 | 5.67e-01 | 0.1323 |
| 55037 | PTCD3 | P5T-E | Human | Esophagus | ESCC | 8.41e-16 | 2.13e-01 | 0.1327 |
| 55037 | PTCD3 | P8T-E | Human | Esophagus | ESCC | 1.45e-20 | 3.31e-01 | 0.0889 |
| 55037 | PTCD3 | P9T-E | Human | Esophagus | ESCC | 9.68e-12 | 2.06e-01 | 0.1131 |
| 55037 | PTCD3 | P10T-E | Human | Esophagus | ESCC | 1.26e-66 | 1.27e+00 | 0.116 |
| 55037 | PTCD3 | P11T-E | Human | Esophagus | ESCC | 6.65e-11 | 3.76e-01 | 0.1426 |
| 55037 | PTCD3 | P12T-E | Human | Esophagus | ESCC | 9.31e-24 | 4.67e-01 | 0.1122 |
| 55037 | PTCD3 | P15T-E | Human | Esophagus | ESCC | 7.85e-25 | 5.87e-01 | 0.1149 |
| 55037 | PTCD3 | P16T-E | Human | Esophagus | ESCC | 6.06e-31 | 5.63e-01 | 0.1153 |
| 55037 | PTCD3 | P17T-E | Human | Esophagus | ESCC | 1.68e-02 | 1.91e-01 | 0.1278 |
| 55037 | PTCD3 | P20T-E | Human | Esophagus | ESCC | 8.45e-21 | 4.70e-01 | 0.1124 |
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| 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. |
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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). |
| 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:014005313 | Esophagus | ESCC | mitochondrial gene expression | 93/8552 | 108/18723 | 1.96e-18 | 2.03e-16 | 93 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:003254314 | Esophagus | ESCC | mitochondrial translation | 68/8552 | 76/18723 | 1.02e-15 | 6.86e-14 | 68 |
| GO:000641712 | Liver | Cirrhotic | regulation of translation | 194/4634 | 468/18723 | 7.28e-16 | 8.79e-14 | 194 |
| GO:0032543 | Liver | Cirrhotic | mitochondrial translation | 40/4634 | 76/18723 | 1.61e-07 | 4.29e-06 | 40 |
| GO:0140053 | Liver | Cirrhotic | mitochondrial gene expression | 49/4634 | 108/18723 | 2.35e-06 | 4.31e-05 | 49 |
| GO:000641722 | Liver | HCC | regulation of translation | 287/7958 | 468/18723 | 8.79e-17 | 8.08e-15 | 287 |
| GO:01400531 | Liver | HCC | mitochondrial gene expression | 82/7958 | 108/18723 | 1.49e-12 | 7.20e-11 | 82 |
| GO:00325431 | Liver | HCC | mitochondrial translation | 62/7958 | 76/18723 | 2.95e-12 | 1.34e-10 | 62 |
| GO:000641720 | Oral cavity | OSCC | regulation of translation | 274/7305 | 468/18723 | 4.39e-18 | 4.63e-16 | 274 |
| GO:01400533 | Oral cavity | OSCC | mitochondrial gene expression | 78/7305 | 108/18723 | 2.37e-12 | 9.86e-11 | 78 |
| GO:00325434 | Oral cavity | OSCC | mitochondrial translation | 59/7305 | 76/18723 | 7.21e-12 | 2.70e-10 | 59 |
| GO:0006417110 | Oral cavity | LP | regulation of translation | 175/4623 | 468/18723 | 4.49e-10 | 2.22e-08 | 175 |
| GO:003254313 | Oral cavity | LP | mitochondrial translation | 43/4623 | 76/18723 | 2.85e-09 | 1.26e-07 | 43 |
| GO:014005312 | Oral cavity | LP | mitochondrial gene expression | 53/4623 | 108/18723 | 3.54e-08 | 1.27e-06 | 53 |
| GO:000641729 | Skin | cSCC | regulation of translation | 226/4864 | 468/18723 | 8.78e-26 | 2.62e-23 | 226 |
| GO:00325436 | Skin | cSCC | mitochondrial translation | 47/4864 | 76/18723 | 4.70e-11 | 2.22e-09 | 47 |
| GO:01400535 | Skin | cSCC | mitochondrial gene expression | 56/4864 | 108/18723 | 8.06e-09 | 2.56e-07 | 56 |
| GO:0006417113 | Thyroid | PTC | regulation of translation | 236/5968 | 468/18723 | 2.70e-17 | 2.52e-15 | 236 |
| GO:01400536 | Thyroid | PTC | mitochondrial gene expression | 51/5968 | 108/18723 | 6.04e-04 | 3.83e-03 | 51 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| TF | 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 |
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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 |
| PTCD3 | SNV | Missense_Mutation | c.391G>A | p.Asp131Asn | p.D131N | Q96EY7 | protein_coding | deleterious(0.05) | possibly_damaging(0.471) | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PTCD3 | SNV | Missense_Mutation | novel | c.2050N>A | p.Asp684Asn | p.D684N | Q96EY7 | protein_coding | tolerated_low_confidence(0.15) | benign(0.346) | TCGA-B6-A3ZX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| PTCD3 | SNV | Missense_Mutation | novel | c.1931N>A | p.Gly644Asp | p.G644D | Q96EY7 | protein_coding | tolerated(0.55) | benign(0.035) | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PTCD3 | insertion | Nonsense_Mutation | novel | c.1846_1847insGTTTGTGAATGGGAACCTTATGCATATTCATGTTTCC | p.Asp616GlyfsTer3 | p.D616Gfs*3 | Q96EY7 | protein_coding | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PTCD3 | insertion | Nonsense_Mutation | novel | c.1961_1962insTACAGTATAGTT | p.Ala654_Ile655insThrValTerLeu | p.A654_I655insTV*L | Q96EY7 | protein_coding | TCGA-AN-A03X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PTCD3 | insertion | Nonsense_Mutation | novel | c.1932_1933insATTGAATAGATCATCATGAAGTCATACTGAATGAATGTTGATAAT | p.Gly644_Leu645insIleGluTerIleIleMetLysSerTyrTerMetAsnValAspAsn | p.G644_L645insIE*IIMKSY*MNVDN | Q96EY7 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| PTCD3 | insertion | Frame_Shift_Ins | novel | c.1248dupT | p.Gln417SerfsTer35 | p.Q417Sfs*35 | Q96EY7 | protein_coding | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PTCD3 | insertion | In_Frame_Ins | rs749173570 | c.30_31insGGCCTCCGCAGCAGGCTT | p.Leu12_Gly17dup | p.L12_G17dup | Q96EY7 | protein_coding | TCGA-Z7-A8R5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | ||
| PTCD3 | SNV | Missense_Mutation | novel | c.1543G>T | p.Asp515Tyr | p.D515Y | Q96EY7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PTCD3 | SNV | Missense_Mutation | rs778632544 | c.1387G>A | p.Asp463Asn | p.D463N | Q96EY7 | protein_coding | tolerated(0.88) | benign(0) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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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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