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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 |
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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 |
| 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 |
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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:2001056111 | Thyroid | PTC | positive regulation of cysteine-type endopeptidase activity | 64/5968 | 148/18723 | 2.33e-03 | 1.23e-02 | 64 |
| GO:00069198 | Thyroid | PTC | activation of cysteine-type endopeptidase activity involved in apoptotic process | 37/5968 | 78/18723 | 2.91e-03 | 1.44e-02 | 37 |
| GO:19015325 | Thyroid | PTC | regulation of hematopoietic progenitor cell differentiation | 18/5968 | 32/18723 | 3.72e-03 | 1.79e-02 | 18 |
| GO:004586234 | Thyroid | ATC | positive regulation of proteolysis | 202/6293 | 372/18723 | 1.07e-16 | 9.42e-15 | 202 |
| GO:004328133 | Thyroid | ATC | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 102/6293 | 209/18723 | 3.61e-06 | 4.03e-05 | 102 |
| GO:005254734 | Thyroid | ATC | regulation of peptidase activity | 200/6293 | 461/18723 | 6.25e-06 | 6.52e-05 | 200 |
| GO:200011633 | Thyroid | ATC | regulation of cysteine-type endopeptidase activity | 111/6293 | 235/18723 | 9.41e-06 | 9.41e-05 | 111 |
| GO:001095233 | Thyroid | ATC | positive regulation of peptidase activity | 94/6293 | 197/18723 | 2.67e-05 | 2.28e-04 | 94 |
| GO:005254834 | Thyroid | ATC | regulation of endopeptidase activity | 181/6293 | 432/18723 | 1.70e-04 | 1.16e-03 | 181 |
| GO:001095033 | Thyroid | ATC | positive regulation of endopeptidase activity | 79/6293 | 179/18723 | 2.09e-03 | 9.86e-03 | 79 |
| GO:190153212 | Thyroid | ATC | regulation of hematopoietic progenitor cell differentiation | 19/6293 | 32/18723 | 2.46e-03 | 1.14e-02 | 19 |
| GO:004328031 | Thyroid | ATC | positive regulation of cysteine-type endopeptidase activity involved in apoptotic process | 58/6293 | 129/18723 | 4.70e-03 | 1.93e-02 | 58 |
| GO:00022448 | Thyroid | ATC | hematopoietic progenitor cell differentiation | 51/6293 | 114/18723 | 8.62e-03 | 3.28e-02 | 51 |
| GO:200105632 | Thyroid | ATC | positive regulation of cysteine-type endopeptidase activity | 64/6293 | 148/18723 | 8.98e-03 | 3.39e-02 | 64 |
| GO:000691922 | Thyroid | ATC | activation of cysteine-type endopeptidase activity involved in apoptotic process | 36/6293 | 78/18723 | 1.43e-02 | 4.92e-02 | 36 |
| 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 |
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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 |
| 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 | SD |
| 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 | CR |
| 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 | SD | |||
| 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 | SD | |||
| 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 | Unknown | PD | ||
| 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 | Unknown | SD |
| 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 | PD |
| 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 | Unknown | PD | |
| 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 | Unknown | SD | |
| 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 | 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 |
| Page: 1 |
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