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Gene: PDCD6 |
Gene summary for PDCD6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDCD6 | Gene ID | 10016 |
| Gene name | programmed cell death 6 | |
| Gene Alias | ALG-2 | |
| Cytomap | 5p15.33 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | O75340 |
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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 |
| 10016 | PDCD6 | GSM4909281 | Human | Breast | IDC | 1.61e-02 | 2.51e-01 | 0.21 |
| 10016 | PDCD6 | GSM4909282 | Human | Breast | IDC | 1.04e-11 | 4.15e-01 | -0.0288 |
| 10016 | PDCD6 | GSM4909285 | Human | Breast | IDC | 2.91e-31 | 6.81e-01 | 0.21 |
| 10016 | PDCD6 | GSM4909288 | Human | Breast | IDC | 3.09e-02 | 8.18e-02 | 0.0988 |
| 10016 | PDCD6 | GSM4909290 | Human | Breast | IDC | 4.62e-03 | 2.82e-01 | 0.2096 |
| 10016 | PDCD6 | GSM4909291 | Human | Breast | IDC | 2.29e-05 | 3.55e-01 | 0.1753 |
| 10016 | PDCD6 | GSM4909293 | Human | Breast | IDC | 7.23e-123 | 1.22e+00 | 0.1581 |
| 10016 | PDCD6 | GSM4909294 | Human | Breast | IDC | 4.03e-10 | 3.25e-01 | 0.2022 |
| 10016 | PDCD6 | GSM4909296 | Human | Breast | IDC | 3.29e-11 | 1.60e-01 | 0.1524 |
| 10016 | PDCD6 | GSM4909297 | Human | Breast | IDC | 3.01e-07 | -3.60e-02 | 0.1517 |
| 10016 | PDCD6 | GSM4909298 | Human | Breast | IDC | 6.37e-07 | 2.93e-01 | 0.1551 |
| 10016 | PDCD6 | GSM4909304 | Human | Breast | IDC | 1.07e-06 | 2.28e-01 | 0.1636 |
| 10016 | PDCD6 | GSM4909308 | Human | Breast | IDC | 2.18e-02 | 2.21e-01 | 0.158 |
| 10016 | PDCD6 | GSM4909311 | Human | Breast | IDC | 1.24e-22 | -3.30e-01 | 0.1534 |
| 10016 | PDCD6 | GSM4909312 | Human | Breast | IDC | 1.80e-10 | -5.38e-02 | 0.1552 |
| 10016 | PDCD6 | GSM4909316 | Human | Breast | IDC | 1.55e-07 | 3.61e-01 | 0.21 |
| 10016 | PDCD6 | GSM4909317 | Human | Breast | IDC | 2.50e-20 | 5.49e-01 | 0.1355 |
| 10016 | PDCD6 | GSM4909318 | Human | Breast | IDC | 1.58e-08 | 5.55e-01 | 0.2031 |
| 10016 | PDCD6 | GSM4909319 | Human | Breast | IDC | 3.04e-31 | -1.81e-01 | 0.1563 |
| 10016 | PDCD6 | GSM4909320 | Human | Breast | IDC | 1.24e-05 | -2.12e-01 | 0.1575 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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. |
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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:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
| GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
| GO:20001169 | Breast | Precancer | regulation of cysteine-type endopeptidase activity | 43/1080 | 235/18723 | 1.30e-11 | 1.83e-09 | 43 |
| GO:00432819 | Breast | Precancer | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 40/1080 | 209/18723 | 1.59e-11 | 2.07e-09 | 40 |
| GO:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
| GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
| GO:00109529 | Breast | Precancer | positive regulation of peptidase activity | 33/1080 | 197/18723 | 3.01e-08 | 1.89e-06 | 33 |
| GO:00313969 | Breast | Precancer | regulation of protein ubiquitination | 33/1080 | 210/18723 | 1.45e-07 | 7.82e-06 | 33 |
| GO:00432808 | Breast | Precancer | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 24/1080 | 129/18723 | 3.13e-07 | 1.50e-05 | 24 |
| GO:00100389 | Breast | Precancer | response to metal ion | 47/1080 | 373/18723 | 3.88e-07 | 1.79e-05 | 47 |
| GO:00109509 | Breast | Precancer | positive regulation of endopeptidase activity | 29/1080 | 179/18723 | 4.23e-07 | 1.90e-05 | 29 |
| GO:20010568 | Breast | Precancer | positive regulation of cysteine-type endopeptidase activity | 25/1080 | 148/18723 | 1.19e-06 | 4.60e-05 | 25 |
| GO:00092667 | Breast | Precancer | response to temperature stimulus | 27/1080 | 178/18723 | 3.85e-06 | 1.21e-04 | 27 |
| GO:00346059 | Breast | Precancer | cellular response to heat | 15/1080 | 69/18723 | 7.08e-06 | 1.95e-04 | 15 |
| GO:00106348 | Breast | Precancer | positive regulation of epithelial cell migration | 25/1080 | 176/18723 | 2.75e-05 | 6.21e-04 | 25 |
| GO:00106319 | Breast | Precancer | epithelial cell migration | 40/1080 | 357/18723 | 4.57e-05 | 9.71e-04 | 40 |
| GO:00901329 | Breast | Precancer | epithelium migration | 40/1080 | 360/18723 | 5.51e-05 | 1.14e-03 | 40 |
| GO:00094088 | Breast | Precancer | response to heat | 18/1080 | 110/18723 | 5.57e-05 | 1.15e-03 | 18 |
| GO:00506736 | Breast | Precancer | epithelial cell proliferation | 46/1080 | 437/18723 | 6.02e-05 | 1.23e-03 | 46 |
| GO:00435426 | Breast | Precancer | endothelial cell migration | 33/1080 | 279/18723 | 7.28e-05 | 1.44e-03 | 33 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 |
| 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 |
| PDCD6 | SNV | Missense_Mutation | novel | c.154N>G | p.Leu52Val | p.L52V | O75340 | protein_coding | deleterious(0) | possibly_damaging(0.544) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| PDCD6 | deletion | Frame_Shift_Del | c.221delG | p.Arg74LeufsTer7 | p.R74Lfs*7 | O75340 | protein_coding | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| PDCD6 | SNV | Missense_Mutation | rs370878298 | c.541N>A | p.Glu181Lys | p.E181K | O75340 | protein_coding | deleterious(0) | probably_damaging(0.921) | TCGA-C5-A7XC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PDCD6 | SNV | Missense_Mutation | rs545985005 | c.302C>T | p.Thr101Met | p.T101M | O75340 | protein_coding | tolerated(0.08) | benign(0.262) | TCGA-VS-A8QC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | PD |
| PDCD6 | SNV | Missense_Mutation | rs139334790 | c.500N>A | p.Arg167His | p.R167H | O75340 | protein_coding | deleterious(0.05) | benign(0.017) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PDCD6 | SNV | Missense_Mutation | c.235N>A | p.Gly79Ser | p.G79S | O75340 | protein_coding | tolerated(0.22) | benign(0.015) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| PDCD6 | SNV | Missense_Mutation | rs767684079 | c.427C>T | p.Arg143Trp | p.R143W | O75340 | protein_coding | deleterious(0.03) | possibly_damaging(0.85) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PDCD6 | SNV | Missense_Mutation | rs373052818 | c.367N>A | p.Gly123Ser | p.G123S | O75340 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3939-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PDCD6 | SNV | Missense_Mutation | novel | c.448N>A | p.Asp150Asn | p.D150N | O75340 | protein_coding | tolerated(0.22) | possibly_damaging(0.852) | TCGA-AD-6548-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PDCD6 | SNV | Missense_Mutation | rs139334790 | c.500N>A | p.Arg167His | p.R167H | O75340 | protein_coding | deleterious(0.05) | benign(0.017) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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 |
| Page: 1 |
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